Histone

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https://en.wikipedia.org/wiki/Histone

Schematic representation of the assembly of the core histones into the nucleosome

In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei and in most Archaeal phyla. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 9 micrometers (0.09 mm) of 30 nm diameter chromatin fibers.

There are five families of histones, which are designated H1/H5 (linker histones), H2, H3, and H4 (core histones). The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer. The tight wrapping of DNA around histones, is to a large degree, a result of electrostatic attraction between the positively charged histones and negatively charged phosphate backbone of DNA.

Histones may be chemically modified through the action of enzymes to regulate gene transcription. The most common modifications are the methylation of arginine or lysine residues or the acetylation of lysine. Methylation can affect how other proteins such as transcription factors interact with the nucleosomes. Lysine acetylation eliminates a positive charge on lysine thereby weakening the electrostatic attraction between histone and DNA, resulting in partial unwinding of the DNA, making it more accessible for gene expression.

Classes and variants

Histone heterooctamer (H3,H4,H2A,H2B) + DNA fragment, Frog

Five major families of histone proteins exist: H1/H5, H2A, H2B, H3, and H4. Histones H2A, H2B, H3 and H4 are known as the core or nucleosomal histones, while histones H1/H5 are known as the linker histones.

The core histones all exist as dimers, which are similar in that they all possess the histone fold domain: three alpha helices linked by two loops. It is this helical structure that allows for interaction between distinct dimers, particularly in a head-tail fashion (also called the handshake motif). The resulting four distinct dimers then come together to form one octameric nucleosome core, approximately 63 Angstroms in diameter (a solenoid (DNA)-like particle). Around 146 base pairs (bp) of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn to give a particle of around 100 Angstroms across. The linker histone H1 binds the nucleosome at the entry and exit sites of the DNA, thus locking the DNA into place and allowing the formation of higher order structure. The most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with approximately 50 base pairs of DNA separating each pair of nucleosomes (also referred to as linker DNA). Higher-order structures include the 30 nm fiber (forming an irregular zigzag) and 100 nm fiber, these being the structures found in normal cells. During mitosis and meiosis, the condensed chromosomes are assembled through interactions between nucleosomes and other regulatory proteins.

Histones are subdivided into canonical replication-dependent histones, whose genes are expressed during the S-phase of the cell cycle and replication-independent histone variants, expressed during the whole cell cycle. In mammals, genes encoding canonical histones are typically clustered along chromosomes in 4 different highly-conserved loci, lack introns and use a stem loop structure at the 3' end instead of a polyA tail. Genes encoding histone variants are usually not clustered, have introns and their mRNAs are regulated with polyA tails.^[10] Complex multicellular organisms typically have a higher number of histone variants providing a variety of different functions. Functionally, histone variants contribute to transcriptional control, epigenetic memory, and DNA repair, serving specialized functions beyond nucleosome packaging which plays distinct roles in chromatin dynamics. For example, H2A.Z is enriched at regulatory elements and promoters of actively transcribed genes, where it modulates nucleosome stability and transcription factor binding. In contrast, H3.3, a replacement variant of Histone H3, is associated with active transcription and is preferentially deposited at enhancer elements and transcribed gene bodies. Another critical variant, CENPA, replaces H3 in centromeric nucleosomes, providing a structural foundation essential for chromosome segregation.

Variants also play essential roles in DNA repair. Variants such as H2A.X are phosphorylated at sites of DNA damage, marking regions for recruitment of repair proteins. This modification, commonly referred to as γH2A.X, serves as a key signal in the cellular response to double-strand breaks, facilitating efficient DNA repair processes. Defects in histone variant regulation have been linked to genome instability, a hallmark of many cancers and age-related diseases.

Recent data are accumulating about the roles of diverse histone variants highlighting the functional links between variants and the delicate regulation of organism development. Histone variants proteins from different organisms, their classification and variant specific features can be found in "HistoneDB 2.0 - Variants" database. Several pseudogenes have also been discovered and identified in very close sequences of their respective functional ortholog genes.

The following is a list of human histone proteins, genes and pseudogenes:

Super family	Family	Replication-dependent genes	Replication-independent genes	Pseudogenes
Linker	H1	H1-1, H1-2, H1-3, H1-4, H1-5, H1-6	H1-0, H1-7, H1-8, H1-10	H1-9P, H1-12P
Core	H2A	H2AC1, H2AC4, H2AC6, H2AC7, H2AC8, H2AC11, H2AC12, H2AC13, H2AC14, H2AC15, H2AC16, H2AC17, H2AC18, H2AC19, H2AC20, H2AC21, H2AC25	H2AZ1, H2AZ2, MACROH2A1, MACROH2A2, H2AX, H2AJ, H2AB1, H2AB2, H2AB3, H2AP, H2AL1Q, H2AL3	H2AC2P, H2AC3P, H2AC5P, H2AC9P, H2AC10P, H2AQ1P, H2AL1MP
	H2B	H2BC1, H2BC3, H2BC4, H2BC5, H2BC6, H2BC7, H2BC8, H2BC9, H2BC10, H2BC11, H2BC12, H2BC13, H2BC14, H2BC15, H2BC17, H2BC18, H2BC21, H2BC26, H2BC12L	H2BK1, H2BW1, H2BW2, H2BW3P, H2BN1	H2BC2P, H2BC16P, H2BC19P, H2BC20P, H2BC27P, H2BL1P, H2BW3P, H2BW4P
	H3	H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12, H3C13, H3C14, H3C15, H3-4	H3-3A, H3-3B, H3-5, H3-7, H3Y1, H3Y2, CENPA	H3C5P, H3C9P, H3P16, H3P44
	H4	H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C7, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15	H4C16	H4C10P

Structure

Steps in nucleosome assembly

The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer, forming two nearly symmetrical halves by tertiary structure (C2 symmetry; one macromolecule is the mirror image of the other). The H2A-H2B dimers and H3-H4 tetramer also show pseudodyad symmetry. The 4 'core' histones (H2A, H2B, H3 and H4) are relatively similar in structure and are highly conserved through evolution, all featuring a 'helix turn helix turn helix' motif (DNA-binding protein motif that recognize specific DNA sequence). They also share the feature of long 'tails' on one end of the amino acid structure - this being the location of post-translational modification (see below).

Archaeal histone only contains a H3-H4 like dimeric structure made out of a single type of unit. Such dimeric structures can stack into a tall superhelix ("hypernucleosome") onto which DNA coils in a manner similar to nucleosome spools. Only some archaeal histones have tails.

The distance between the spools around which eukaryotic cells wind their DNA has been determined to range from 59 to 70 Å.

In all, histones make five types of interactions with DNA:

• Salt bridges and hydrogen bonds between side chains of basic amino acids (especially lysine and arginine) and phosphate oxygens on DNA
• Helix-dipoles form alpha-helixes in H2B, H3, and H4 cause a net positive charge to accumulate at the point of interaction with negatively charged phosphate groups on DNA
• Hydrogen bonds between the DNA backbone and the amide group on the main chain of histone proteins
• Nonpolar interactions between the histone and deoxyribose sugars on DNA
• Non-specific minor groove insertions of the H3 and H2B N-terminal tails into two minor grooves each on the DNA molecule

The highly basic nature of histones, aside from facilitating DNA-histone interactions, contributes to their water solubility.

Histones are subject to post translational modification by enzymes primarily on their N-terminal tails, but also in their globular domains. Such modifications include methylation, citrullination, acetylation, phosphorylation, SUMOylation, ubiquitination, and ADP-ribosylation. This affects their function of gene regulation.

In general, genes that are active have less bound histone, while inactive genes are highly associated with histones during interphase. It also appears that the structure of histones has been evolutionarily conserved, as any deleterious mutations would be severely maladaptive. All histones have a highly positively charged N-terminus with many lysine and arginine residues.

Evolution and species distribution

Core histones are found in the nuclei of eukaryotic cells and in most Archaeal phyla, but not in bacteria. The unicellular algae known as dinoflagellates were previously thought to be the only eukaryotes that completely lack histones, but later studies showed that their DNA still encodes histone genes. Unlike the core histones, homologs of the lysine-rich linker histone (H1) proteins are found in bacteria, otherwise known as nucleoprotein HC1/HC2.

It has been proposed that core histone proteins are evolutionarily related to the helical part of the extended AAA+ ATPase domain, the C-domain, and to the N-terminal substrate recognition domain of Clp/Hsp100 proteins. Despite the differences in their topology, these three folds share a homologous helix-strand-helix (HSH) motif. It's also proposed that they may have evolved from ribosomal proteins (RPS6/RPS15), both being short and basic proteins.

Archaeal histones may well resemble the evolutionary precursors to eukaryotic histones. Histone proteins are among the most highly conserved proteins in eukaryotes, emphasizing their important role in the biology of the nucleus. In contrast mature sperm cells largely use protamines to package their genomic DNA, most likely because this allows them to achieve an even higher packaging ratio.

There are some variant forms in some of the major classes. They share amino acid sequence homology and core structural similarity to a specific class of major histones but also have their own feature that is distinct from the major histones. These minor histones usually carry out specific functions of the chromatin metabolism. For example, histone H3-like CENPA is associated with only the centromere region of the chromosome. Histone H2A variant H2A.Z is associated with the promoters of actively transcribed genes and also involved in the prevention of the spread of silent heterochromatin. Furthermore, H2A.Z has roles in chromatin for genome stability. Another H2A variant H2A.X is phosphorylated at S139 in regions around double-strand breaks and marks the region undergoing DNA repair. Histone H3.3 is associated with the body of actively transcribed genes.

Function

Basic units of chromatin structure

Compacting DNA strands

Histones act as spools around which DNA winds. This enables the compaction necessary to fit the large genomes of eukaryotes inside cell nuclei: the compacted molecule is 40,000 times shorter than an unpacked molecule.

Chromatin regulation

Histone tails and their function in chromatin formation

Histones undergo posttranslational modifications that alter their interaction with DNA and nuclear proteins. The H3 and H4 histones have long tails protruding from the nucleosome, which can be covalently modified at several places. Modifications of the tail include methylation, acetylation, phosphorylation, ubiquitination, SUMOylation, citrullination, and ADP-ribosylation. The core of the histones H2A and H2B can also be modified. Combinations of modifications, known as histone marks, are thought to constitute a code, the so-called "histone code". Histone modifications act in diverse biological processes such as gene regulation, DNA repair, chromosome condensation (mitosis) and spermatogenesis (meiosis).

The common nomenclature of histone modifications is:

• The name of the histone (e.g., H3)
• The single-letter amino acid abbreviation (e.g., K for Lysine) and the amino acid position in the protein
• The type of modification (Me: methyl, P: phosphate, Ac: acetyl, Ub: ubiquitin)
• The number of modifications (only Me is known to occur in more than one copy per residue. 1, 2 or 3 is mono-, di- or tri-methylation)

So H3K4me1 denotes the monomethylation of the 4th residue (a lysine) from the start (i.e., the N-terminal) of the H3 protein.

Examples of histone modifications in transcriptional regulation

Type of modification	Histone
	H3K4	H3K9	H3K14	H3K27	H3K79	H3K36	H4K20	H2BK5	H2BK20
mono-methylation	activation	activation		activation	activation		activation	activation
di-methylation		repression		repression	activation
tri-methylation	activation	repression		repression	activation, repression	activation	repression
acetylation	activation	activation	activation	activation					activation

Modification

Schematic representation of histone modifications. Based on Rodriguez-Paredes and Esteller, Nature, 2011

A huge catalogue of histone modifications have been described, but a functional understanding of most is still lacking. Collectively, it is thought that histone modifications may underlie a histone code, whereby combinations of histone modifications have specific meanings. However, most functional data concerns individual prominent histone modifications that are biochemically amenable to detailed study.

Chemistry

Lysine methylation

The addition of one, two, or many methyl groups to lysine has little effect on the chemistry of the histone; methylation leaves the charge of the lysine intact and adds a minimal number of atoms so steric interactions are mostly unaffected. However, proteins containing Tudor, chromo or PHD domains, amongst others, can recognise lysine methylation with exquisite sensitivity and differentiate mono, di and tri-methyl lysine, to the extent that, for some lysines (e.g.: H4K20) mono, di and tri-methylation appear to have different meanings. Because of this, lysine methylation tends to be a very informative mark and dominates the known histone modification functions.

Glutamine serotonylation

Recently it has been shown, that the addition of a serotonin group to the position 5 glutamine of H3, happens in serotonergic cells such as neurons. This is part of the differentiation of the serotonergic cells. This post-translational modification happens in conjunction with the H3K4me3 modification. The serotonylation potentiates the binding of the general transcription factor TFIID to the TATA box.

Arginine methylation

What was said above of the chemistry of lysine methylation also applies to arginine methylation, and some protein domains—e.g., Tudor domains—can be specific for methyl arginine instead of methyl lysine. Arginine is known to be mono- or di-methylated, and methylation can be symmetric or asymmetric, potentially with different meanings.

Arginine citrullination

Enzymes called peptidylarginine deiminases (PADs) hydrolyze the imine group of arginines and attach a keto group, so that there is one less positive charge on the amino acid residue. This process has been involved in the activation of gene expression by making the modified histones less tightly bound to DNA and thus making the chromatin more accessible. PADs can also produce the opposite effect by removing or inhibiting mono-methylation of arginine residues on histones and thus antagonizing the positive effect arginine methylation has on transcriptional activity.

Lysine acetylation

Addition of an acetyl group has a major chemical effect on lysine as it neutralises the positive charge. This reduces electrostatic attraction between the histone and the negatively charged DNA backbone, loosening the chromatin structure; highly acetylated histones form more accessible chromatin and tend to be associated with active transcription. Lysine acetylation appears to be less precise in meaning than methylation, in that histone acetyltransferases tend to act on more than one lysine; presumably this reflects the need to alter multiple lysines to have a significant effect on chromatin structure. The modification includes H3K27ac.

Serine/threonine/tyrosine phosphorylation

Addition of a negatively charged phosphate group can lead to major changes in protein structure, leading to the well-characterised role of phosphorylation in controlling protein function. It is not clear what structural implications histone phosphorylation has, but histone phosphorylation has clear functions as a post-translational modification, and binding domains such as BRCT have been characterised.

Effects on transcription

Most well-studied histone modifications are involved in control of transcription.

Actively transcribed genes

Two histone modifications are particularly associated with active transcription:

Trimethylation of H3 lysine 4 (H3K4me3)

This trimethylation occurs at the promoter of active genes and is performed by the COMPASS complex. Despite the conservation of this complex and histone modification from yeast to mammals, it is not entirely clear what role this modification plays. However, it is an excellent mark of active promoters and the level of this histone modification at a gene's promoter is broadly correlated with transcriptional activity of the gene. The formation of this mark is tied to transcription in a rather convoluted manner: early in transcription of a gene, RNA polymerase II undergoes a switch from initiating' to 'elongating', marked by a change in the phosphorylation states of the RNA polymerase II C terminal domain (CTD). The same enzyme that phosphorylates the CTD also phosphorylates the Rad6 complex, which in turn adds a ubiquitin mark to H2B K123 (K120 in mammals). H2BK123Ub occurs throughout transcribed regions, but this mark is required for COMPASS to trimethylate H3K4 at promoters.

Trimethylation of H3 lysine 36 (H3K36me3)

This trimethylation occurs in the body of active genes and is deposited by the methyltransferase Set2. This protein associates with elongating RNA polymerase II, and H3K36Me3 is indicative of actively transcribed genes. H3K36Me3 is recognised by the Rpd3 histone deacetylase complex, which removes acetyl modifications from surrounding histones, increasing chromatin compaction and repressing spurious transcription. Increased chromatin compaction prevents transcription factors from accessing DNA, and reduces the likelihood of new transcription events being initiated within the body of the gene. This process therefore helps ensure that transcription is not interrupted.

Repressed genes

Three histone modifications are particularly associated with repressed genes:

Trimethylation of H3 lysine 27 (H3K27me3)

This histone modification is deposited by the polycomb complex PRC2. It is a clear marker of gene repression, and is likely bound by other proteins to exert a repressive function. Another polycomb complex, PRC1, can bind H3K27me3 and adds the histone modification H2AK119Ub which aids chromatin compaction. Based on this data it appears that PRC1 is recruited through the action of PRC2, however, recent studies show that PRC1 is recruited to the same sites in the absence of PRC2.

Di and tri-methylation of H3 lysine 9 (H3K9me2/3)

H3K9me2/3 is a well-characterised marker for heterochromatin, and is therefore strongly associated with gene repression. The formation of heterochromatin has been best studied in the yeast Schizosaccharomyces pombe, where it is initiated by recruitment of the RNA-induced transcriptional silencing (RITS) complex to double stranded RNAs produced from centromeric repeats. RITS recruits the Clr4 histone methyltransferase which deposits H3K9me2/3. This process is called histone methylation. H3K9Me2/3 serves as a binding site for the recruitment of Swi6 (heterochromatin protein 1 or HP1, another classic heterochromatin marker) which in turn recruits further repressive activities including histone modifiers such as histone deacetylases and histone methyltransferases.

Trimethylation of H4 lysine 20 (H4K20me3)

This modification is tightly associated with heterochromatin, although its functional importance remains unclear. This mark is placed by the Suv4-20h methyltransferase, which is at least in part recruited by heterochromatin protein 1.

Bivalent promoters

Analysis of histone modifications in embryonic stem cells (and other stem cells) revealed many gene promoters carrying both H3K4Me3 and H3K27Me3, in other words these promoters display both activating and repressing marks simultaneously. This peculiar combination of modifications marks genes that are poised for transcription; they are not required in stem cells, but are rapidly required after differentiation into some lineages. Once the cell starts to differentiate, these bivalent promoters are resolved to either active or repressive states depending on the chosen lineage.

Other functions

DNA damage repair

Marking sites of DNA damage is an important function for histone modifications. Without a repair marker, DNA would get destroyed by damage accumulated from sources such as the ultraviolet radiation of the sun.

Phosphorylation of H2AX at serine 139 (γH2AX)

Phosphorylated H2AX (also known as gamma H2AX) is a marker for DNA double strand breaks, and forms part of the response to DNA damage. H2AX is phosphorylated early after detection of DNA double strand break, and forms a domain extending many kilobases either side of the damage. Gamma H2AX acts as a binding site for the protein MDC1, which in turn recruits key DNA repair proteins and as such, gamma H2AX forms a vital part of the machinery that ensures genome stability.

Acetylation of H3 lysine 56 (H3K56Ac)

H3K56Acx is required for genome stability. H3K56 is acetylated by the p300/Rtt109 complex, but is rapidly deacetylated around sites of DNA damage. H3K56 acetylation is also required to stabilise stalled replication forks, preventing dangerous replication fork collapses. Although in general mammals make far greater use of histone modifications than microorganisms, a major role of H3K56Ac in DNA replication exists only in fungi, and this has become a target for antibiotic development.

Trimethylation of H3 lysine 36 (H3K36me3)

H3K36me3 has the ability to recruit the MSH2-MSH6 (hMutSα) complex of the DNA mismatch repair pathway. Consistently, regions of the human genome with high levels of H3K36me3 accumulate less somatic mutations due to mismatch repair activity.

Chromosome condensation

Phosphorylation of H3 at serine 10 (phospho-H3S10)

The mitotic kinase aurora B phosphorylates histone H3 at serine 10, triggering a cascade of changes that mediate mitotic chromosome condensation. Condensed chromosomes therefore stain very strongly for this mark, but H3S10 phosphorylation is also present at certain chromosome sites outside mitosis, for example in pericentric heterochromatin of cells during G2. H3S10 phosphorylation has also been linked to DNA damage caused by R-loop formation at highly transcribed sites.

Phosphorylation H2B at serine 10/14 (phospho-H2BS10/14)

Phosphorylation of H2B at serine 10 (yeast) or serine 14 (mammals) is also linked to chromatin condensation, but for the very different purpose of mediating chromosome condensation during apoptosis. This mark is not simply a late acting bystander in apoptosis as yeast carrying mutations of this residue are resistant to hydrogen peroxide-induced apoptotic cell death.

Addiction

Epigenetic modifications of histone tails in specific regions of the brain are of central importance in addictions. Once particular epigenetic alterations occur, they appear to be long lasting "molecular scars" that may account for the persistence of addictions.

Cigarette smokers (about 15% of the US population) are usually addicted to nicotine. After 7 days of nicotine treatment of mice, acetylation of both histone H3 and histone H4 was increased at the FosB promoter in the nucleus accumbens of the brain, causing 61% increase in FosB expression. This would also increase expression of the splice variant Delta FosB. In the nucleus accumbens of the brain, Delta FosB functions as a "sustained molecular switch" and "master control protein" in the development of an addiction.

About 7% of the US population is addicted to alcohol. In rats exposed to alcohol for up to 5 days, there was an increase in histone 3 lysine 9 acetylation in the pronociceptin promoter in the brain amygdala complex. This acetylation is an activating mark for pronociceptin. The nociceptin/nociceptin opioid receptor system is involved in the reinforcing or conditioning effects of alcohol.

Methamphetamine addiction occurs in about 0.2% of the US population. Chronic methamphetamine use causes methylation of the lysine in position 4 of histone 3 located at the promoters of the c-fos and the C-C chemokine receptor 2 (ccr2) genes, activating those genes in the nucleus accumbens (NAc). c-fos is well known to be important in addiction. The ccr2 gene is also important in addiction, since mutational inactivation of this gene impairs addiction.

Histone Chaperones

Histone chaperones (biology) are specialized proteins that assist in the proper handling, transport, and assembly of histones, preventing their aggregation and ensuring their appropriate deposition onto DNA. These proteins play a crucial role in regulating nucleosome assembly and disassembly, influencing transcriptional activity, DNA replication, and repair. Unlike enzymatic chromatin remodeling, histone chaperones function by binding histones in a regulated manner, modulating chromatin structure without direct catalytic activity.

One key function of histone chaperones is maintaining a reservoir of histones, regulating their supply to ensure proper chromatin formation. During DNA replication and transcription (biology), histone chaperones such as ASF1 and FACT facilitate nucleosome reassembly, ensuring the preservation of histone modifications that define cellular identity. Moreover, histone chaperones contribute to nucleosome disassembly in response to cellular stress or DNA damage, thereby allowing access to repair machinery.

Histone chaperones also participate in the selective deposition of histone variants, which are functionally distinct from canonical histones. For example, HIRA is a chaperone that specifically deposits the histone variant H3.3, a marker of active chromatin regions. Similarly, CAF-1 is responsible for incorporating H3.1 and H3.2 into newly replicated DNA, highlighting the functional specialization within chaperone networks.

Given their critical roles, misregulation of histone chaperones has been implicated in diseases such as cancer. Aberrant chaperone activity can lead to improper histone deposition, genome instability, and altered gene expression, contributing to tumorigenesis. Current research is exploring histone chaperones as potential therapeutic targets, particularly in cancers characterized by disrupted chromatin landscapes.

Chaperone Networks

The coordinated action of multiple histone chaperones forms an intricate network responsible for histone transport, Chromatin assembly factor 1, and genome maintenance. Chaperone networks facilitate the transport of histones which are synthesized in the cytoplasm and must be escorted to the cell nucleus. This network ensures histones are deposited at the appropriate genomic locations, maintaining chromatin integrity and function.

Histone chaperones play a crucial role in responding to DNA damage by regulating chromatin accessibility. For example, in response to double strand breaks, chaperones such as FACT and ASF1 help disassemble nucleosomes at damage sites, allowing repair factors to access the lesion. Once repair is completed, these chaperones facilitate the reassembly of nucleosomes, restoring chromatin structure and ensuring epigenetic information is maintained.

In addition to their role in genome stability, histone chaperones contribute to epigenetic inheritance. During cell division, chromatin states must be faithfully propagated to daughter cells. Chaperones help distribute parental histones onto newly synthesized DNA strands, preserving histone modifications and ensuring continuity of cellular identity. Disruptions in these processes can lead to epigenetic abnormalities associated with developmental disorders.

Synthesis

The first step of chromatin structure duplication is the synthesis of histone proteins: H1, H2A, H2B, H3, H4. These proteins are synthesized during S phase of the cell cycle. There are different mechanisms which contribute to the increase of histone synthesis.

Yeast

Yeast carry one or two copies of each histone gene, which are not clustered but rather scattered throughout chromosomes. Histone gene transcription is controlled by multiple gene regulatory proteins such as transcription factors which bind to histone promoter regions. In budding yeast, the candidate gene for activation of histone gene expression is SBF. SBF is a transcription factor that is activated in late G1 phase, when it dissociates from its repressor Whi5. This occurs when Whi5 is phosphorylated by Cdc8 which is a G1/S Cdk. Suppression of histone gene expression outside of S phases is dependent on Hir proteins which form inactive chromatin structure at the locus of histone genes, causing transcriptional activators to be blocked.

Metazoan

In metazoans the increase in the rate of histone synthesis is due to the increase in processing of pre-mRNA to its mature form as well as decrease in mRNA degradation; this results in an increase of active mRNA for translation of histone proteins. The mechanism for mRNA activation has been found to be the removal of a segment of the 3' end of the mRNA strand, and is dependent on association with stem-loop binding protein (SLBP). SLBP also stabilizes histone mRNAs during S phase by blocking degradation by the 3'hExo nuclease. SLBP levels are controlled by cell-cycle proteins, causing SLBP to accumulate as cells enter S phase and degrade as cells leave S phase. SLBP are marked for degradation by phosphorylation at two threonine residues by cyclin dependent kinases, possibly cyclin A/ cdk2, at the end of S phase. Metazoans also have multiple copies of histone genes clustered on chromosomes which are localized in structures called Cajal bodies as determined by genome-wide chromosome conformation capture analysis (4C-Seq).

Link between cell-cycle control and synthesis

Nuclear protein Ataxia-Telangiectasia (NPAT), also known as nuclear protein coactivator of histone transcription, is a transcription factor which activates histone gene transcription on chromosomes 1 and 6 of human cells. NPAT is also a substrate of cyclin E-Cdk2, which is required for the transition between G1 phase and S phase. NPAT activates histone gene expression only after it has been phosphorylated by the G1/S-Cdk cyclin E-Cdk2 in early S phase. This shows an important regulatory link between cell-cycle control and histone synthesis.

History

Histones were discovered in 1884 by Albrecht Kossel. The word "histone" dates from the late 19th century and is derived from the German word "Histon", a word itself of uncertain origin, perhaps from Ancient Greek ἵστημι (hístēmi, “make stand”) or ἱστός (histós, “loom”).

In the early 1960s, before the types of histones were known and before histones were known to be highly conserved across taxonomically diverse organisms, James F. Bonner and his collaborators began a study of these proteins that were known to be tightly associated with the DNA in the nucleus of higher organisms. Bonner and his postdoctoral fellow Ru Chih C. Huang showed that isolated chromatin would not support RNA transcription in the test tube, but if the histones were extracted from the chromatin, RNA could be transcribed from the remaining DNA. Their paper became a citation classic. Paul T'so and James Bonner had called together a World Congress on Histone Chemistry and Biology in 1964, in which it became clear that there was no consensus on the number of kinds of histone and that no one knew how they would compare when isolated from different organisms. Bonner and his collaborators then developed methods to separate each type of histone, purified individual histones, compared amino acid compositions in the same histone from different organisms, and compared amino acid sequences  of the same histone from different organisms in collaboration with Emil Smith from UCLA. For example, they found Histone IV sequence to be highly conserved between peas and calf thymus. However, their work on the biochemical characteristics of individual histones did not reveal how the histones interacted with each other or with DNA to which they were tightly bound.

Also in the 1960s, Vincent Allfrey and Alfred Mirsky had suggested, based on their analyses of histones, that acetylation and methylation of histones could provide a transcriptional control mechanism, but did not have available the kind of detailed analysis that later investigators were able to conduct to show how such regulation could be gene-specific. Until the early 1990s, histones were dismissed by most as inert packing material for eukaryotic nuclear DNA, a view based in part on the models of Mark Ptashne and others, who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, as is the case in bacteria.

During the 1980s, Yahli Lorch and Roger Kornberg showed that a nucleosome on a core promoter prevents the initiation of transcription in vitro, and Michael Grunstein demonstrated that histones repress transcription in vivo, leading to the idea of the nucleosome as a general gene repressor. Relief from repression is believed to involve both histone modification and the action of chromatin-remodeling complexes. Vincent Allfrey and Alfred Mirsky had earlier proposed a role of histone modification in transcriptional activation, regarded as a molecular manifestation of epigenetics. Michael Grunstein and David Allis found support for this proposal, in the importance of histone acetylation for transcription in yeast and the activity of the transcriptional activator Gcn5 as a histone acetyltransferase.

The discovery of the H5 histone appears to date back to the 1970s, and it is now considered an isoform of Histone H1.

ChIP-on-chip

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/ChIP-on-chip

Workflow overview of a ChIP-on-chip experiment.

ChIP-on-chip (also known as ChIP-chip) is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray ("chip"). Like regular ChIP, ChIP-on-chip is used to investigate interactions between proteins and DNA in vivo. Specifically, it allows the identification of the cistrome, the sum of binding sites, for DNA-binding proteins on a genome-wide basis. Whole-genome analysis can be performed to determine the locations of binding sites for almost any protein of interest. As the name of the technique suggests, such proteins are generally those operating in the context of chromatin. The most prominent representatives of this class are transcription factors, replication-related proteins, like origin recognition complex protein (ORC), histones, their variants, and histone modifications.

The goal of ChIP-on-chip is to locate protein binding sites that may help identify functional elements in the genome. For example, in the case of a transcription factor as a protein of interest, one can determine its transcription factor binding sites throughout the genome. Other proteins allow the identification of promoter regions, enhancers, repressors and silencing elements, insulators, boundary elements, and sequences that control DNA replication. If histones are subject of interest, it is believed that the distribution of modifications and their localizations may offer new insights into the mechanisms of regulation.

One of the long-term goals ChIP-on-chip was designed for is to establish a catalogue of (selected) organisms that lists all protein-DNA interactions under various physiological conditions. This knowledge would ultimately help in the understanding of the machinery behind gene regulation, cell proliferation, and disease progression. Hence, ChIP-on-chip offers both potential to complement our knowledge about the orchestration of the genome on the nucleotide level and information on higher levels of information and regulation as it is propagated by research on epigenetics.

Technological platforms

See also: DNA microarray and Immunoprecipitation

The technical platforms to conduct ChIP-on-chip experiments are DNA microarrays, or "chips". They can be classified and distinguished according to various characteristics:

Probe type: DNA arrays can comprise either mechanically spotted cDNAs or PCR-products, mechanically spotted oligonucleotides, or oligonucleotides that are synthesized in situ. The early versions of microarrays were designed to detect RNAs from expressed genomic regions (open reading frames aka ORFs). Although such arrays are perfectly suited to study gene expression profiles, they have limited importance in ChIP experiments since most "interesting" proteins with respect to this technique bind in intergenic regions. Nowadays, even custom-made arrays can be designed and fine-tuned to match the requirements of an experiment. Also, any sequence of nucleotides can be synthesized to cover genic as well as intergenic regions.

Probe size: Early version of cDNA arrays had a probe length of about 200bp. Latest array versions use oligos as short as 70- (Microarrays, Inc.) to 25-mers (Affymetrix). (Feb 2007)

Probe composition: There are tiled and non-tiled DNA arrays. Non-tiled arrays use probes selected according to non-spatial criteria, i.e., the DNA sequences used as probes have no fixed distances in the genome. Tiled arrays, however, select a genomic region (or even a whole genome) and divide it into equal chunks. Such a region is called tiled path. The average distance between each pair of neighboring chunks (measured from the center of each chunk) gives the resolution of the tiled path. A path can be overlapping, end-to-end or spaced.

Array size: The first microarrays used for ChIP-on-Chip contained about 13,000 spotted DNA segments representing all ORFs and intergenic regions from the yeast genome. Nowadays, Affymetrix offers whole-genome tiled yeast arrays with a resolution of 5bp (all in all 3.2 million probes). Tiled arrays for the human genome become more and more powerful, too. Just to name one example, Affymetrix offers a set of seven arrays with about 90 million probes, spanning the complete non-repetitive part of the human genome with about 35bp spacing. (Feb 2007) Besides the actual microarray, other hard- and software equipment is necessary to run ChIP-on-chip experiments. It is generally the case that one company's microarrays can not be analyzed by another company's processing hardware. Hence, buying an array requires also buying the associated workflow equipment. The most important elements are, among others, hybridization ovens, chip scanners, and software packages for subsequent numerical analysis of the raw data.

Workflow of a ChIP-on-chip experiment

Starting with a biological question, a ChIP-on-chip experiment can be divided into three major steps: The first is to set up and design the experiment by selecting the appropriate array and probe type. Second, the actual experiment is performed in the wet-lab. Last, during the dry-lab portion of the cycle, gathered data are analyzed to either answer the initial question or lead to new questions so that the cycle can start again.

Wet-lab portion of the workflow

Workflow overview of the wet-lab portion of a ChIP-on-chip experiment.

In the first step, the protein of interest (POI) is cross-linked with the DNA site it binds to in an in vitro environment. Usually this is done by a gentle formaldehyde fixation that is reversible with heat.

Then, the cells are lysed and the DNA is sheared by sonication or using micrococcal nuclease. This results in double-stranded chunks of DNA fragments, normally 1 kb or less in length. Those that were cross-linked to the POI form a POI-DNA complex.

In the next step, only these complexes are filtered out of the set of DNA fragments, using an antibody specific to the POI. The antibodies may be attached to a solid surface, may have a magnetic bead, or some other physical property that allows separation of cross-linked complexes and unbound fragments. This procedure is essentially an immunoprecipitation (IP) of the protein. This can be done either by using a tagged protein with an antibody against the tag (ex. FLAG, HA, c-myc) or with an antibody to the native protein.

The cross-linking of POI-DNA complexes is reversed (usually by heating) and the DNA strands are purified. For the rest of the workflow, the POI is no longer necessary.

After an amplification and denaturation step, the single-stranded DNA fragments are labeled with a fluorescent tag such as Cy5 or Alexa 647.

Finally, the fragments are poured over the surface of the DNA microarray, which is spotted with short, single-stranded sequences that cover the genomic portion of interest. Whenever a labeled fragment "finds" a complementary fragment on the array, they will hybridize and form again a double-stranded DNA fragment.

Dry-lab portion of the workflow

See also: DNA microarray

Workflow overview of the dry-lab portion of a ChIP-on-chip experiment.

After a sufficiently large time frame to allow hybridization, the array is illuminated with fluorescent light. Those probes on the array that are hybridized to one of the labeled fragments emit a light signal that is captured by a camera. This image contains all raw data for the remaining part of the workflow.

This raw data, encoded as false-color image, needs to be converted to numerical values before the actual analysis can be done. The analysis and information extraction of the raw data often remains the most challenging part for ChIP-on-chip experiments. Problems arise throughout this portion of the workflow, ranging from the initial chip read-out, to suitable methods to subtract background noise, and finally to appropriate algorithms that normalize the data and make it available for subsequent statistical analysis, which then hopefully lead to a better understanding of the biological question that the experiment seeks to address. Furthermore, due to the different array platforms and lack of standardization between them, data storage and exchange is a huge problem. Generally speaking, the data analysis can be divided into three major steps:

During the first step, the captured fluorescence signals from the array are normalized, using control signals derived from the same or a second chip. Such control signals tell which probes on the array were hybridized correctly and which bound nonspecifically.

In the second step, numerical and statistical tests are applied to control data and IP fraction data to identify POI-enriched regions along the genome. The following three methods are used widely: median percentile rank, single-array error, and sliding-window. These methods generally differ in how low-intensity signals are handled, how much background noise is accepted, and which trait for the data is emphasized during the computation. In the recent past, the sliding-window approach seems to be favored and is often described as most powerful.

In the third step, these regions are analyzed further. If, for example, the POI was a transcription factor, such regions would represent its binding sites. Subsequent analysis then may want to infer nucleotide motifs and other patterns to allow functional annotation of the genome.

Strengths and weaknesses

Using tiled arrays, ChIP-on-chip allows for high resolution of genome-wide maps. These maps can determine the binding sites of many DNA-binding proteins like transcription factors and also chromatin modifications.

Although ChIP-on-chip can be a powerful technique in the area of genomics, it is very expensive. Most published studies using ChIP-on-chip repeat their experiments at least three times to ensure biologically meaningful maps. The cost of the DNA microarrays is often a limiting factor to whether a laboratory should proceed with a ChIP-on-chip experiment. Another limitation is the size of DNA fragments that can be achieved. Most ChIP-on-chip protocols utilize sonication as a method of breaking up DNA into small pieces. However, sonication is limited to a minimal fragment size of 200 bp. For higher resolution maps, this limitation should be overcome to achieve smaller fragments, preferably to single nucleosome resolution. As mentioned previously, the statistical analysis of the huge amount of data generated from arrays is a challenge and normalization procedures should aim to minimize artifacts and determine what is really biologically significant. So far, application to mammalian genomes has been a major limitation, for example, due to the significant percentage of the genome that is occupied by repeats. However, as ChIP-on-chip technology advances, high resolution whole mammalian genome maps should become achievable.

Antibodies used for ChIP-on-chip can be an important limiting factor. ChIP-on-chip requires highly specific antibodies that must recognize its epitope in free solution and also under fixed conditions. If it is demonstrated to successfully immunoprecipitate cross-linked chromatin, it is termed "ChIP-grade". Companies that provide ChIP-grade antibodies include Abcam, Cell Signaling Technology, Santa Cruz, and Upstate. To overcome the problem of specificity, the protein of interest can be fused to a tag like FLAG or HA that are recognized by antibodies. An alternative to ChIP-on-chip that does not require antibodies is DamID.

Also available are antibodies against a specific histone modification like H3 tri methyl K4. As mentioned before, the combination of these antibodies and ChIP-on-chip has become extremely powerful in determining whole genome analysis of histone modification patterns and will contribute tremendously to our understanding of the histone code and epigenetics.

A study demonstrating the non-specific nature of DNA binding proteins has been published in PLoS Biology. This indicates that alternate confirmation of functional relevancy is a necessary step in any ChIP-chip experiment.

History

A first ChIP-on-chip experiment was performed in 1999 to analyze the distribution of cohesin along budding yeast chromosome III. Although the genome was not completely represented, the protocol in this study remains equivalent as those used in later studies. The ChIP-on-chip technique using all of the ORFs of the genome (that nevertheless remains incomplete, missing intergenic regions) was then applied successfully in three papers published in 2000 and 2001. The authors identified binding sites for individual transcription factors in the budding yeast Saccharomyces cerevisiae. In 2002, Richard Young's group determined the genome-wide positions of 106 transcription factors using a c-Myc tagging system in yeast. The first demonstration of the mammalian ChIp-on-chip technique reported the isolation of nine chromatin fragments containing weak and strong E2F binding site was done by Peggy Farnham's lab in collaboration with Michael Zhang's lab and published in 2001. This study was followed several months later in a collaboration between the Young lab with the laboratory of Brian Dynlacht which used the ChIP-on-chip technique to show for the first time that E2F targets encode components of the DNA damage checkpoint and repair pathways, as well as factors involved in chromatin assembly/condensation, chromosome segregation, and the mitotic spindle checkpoint Other applications for ChIP-on-chip include DNA replication, recombination, and chromatin structure. Since then, ChIP-on-chip has become a powerful tool in determining genome-wide maps of histone modifications and many more transcription factors. ChIP-on-chip in mammalian systems has been difficult due to the large and repetitive genomes. Thus, many studies in mammalian cells have focused on select promoter regions that are predicted to bind transcription factors and have not analyzed the entire genome. However, whole mammalian genome arrays have recently become commercially available from companies like Nimblegen. In the future, as ChIP-on-chip arrays become more and more advanced, high resolution whole genome maps of DNA-binding proteins and chromatin components for mammals will be analyzed in more detail.

Alternatives

Introduced in 2007, ChIP sequencing (ChIP-seq) is a technology that uses chromatin immunoprecipitation to crosslink the proteins of interest to the DNA but then instead of using a micro-array, it uses the more accurate, higher throughput method of sequencing to localize interaction points.

DamID is an alternative method that does not require antibodies.

ChIP-exo uses exonuclease treatment to achieve up to single base pair resolution.

CUT&RUN sequencing uses antibody recognition with targeted enzymatic cleavage to address some technical limitations of ChIP.

https://en.wikipedia.org/wiki/Organ-on-a-chip#Human-on-a-chip

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Organ-on-a-chip#Human-on-a-chip

Researchers are working towards building a multi-channel 3D microfluidic cell culture system that compartmentalizes microenvironments in which 3D cellular aggregates are cultured to mimic multiple organs in the body. Most organ-on-a-chip models today only culture one cell type, so even though they may be valid models for studying whole organ functions, the systemic effect of a drug on the human body is not verified.

In particular, an integrated cell culture analog (μCCA) was developed and included lung cells, drug-metabolizing liver and fat cells. The cells were linked in a 2D fluidic network with culture medium circulating as a blood surrogate, thus efficiently providing a nutritional delivery transport system, while simultaneously removing wastes from the cells. "The development of the μCCA laid the foundation for a realistic in vitro pharmacokinetic model and provided an integrated biomimetic system for culturing multiple cell types with high fidelity to in vivo situations", claim C. Zhang et al. They have developed a microfluidic human-on-a-chip, culturing four different cell types to mimic four human organs: liver, lung, kidney and fat. They focused on developing a standard serum-free culture media that would be valuable to all cell types included in the device. Optimized standard media are generally targeted to one specific cell-type, whereas a human-on-a-chip will evidently require a common medium (CM). In fact, they claim to have identified a cell culture CM that, when used to perfuse all cell cultures in the microfluidic device, maintains the cells' functional levels. Heightening the sensitivity of the in vitro cultured cells ensures the validity of the device, or that any drug injected into the microchannels will stimulate an identical physiological and metabolic reaction from the sample cells as whole organs in humans.

A human-on-a-chip design that allows tuning microfluidic transport to multiple tissues using a single fluidic actuator was designed and evaluated for modelling prediabetic hyperglycaemia using liver and pancreatic tissues.

With more extensive development of these kinds of chips, pharmaceutical companies will potentially be able to measure direct effects of one organ's reaction on another. For instance, the delivery of biochemical substances would be screened to confirm that even though it may benefit one cell type, it does not compromise the functions of others. It is probably already possible to print these organs with 3D printers, but the cost is too high. Designing whole body biomimetic devices addresses a major reservation that pharmaceutical companies have towards organs-on-chips, namely the isolation of organs. As these devices become more and more accessible, the complexity of the design increases exponentially. Systems will soon have to simultaneously provide mechanical perturbation and fluid flow through a circulatory system. "Anything that requires dynamic control rather than just static control is a challenge", says Takayama from the University of Michigan. This challenge has been partially tackled by tissue engineering Linda Griffith group from MIT. A complex multi-organ-on-a-chip was developed to have 4, 7, or 10 organs interconnected through fluidic control. The system is able to maintain the function of these organs for weeks.

Peristalsis

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Peristalsis

A time-space diagram of a peristaltic wave after a water swallow. High-pressure values are red, zero pressure is blue-green. The ridge in the upper part of the picture is the high pressure of the upper esophageal sphincter which only opens for a short time to let water pass.

Peristalsis (/ˌpɛrɪˈstælsɪs/ PERR-ih-STAL-siss, US also /-ˈstɔːl-/ -⁠STAWL-) is a type of intestinal motility, characterized by radially symmetrical contraction and relaxation of muscles that propagate in a wave down a tube, in an anterograde direction. Peristalsis is progression of coordinated contraction of involuntary circular muscles, which is preceded by a simultaneous contraction of the longitudinal muscle and relaxation of the circular muscle in the lining of the gut.

In much of a digestive tract, such as the human gastrointestinal tract, smooth muscle tissue contracts in sequence to produce a peristaltic wave, which propels a ball of food (called a bolus before being transformed into chyme in the stomach) along the tract. The peristaltic movement comprises relaxation of circular smooth muscles, then their contraction behind the chewed material to keep it from moving backward, then longitudinal contraction to push it forward.

Earthworms use a similar mechanism to drive their locomotion, and some modern machinery imitate this design.

The word comes from Neo-Latin and is derived from the Greek peristellein, "to wrap around," from peri-, "around" + stellein, "draw in, bring together; set in order".

Human physiology

Peristalsis is generally directed caudal, that is, towards the anus. This sense of direction might be attributable to the polarisation of the myenteric plexus. Because of the reliance of the peristaltic reflex on the myenteric plexus, it is also referred to as the myenteric reflex.

Mechanism of the peristaltic reflex

The food bolus causes a stretch of the gut smooth muscle that causes serotonin to be secreted to sensory neurons, which then get activated. These sensory neurons, in turn, activate neurons of the myenteric plexus, which then proceed to split into two cholinergic pathways: a retrograde and an anterograde. Activated neurons of the retrograde pathway release substance molecules alsoP and acetylcholine to contract the smooth muscle behind the bolus. The activated neurons of the anterograde pathway instead release nitric oxide and vasoactive intestinal polypeptide to relax the smooth muscle caudal to the bolus. This allows the food bolus to effectively be pushed forward along the digestive tract.

Esophagus

After food is chewed into a bolus, it is swallowed and moved through the esophagus. Smooth muscles contract behind the bolus to prevent it from being squeezed back into the mouth. Then rhythmic, unidirectional waves of contractions work to rapidly force the food into the stomach. The migrating motor complex (MMC) helps trigger peristaltic waves. This process works in one direction only, and its sole esophageal function is to move food from the mouth into the stomach (the MMC also functions to clear out remaining food in the stomach to the small bowel and remaining particles in the small bowel into the colon).

A simplified image showing peristalsis

In the esophagus, two types of peristalsis occur:

• First, there is a primary peristaltic wave, which occurs when the bolus enters the esophagus during swallowing. The primary peristaltic wave forces the bolus down the esophagus and into the stomach in a wave lasting about 8–9 seconds. The wave travels down to the stomach even if the bolus of food descends at a greater rate than the wave itself, and continues even if for some reason the bolus gets stuck further up the esophagus.
• If the bolus gets stuck or moves slower than the primary peristaltic wave (as can happen when it is poorly lubricated), then stretch receptors in the esophageal lining are stimulated and a local reflex response causes a secondary peristaltic wave around the bolus, forcing it further down the esophagus, and these secondary waves continue indefinitely until the bolus enters the stomach. The process of peristalsis is controlled by the medulla oblongata. Esophageal peristalsis is typically assessed by performing an esophageal motility study.
• A third type of peristalsis, tertiary peristalsis, is dysfunctional and involves irregular, diffuse, simultaneous contractions. These contractions are suspect in esophageal dysmotility and present on a barium swallow as a "corkscrew esophagus".

During vomiting, the propulsion of food up the esophagus and out the mouth comes from the contraction of the abdominal muscles; peristalsis does not reverse in the esophagus.

Stomach

When a peristaltic wave reaches at the end of the esophagus, the cardiac sphincter (gastroesophageal sphincter) opens, allowing the passage of bolus into the stomach. The gastroesophageal sphincter normally remains closed and does not allow the stomach's food contents to move back. The churning movements of the stomach's thick muscular wall blend the food thoroughly with the acidic gastric juice, producing a mixture called the chyme. The muscularis layer of the stomach is thickest and maximum peristalsis occurs here. After short intervals, the pyloric sphincter keeps on opening and closing so the chyme is fed into the intestine in installments.

Small intestine

Once processed and digested by the stomach, the semifluid chyme is passed through the pyloric sphincter into the small intestine. Once past the stomach, a typical peristaltic wave lasts only a few seconds, traveling at only a few centimeters per second. Its primary purpose is to mix the chyme in the intestine rather than to move it forward in the intestine. Through this process of mixing and continued digestion and absorption of nutrients, the chyme gradually works its way through the small intestine to the large intestine.

In contrast to peristalsis, segmentation contractions result in that churning and mixing without pushing materials further down the digestive tract.

Large intestine

Although the large intestine has peristalsis of the type that the small intestine uses, it is not the primary propulsion. Instead, general contractions called mass action contractions occur one to three times per day in the large intestine, propelling the chyme (now feces) toward the rectum. Mass movements often tend to be triggered by meals, as the presence of chyme in the stomach and duodenum prompts them (gastrocolic reflex). Minimum peristalsis is found in the rectum part of the large intestine as a result of the thinnest muscularis layer.

Lymph

The human lymphatic system has no central pump. Instead, lymph circulates through peristalsis in the lymph capillaries as well as valves in the capillaries, compression during contraction of adjacent skeletal muscle, and arterial pulsation.

Sperm

During ejaculation, the smooth muscle in the walls of the vasa deferentia contract reflexively in peristalsis, propelling sperm from the testicles to the urethra.

Earthworms

A simplified image showing Earthworm movement via peristalsis

The earthworm is a limbless annelid worm with a hydrostatic skeleton that moves by peristalsis. Its hydrostatic skeleton consists of a fluid-filled body cavity surrounded by an extensible body wall. The worm moves by radially constricting the anterior portion of its body, increasing length via hydrostatic pressure. This constricted region propagates posteriorly along the worm's body. As a result, each segment is extended forward, then relaxes and re-contacts the substrate, with hair-like setae preventing backward slipping. Various other invertebrates, such as caterpillars and millipedes, also move by peristalsis.

Machinery

A peristaltic pump is a positive-displacement pump in which a motor pinches advancing portions of a flexible tube to propel a fluid within the tube. The pump isolates the fluid from the machinery, which is important if the fluid is abrasive or must remain sterile.

Robots have been designed that use peristalsis to achieve locomotion, as the earthworm uses it.

Related terms

Aperistalsis refers to a lack of propulsion. It can result from achalasia of the smooth muscle involved.

Basal electrical rhythm is a slow wave of electrical activity that can initiate a contraction.

Catastalsis is a related intestinal muscle process.

Ileus is a disruption of the normal propulsive ability of the gastrointestinal tract caused by the failure of peristalsis.

Retroperistalsis, the reverse of peristalsis

Segmentation contractions are another type of intestinal motility.

Intestinal desmosis, the atrophy of the tendinous plexus layer, may cause disturbed gut motility.

Intestine-on-a-chip

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Intestine-on-a-chip

Intestines-on-a-chip (gut-on-a-chip, mini-intestine) are microfluidic bioengineered 3D-models of the real organ, which better mimic physiological features than conventional 3D intestinal organoid culture. A variety of different intestine-on-a-chip models systems have been developed and refined, all holding their individual strengths and weaknesses and collectively holding great promise to the ultimate goal of establishing these systems as reliable high-throughput platforms for drug testing and personalised medicine. The intestine is a highly complex organ system performing a diverse set of vital tasks, from nutrient digestion and absorption, hormone secretion, and immunological processes to neuronal activity, which makes it particularly challenging to model in vitro.

Conventional intestine models

Conventional intestinal models, such as traditional 2D cell culture of immortalised cell lines (e.g. CaCo2 or HT29), transwell cultures, Ussing chambers, and everted gut sacs, have been used extensively to understand better (patho-)physiological processes in the intestine. However, many intestinal functions are difficult to recapitulate and study using such simplistic models. Thus, these systems' translational and experimental value is limited.

In 2009, the development of intestinal organoids marked a milestone in the in vitro modelling of intestinal tissue. Intestinal organoids mimic the in vivo stem cell niche as intestinal stem cells spontaneously give rise to a closed, cystic mini-tissue with outward-facing buds representing the characteristic crypt-villus architecture of the intestinal epithelium. Intestinal organoids can contain all the different cell types of the intestinal epithelium, e.g. enterocytes, goblet cells, Paneth cells and enteroendocrine cells. Together with the accurate representation of the tissue architecture and cell-type composition, organoids have been shown to also exhibit key functional similarities to the native tissue. Furthermore, their long-term stability in culture, derivation from healthy and diseased origin and genetic manipulation possibilities make intestinal organoids a useful though simplistic model for large spread use as a platform for functional studies and disease modelling.

Nevertheless, several limitations restrict their usefulness as an intestinal model. First and foremost, the organoids' closed cystic structure makes their inner (apical) surface inaccessible, and separate treatment of apical and basolateral sides — and thus transport studies — highly cumbersome. Moreover, this closed cystic structure implies that intestinal organoids accumulate shed dead cells in their lumen putting spatial strain on the organoids, thus impeding undisturbed organoid culture over longer periods of time without disruption by mechanical disruption and passaging. Furthermore, intestinal organoid cultures suffer from strongly variable sizes, shapes, morphologies and localisations between single organoids in their 3D culture environment.

Intestine-on-a-chip models

Although organoids usually are referred to as miniature organs, they lack vital features to mimic organ-level complexity. For this reason, biofabricated devices have been developed, which surpass organoid limitations. Especially microfluidic devices hold great potential as platforms for in vitro models of organs, as they enable perfusion mimicking the function of blood circulation in tissues. Apart from fluidic flow, other culture parameters are incorporated into intestine-on-a-chip devices, including architectural cues, mechanical stimulation, oxygen gradients and co-cultures with other cell populations and the microbiota, to more accurately display the physiological behaviour of the actual organ.

Microfluidics

Opposite to traditional static cell culture, in microfluidic devices, fluid flows can be created, which closely mimick physiological fluid flow patterns. Fluid flow introduces physiological shear stress to cell surfaces, introduces apical delivery of nutrients and growth factors and enables the establishment of chemical gradients of, e.g. growth factors, which are vital for proper organ development. Overall, microfluidic devices increase the control over the organ-specific microenvironment, which allows for more precise models.

Different technologies have been used to introduce microfluidic flows in intestine-on-a-chip devices, including peristaltic pumps, syringe pumps, pressure generators and pumpless systems driven by hydrostatic pressure and gravity. An example of a gravity-driven microfluidic intestine-on-a-chip device is the OrganoPlate platform by Mimetas, which has been used as a disease model for inflammatory bowel disease by Beaurivage et al.

Mechanical stimulation

Beginning from the early stages of embryonic development up to the post-natal life, the intestine is constantly exposed to a wide range of mechanical forces. Peristalsis, the involuntary and cyclic propulsion of intestinal contents, is an essential part of the digestive process. It facilitates food digestion, nutrient absorption and intestinal emptying on a macro scale and applies shear stress and radial pressure on the intestinal epithelium on a micro-scale. In particular, mechanical factors were shown to influence intestinal development and homeostasis, such as gut looping, villi formation, and crypt localisation. Moreover, the chronic absence of mechanical stimuli in the human intestine has been associated with intestinal morbidity.

A prominent example where both mechanical stimulations in the form of peristalsis and microfluidic flow are used in combination is the Emulate intestine-on-a-chip system. The system consists of a two-way central cell culture microchannel, which is separated by a porous, extracellular matrix-coated, PDMS membrane allowing the separate culture of two different cell populations in the upper and lower microchannel. The central chamber is enclosed by two vacuum chambers running in parallel. The application of vacuum allows the cyclic unidirectional expansion of the porous membrane separating the channels to mimic peristaltic motion.

Architectural cues

As in traditional organoid culture, introducing a third culture dimension is critical for a better representation of the microanatomy of a tissue. Since 3D cell cultures implement more physiologically relevant biochemical and mechanical cues, 3D cultures generally achieve better cell viability and a more physiological transcriptome and proteome. Moreover, tissue homeostasis processes such as proliferation, differentiation and cell death are represented in a more physiological manner. The 3D support of cell cultures is commonly based on hydrogels, which mimick the native extracellular matrix. Cells can either be embedded into hydrogels or grown on a predefined micro-engineered hydrogel surface. The most commonly used hydrogel for 3D intestinal systems is Matrigel, a solubilised basement membrane extract from mouse sarcoma. However, Matrigel has significant disadvantages such as a xenogeneic origin, bath-to-batch variability, high cost and a poorly defined composition. As these factors hinder clinical translation, other hydrogels are increasingly used in 3D intestinal models, including fibrin, collagen, hyaluronic acid and PEG-based synthetic hydrogels.

In tissue engineering, microfabrication techniques are of critical importance, especially in modelling the tissue microenvironment. Apart from designing and fabricating the microfluidic device itself, microfabrication techniques are also used to create 3D microstructures which allow the patterning of cell culture surfaces closely resembling the native tissue topography, i.e. the crypt-villus-axis.

A prominent example of an intestine-on-a-chip system relying on architectural cues is the homeostatic mini-intestines by Nikolaev et al. They use microfabricated intestine-on-a-chip devices with a hydrogel chamber. The collagen-Matrigel-mix hydrogel is laser-ablated to generate a microchannel for a tubular intestinal lumen with crypt structures. The culture of intestinal stem cells in this device results in their self-organisation into a functional epithelium with the physiological spatial arrangement of the crypt-villus domains. These mini-intestines allow for an extended long term culture and give rise to rare intestinal cell types not commonly found in other 3D models. Another example for architecturally driven morphogenesis of intestine-on-a-chip models are the surface patterning techniques published by Gjorevski et al., they developed microfabricated devices to pattern hydrogel surfaces in order to reproducibly direct intestinal organoid geometry, size and cell distributions.

These examples show, that intestine-on-a-chip systems with extrinsically guided morphogenesis enable spatial and temporal control of signalling gradients and may provide a platform to extensively study intestinal morphogenesis, stem cell maintenance, crypt dynamics, and epithelial regeneration.^[1]

Co-culturing

The healthy intestine has a wide range of different functions, which requires a vast set of different cell types to fulfil them. The primary intestinal function, the absorption of nutrients, requires close contact between the intestinal epithelium and blood and lymph endothelial cells. Moreover, the intestinal microbiota plays a critical part in the digestion of food, which makes a reliable immune defence indispensable. Furthermore, muscle and nerve cells control peristalsis and satiety. Finally, mesenchymal cells are essential components of the intestinal stem cell niche as they provide physical support and secrete growth factors. Thus, incorporating different cell types in intestine-on-a-chip systems is vital to model different aspects of intestinal functions adequately.

First steps were taken in co-culturing the intestinal epithelium and the microbiota in intestine-on-a-chip systems. Examples are the establishment of an in vitro model for intestinal Shigella flexneri infection using the Emulate intestine-on-a-chip system or the recreation of a complex faeces-derived microbiota population with both aerobic and anaerobic species. Similarly, researchers have tried to recreate an immunocompetent intestinal epithelium in intestine-on-a-chip systems, by co-culturing the intestinal epithelium with peripheral blood mononuclear cells, monocytes, macrophages or neutrophils. Moreover, the epithelial-endothelial interface has been modelled in several different systems by culturing endothelial monolayers and the intestinal epithelium on opposite sides of a porous membrane.

Apart from co-culturing intestinal cells with other cell types, also the cell population of the intestinal epithelium is of high relevance. While some rather simplistic approaches use immortalised cell lines as cell source for an intestinal epithelium, there is a shift towards the use of organoid-derived intestinal stem cells, which allows the derivation of intestinal epithelia with a more physiological cell type composition.