Androgyny

From Wikipedia, the free encyclopedia

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

Androgyny is the combination of masculine and feminine characteristics into an ambiguous form. Androgyny may be expressed with regard to biological sex, gender identity, gender expression, or sexual identity. 

When androgyny refers to mixed biological sex characteristics in humans, it often refers to intersex people. As a gender identity, androgynous individuals may refer to themselves as non-binary, genderqueer, or gender neutral. As a form of gender expression, androgyny can be achieved through personal grooming or fashion. Androgynous gender expression has waxed and waned in popularity in different cultures and throughout history.

Etymology

Androgyny as a noun came into use c. 1850, nominalizing the adjective androgynous. The adjective use dates from the early 17th century and is itself derived from the older French (14th Century) and English (c. 1550) term androgyne. The terms are ultimately derived from Ancient Greek: ἀνδρόγυνος, from ἀνήρ, stem ἀνδρ- (anér, andr-, meaning man) and γυνή (gunē, gyné, meaning woman) through the Latin: androgynus, The older word form androgyne is still in use as a noun with an overlapping set of meanings.

History

Androgyny among humans – expressed in terms of biological sex characteristics, gender identity, or gender expression – is attested to from earliest history and across world cultures. In ancient Sumer, androgynous and hermaphroditic men were heavily involved in the cult of Inanna. A set of priests known as gala worked in Inanna's temples, where they performed elegies and lamentations. Gala took female names, spoke in the eme-sal dialect, which was traditionally reserved for women, and appear to have engaged in homosexual intercourse. In later Mesopotamian cultures, kurgarrū and assinnu were servants of the goddess Ishtar (Inanna's East Semitic equivalent), who dressed in female clothing and performed war dances in Ishtar's temples. Several Akkadian proverbs seem to suggest that they may have also engaged in homosexual intercourse. Gwendolyn Leick, an anthropologist known for her writings on Mesopotamia, has compared these individuals to the contemporary Indian hijra. In one Akkadian hymn, Ishtar is described as transforming men into women.

The ancient Greek myth of Hermaphroditus and Salmacis, two divinities who fused into a single immortal – provided a frame of reference used in Western culture for centuries. Androgyny and homosexuality are seen in Plato's Symposium in a myth that Aristophanes tells the audience. People used to be spherical creatures, with two bodies attached back to back who cartwheeled around. There were three sexes: the male-male people who descended from the sun, the female-female people who descended from the earth, and the male-female people who came from the moon. This last pairing represented the androgynous couple. These sphere people tried to take over the gods and failed. Zeus then decided to cut them in half and had Apollo repair the resulting cut surfaces, leaving the navel as a reminder to not defy the gods again. If they did, he would cleave them in two again to hop around on one leg. Plato states in this work that homosexuality is not shameful. This is one of the earlier written references to androgyny. Other early references to androgyny include astronomy, where androgyn was a name given to planets that were sometimes warm and sometimes cold.

Philosophers such as Philo of Alexandria, and early Christian leaders such as Origen and Gregory of Nyssa, continued to promote the idea of androgyny as humans' original and perfect state during late antiquity.” In medieval Europe, the concept of androgyny played an important role in both Christian theological debate and Alchemical theory. Influential Theologians such as John of Damascus and John Scotus Eriugena continued to promote the pre-fall androgyny proposed by the early Church Fathers, while other clergy expounded and debated the proper view and treatment of contemporary “hermaphrodites.”

Western esotericism’s embrace of androgyny continued into the modern period. A 1550 anthology of Alchemical thought, De Alchemia, included the influential Rosary of the Philosophers, which depicts the sacred marriage of the masculine principle (Sol) with the feminine principle (Luna) producing the "Divine Androgyne," a representation of Alchemical Hermetic beliefs in dualism, transformation, and the transcendental perfection of the union of opposites. The symbolism and meaning of androgyny was a central preoccupation of the German mystic Jakob Böhme and the Swedish philosopher Emanuel Swedenborg. The philosophical concept of the “Universal Androgyne” (or “Universal Hermaphrodite”) – a perfect merging of the sexes that predated the current corrupted world and/or was the utopia of the next – also plays a central role in Rosicrucian doctrine and in philosophical traditions such as Swedenborgianism and Theosophy. Twentieth century architect Claude Fayette Bragdon expressed the concept mathematically as a magic square, using it as building block in many of his most noted buildings.

Symbols and iconography

The Caduceus

 

In the ancient and medieval worlds, androgynous people and/or hermaphrodites were represented in art by the caduceus, a wand of transformative power in ancient Greco-Roman mythology. The caduceus was created by Tiresias and represents his transformation into a woman by Juno in punishment for striking at mating snakes. The caduceus was later carried by Hermes/Mercury and was the basis for the astronomical symbol for the planet Mercury and the botanical sign for hermaphrodite. That sign is now sometimes used for transgender people.

Another common androgyny icon in the medieval and early modern period was the Rebis, a conjoined male and female figure, often with solar and lunar motifs. Still another symbol was what is today called sun cross, which united the cross (or saltire) symbol for male with the circle for female. This sign is now the astronomical symbol for the planet Earth.

Mercury symbol derived from the Caduceus

 

A Rebis from 1617

 

"Rose and Cross" Androgyne symbol

Alternate "rose and cross" version

Biological

Historically, the word androgynous was applied to humans with a mixture of male and female sex characteristics, and was sometimes used synonymously with the term hermaphrodite. In some disciplines, such as botany, androgynous and hermaphroditic are still used interchangeably.

When androgyny is used to refer to physical traits, it often refers to a person whose biological sex is difficult to discern at a glance because of their mixture of male and female characteristics. Because androgyny encompasses additional meanings related to gender identity and gender expression that are distinct from biological sex, today the word androgynous is rarely used to formally describe mixed biological sex characteristics in humans. In modern English, the word intersex is used to more precisely describe individuals with mixed or ambiguous sex characteristics. However, both intersex and non-intersex people can exhibit a mixture of male and female sex traits such as hormone levels, type of internal and external genitalia, and the appearance of secondary sex characteristics.

Psychological

Though definitions of androgyny vary throughout the scientific community, it is generally supported that androgyny represents a blending of traits associated with both masculinity and femininity. In psychological study, various measures have been used to characterize gender, such as the Bem Sex Role Inventory, the Personal Attributes Questionnaire.

Broadly speaking, masculine traits are categorized as agentic and instrumental, dealing with assertiveness and analytical skill. Feminine traits are categorized as communal and expressive, dealing with empathy and subjectivity. Androgynous individuals exhibit behavior that extends beyond what is normally associated with their given sex. Due to the possession of both masculine and feminine characteristics, androgynous individuals have access to a wider array of psychological competencies in regards to emotional regulation, communication styles, and situational adaptability. Androgynous individuals have also been associated with higher levels of creativity and mental health.

Bem Sex-Role Inventory

The Bem Sex-Role Inventory (BSRI) was constructed by the early leading proponent of androgyny, Sandra Bem (1977). The BSRI is one of the most widely used gender measures. Based on an individual's responses to the items in the BSRI, they are classified as having one of four gender role orientations: masculine, feminine, androgynous, or undifferentiated. Bem understood that both masculine and feminine characteristics could be expressed by anyone and it would determine those gender role orientations.

An androgynous person is an individual who has a high degree of both feminine (expressive) and masculine (instrumental) traits. A feminine individual is ranked high on feminine (expressive) traits and ranked low on masculine (instrumental) traits. A masculine individual is ranked high on instrumental traits and ranked low on expressive traits. An undifferentiated person is low on both feminine and masculine traits.

According to Sandra Bem, androgynous individuals are more flexible and more mentally healthy than either masculine or feminine individuals; undifferentiated individuals are less competent. More recent research has debunked this idea, at least to some extent, and Bem herself has found weaknesses in her original pioneering work. Now she prefers to work with gender schema theory.

One study found that masculine and androgynous individuals had higher expectations for being able to control the outcomes of their academic efforts than feminine or undifferentiated individuals.

Personal Attribues Questionnaire

The Personal Attributes Questionnaire (PAQ) was developed in the 70s by Janet Spence, Robert Helmreich, and Joy Stapp. This test asked subjects to complete to a survey consisting of three sets of scales relating to masculinity, femininity, and masculinity-femininity. These scales had sets of adjectives commonly associated with males, females, and both. These descriptors were chosen based on typical characteristics as rated by a population of undergrad students. Similar to the BSRI, the PAQ labeled androgynous individuals as people who ranked highly in both the areas of masculinity and femininity. However, Spence and Helmreich considered androgyny to be a descriptor of high levels of masculinity and femininity as opposed to a category in and of itself.

Gender identity

An individual's gender identity, a personal sense of one's own gender, may be described as androgynous if they feel that they have both masculine and feminine aspects. The word androgyne can refer to a person who does not fit neatly into one of the typical masculine or feminine gender roles of their society, but is uncommon. Many androgynous individuals identify as being mentally or emotionally both masculine and feminine. They may identify as "gender-neutral", "genderqueer", or "non-binary". A person who is androgynous may engage freely in what is seen as masculine or feminine behaviors as well as tasks. They have a balanced identity that includes the virtues of both men and women and may disassociate the task with what gender they may be socially or physically assigned to. People who are androgynous disregard what traits are culturally constructed specifically for males and females within a specific society, and rather focus on what behavior is most effective within the situational circumstance.

Many non-western cultures recognize additional androgynous gender identities. Jewish culture recognizes the Tumtum and Androgynos genders. In Chinese culture exists the Yinyang ren gender. The Bugis of Indonesia recognize five genders, Bissu representing the androgynous category. In Hawaiian culture, the third gender Māhū is recognized. In Oaxacan Zapotec culture, the Muxe are recognized as a third gender. In India, the Hijra is the third androgynous gender. Samoans accept Fa’afafine as a third gender. Native American culture includes Two Spirit as a general third gender.

Gender expression

Gender expression, which includes a mixture of masculine and feminine characteristics, can be described as androgynous. The categories of masculine and feminine in gender expression are socially constructed, and rely on shared conceptions of clothing, behavior, communication style, and other aspects of presentation. In some cultures, androgynous gender expression has been celebrated, while in others, androgynous expression has been limited or suppressed. To say that a culture or relationship is androgynous is to say that it lacks rigid gender roles, or has blurred lines between gender roles. 

The word genderqueer is often used by androgynous individuals to refer to themselves, but the terms genderqueer and androgynous are neither equivalent nor interchangeable. Genderqueer is not specific to androgynes, and does not denote gender identity. It may refer to any person, cisgender or transgender, whose behavior falls outside conventional gender norms. Furthermore, genderqueer, by virtue of its ties with queer culture, carries sociopolitical connotations that androgyny does not carry. For these reasons, some androgynes may find the label genderqueer inaccurate, inapplicable, or offensive. Androgneity is considered by some to be a viable alternative to androgyn for differentiating internal (psychological) factors from external (visual) factors.

Terms such as bisexual, heterosexual, and homosexual have less meaning for androgynous individuals who do not identify as men or women to begin with. Infrequently the words gynephilia and androphilia are used, and some describe themselves as androsexual. These words refer to the gender of the person someone is attracted to, but do not imply any particular gender on the part of the person who is feeling the attraction.

Louise Brooks exemplified the flapper. Flappers challenged traditional gender roles, had boyish hair cuts and androgynous figures.

Androgyny in fashion

Throughout most of twentieth century Western history, social rules have restricted people's dress according to gender. Trousers were traditionally a male form of dress, frowned upon for women. However, during the 1800s, female spies were introduced and Vivandières wore a certain uniform with a dress over trousers. Women activists during that time would also decide to wear trousers, for example Luisa Capetillo, a women's rights activist and the first woman in Puerto Rico to wear trousers in public.

Coco Chanel wearing a sailor's jersey and trousers. 1928

 

In the 1900s, starting around World War I traditional gender roles blurred and fashion pioneers such as Paul Poiret and Coco Chanel introduced trousers to women's fashion. The "flapper style" for women of this era included trousers and a chic bob, which gave women an androgynous look. Coco Chanel, who had a love for wearing trousers herself, created trouser designs for women such as beach pajamas and horse-riding attire. During the 1930s, glamorous actresses such as Marlene Dietrich fascinated and shocked many with their strong desire to wear trousers and adopt the androgynous style. Dietrich is remembered as one of the first actresses to wear trousers in a premiere.

Yves Saint Laurent, the tuxedo suit "Le Smoking", created in 1966

 

Throughout the 1960s and 1970s, the women's liberation movement is likely to have contributed to ideas and influenced fashion designers, such as Yves Saint Laurent. Yves Saint Laurent designed the Le Smoking suit and first introduced in 1966, and Helmut Newton’s erotized androgynous photographs of it made Le Smoking iconic and classic. The Le Smoking tuxedo was a controversial statement of femininity and has revolutionized trousers.

Elvis Presley, however is considered to be the one who introduced the androgynous style in rock'n'roll and made it the standard template for rock'n'roll front-men since the 1950s. His pretty face and use of eye makeup often made people think he was a rather "effeminate guy", but Elvis Presley was considered as the prototype for the looks of rock'n'roll. The Rolling Stones, says Mick Jagger became androgynous "straightaway unconsciously" because of him.

However, the upsurge of androgynous dressing for men really began after during the 1960s and 1970s. When the Rolling Stones played London's Hyde Park in 1969, Mick Jagger wore a white "man's dress" designed by British designer Mr Fish. Mr Fish, also known as Michael Fish, was the most fashionable shirt-maker in London, the inventor of the Kipper tie, and a principal taste-maker of the Peacock revolution in men's fashion. His creation for Mick Jagger was considered to be the epitome of the swinging 60s. From then on, the androgynous style was being adopted by many celebrities. 

Annie Lennox was known for her androgyny in the 1980s

 

During the 1970s, Jimi Hendrix was wearing high heels and blouses quite often, and David Bowie presented his alter ego Ziggy Stardust, a character that was a symbol of sexual ambiguity when he launched the album The Rise and Fall of Ziggy Stardust and Spiders from Mars. This was when androgyny entered the mainstream in the 1970s and had a big influence in pop culture. Another significant influence during this time included John Travolta, one of the androgynous male heroes of the post-counter-culture disco era in the 1970s, who starred in Grease and Saturday Night Fever.

Continuing into the 1980s, the rise of avant-garde fashion designers like Yohji Yamamoto, challenged the social constructs around gender. They reinvigorated androgyny in fashion, addressing gender issues. This was also reflected within pop culture icons during the 1980s, such as David Bowie and Annie Lennox.

Power dressing for women became even more prominent within the 1980s which was previously only something done by men in order to look structured and powerful. However, during the 1980s this began to take a turn as women were entering jobs with equal roles to the men. In the article “The Menswear Phenomenon” by Kathleen Beckett written for Vogue in 1984 the concept of power dressing is explored as women entered these jobs they had no choice but to tailor their wardrobes accordingly, eventually leading the ascension of power dressing as a popular style for women. Women begin to find through fashion they can incite men to pay more attention to the seduction of their mental prowess rather, than the physical attraction of their appearance. This influence in the fashion world quickly makes its way to the world of film, with movies like "Working Girl" using power dressing women as their main subject matter. 

Androgynous fashion made its most powerful in the 1980s debut through the work of Yohji Yamamoto and Rei Kawakubo, who brought in a distinct Japanese style that adopted distinctively gender ambiguous theme. These two designers consider themselves to very much a part of the avant-garde, reinvigorating Japanism. Following a more anti-fashion approach and deconstructing garments, in order to move away from the more mundane aspects of current Western fashion. This would end up leading a change in Western fashion in the 1980s that would lead on for more gender friendly garment construction. This is because designers like Yamamoto believe that the idea of androgyny should be celebrated, as it is an unbiased way for an individual to identify with one's self and that fashion is purely a catalyst for this.

Also during the 1980s, Grace Jones's a famous singer and fashion model gender-thwarted appearance in the 1980s which startled the public, but her androgynous style of heavily derivative of power dressing and eccentric personality has inspired many, and has become an androgynous style icon for modern celebrities. This was seen as controversial but from then on, there was a rise of unisex designers later in the 1990s and the androgynous style was widely adopted by many.

In 2016, Louis Vuitton revealed that Jaden Smith would star in their womenswear campaign. Because of events like this, gender fluidity in fashion is being vigorously discussed in the media, with the concept being articulated by Lady Gaga, Ruby Rose, and in Tom Hooper's film The Danish Girl. Jaden Smith and other young individuals, such as Lily-Rose Depp, have inspired the movement with his appeal for clothes to be non-gender specific, meaning that men can wear skirts and women can wear boxer shorts if they so wish.

Alternatives

An alternative to androgyny is gender-role transcendence: the view that individual competence should be conceptualized on a personal basis rather than on the basis of masculinity, femininity, or androgyny.

In agenderism, the division of people into women and men (in the psychical sense), is considered erroneous and artificial. Agendered individuals are those who reject genderic labeling in conception of self-identity and other matters. They see their subjectivity through the term person instead of woman or man. According to E. O. Wright, genderless people can have traits, behaviors and dispositions that correspond to what is currently viewed as feminine and masculine, and the mix of these would vary across persons. Nevertheless, it doesn't suggest that everyone would be androgynous in their identities and practices in the absence of gendered relations. What disappears in the idea of genderlessness is any expectation that some characteristics and dispositions are strictly attributed to a person of any biological sex.

Contemporary trends

Jennifer Miller, bearded woman

 

X Japan founder Yoshiki is often labelled androgynous, known for having worn lace dresses and acting effeminate during performances

 

South Korean pop star G-Dragon is often noted for his androgynous looks

 

Androgyny has been gaining more prominence in popular culture in the early 21st century. Both fashion industries and pop culture have accepted and even popularised the "androgynous" look, with several current celebrities being hailed as creative trendsetters.

The rise of the metrosexual in the first decade of the 2000s has also been described as a related phenomenon associated with this trend. Traditional gender stereotypes have been challenged and reset in recent years dating back to the 1960s, the hippie movement and flower power. Artists in film such as Leonardo DiCaprio sported the "skinny" look in the 1990s, a departure from traditional masculinity which resulted in a fad known as "Leo Mania". This trend came long after musical superstars such as David Bowie, Boy George, Prince, Pete Burns and Annie Lennox challenged the norms in the 1970s and had elaborate cross gender wardrobes by the 1980s. Musical stars such as Brett Anderson of the British band Suede, Marilyn Manson and the band Placebo have used clothing and makeup to create an androgyny culture throughout the 1990s and the first decade of the 2000s.

While the 1990s unrolled and fashion developed an affinity for unisex clothes there was a rise of designers who favored that look, like Helmut Lang, Giorgio Armani and Pierre Cardin, the trends in fashion hit the public mainstream in the 2000s (decade) that featured men sporting different hair styles: longer hair, hairdyes, hair highlights. Men in catalogues started wearing jewellery, make up, visual kei, designer stubble. These styles have become a significant mainstream trend of the 21st century, both in the western world and in Asia. Japanese and Korean cultures have featured the androgynous look as a positive attribute in society, as depicted in both K-pop, J-pop, in anime and manga, as well as the fashion industry.

XY sex-determination system

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/XY_sex-determination_system

 

Drosophila sex-chromosomes

 

Pollen cones of a male Ginkgo biloba tree, a dioecious species

 

Ovules of a female Ginkgo biloba tree

 

The XY sex-determination system is found in humans, most other mammals, some insects (Drosophila), some snakes, and some plants (Ginkgo). In this system, the sex of an individual is determined by a pair of sex chromosomes. Females typically have two of the same kind of sex chromosome (XX) and are called the homogametic sex. Males typically have two different kinds of sex chromosomes (XY) and are called the heterogametic sex.

 

In humans, the presence of the Y chromosome is responsible for triggering male development; in the absence of the Y chromosome, the fetus will undergo female development. More specifically, it is the SRY gene located on the Y chromosome that is of importance to male differentiation. Variations to the sex gene karyotype could include rare disorders such as XX males (often due to translocation of the SRY gene to the X chromosome) or XY gonadal dysgenesis in people who are externally female (due to mutations in the SRY gene). In addition, other rare genetic variations such as Turner's (XO) and Klinefelter's (XXY) are seen as well.

The XY system contrasts in several ways with the ZW sex-determination system found in birds, some insects, many reptiles, and various other animals, in which the heterogametic sex is female. It had been thought for several decades that, in all snakes, sex was determined by the ZW system, but there had been observations of unexpected effects in the genetics of species in the families Boidae and Pythonidae; for example, parthenogenic reproduction produced only females rather than males, which is the opposite of what is to be expected in the ZW system. In the early years of the 21st century such observations prompted research that demonstrated that all pythons and boas so far investigated definitely have the XY system of sex determination.

A temperature-dependent sex determination system is found in some reptiles.

Mechanisms

All animals have a set of DNA coding for genes present on chromosomes. In humans, most mammals, and some other species, two of the chromosomes, called the X chromosome and Y chromosome, code for sex. In these species, one or more genes are present on their Y chromosome that determine maleness. In this process, an X chromosome and a Y chromosome act to determine the sex of offspring, often due to genes located on the Y chromosome that code for maleness. Offspring have two sex chromosomes: an offspring with two X chromosomes will develop female characteristics, and an offspring with an X and a Y chromosome will develop male characteristics.

Humans

Human male XY chromosomes after G-banding

 

In humans, half of spermatozoons carry X chromosome and the other half Y chromosome. A single gene (SRY) present on the Y chromosome acts as a signal to set the developmental pathway towards maleness. Presence of this gene starts off the process of virilization. This and other factors result in the sex differences in humans. The cells in females, with two X chromosomes, undergo X-inactivation, in which one of the two X chromosomes is inactivated. The inactivated X chromosome remains within a cell as a Barr body.

Humans, as well as some other organisms, can have a rare chromosomal arrangement that is contrary to their phenotypic sex; for example, XX males or XY gonadal dysgenesis (see androgen insensitivity syndrome). Additionally, an abnormal number of sex chromosomes (aneuploidy) may be present, such as Turner's syndrome, in which a single X chromosome is present, and Klinefelter's syndrome, in which two X chromosomes and a Y chromosome are present, XYY syndrome and XXYY syndrome. Other less common chromosomal arrangements include: triple X syndrome, 48, XXXX, and 49, XXXXX.

Other animals

In most mammals, sex is determined by presence of the Y chromosome. "Female" is the default sex, due to the absence of the Y chromosome. In the 1930s, Alfred Jost determined that the presence of testosterone was required for Wolffian duct development in the male rabbit.

SRY is a sex-determining gene on the Y chromosome in the therians (placental mammals and marsupials). Non-human mammals use several genes on the Y chromosome. Not all male-specific genes are located on the Y chromosome. Platypus, a monotreme, use five pairs of different XY chromosomes with six groups of male-linked genes, AMH being the master switch. Other species (including most Drosophila species) use the presence of two X chromosomes to determine femaleness: one X chromosome gives putative maleness, but the presence of Y chromosome genes is required for normal male development.

Other systems

Birds and many insects have a similar system of sex determination (ZW sex-determination system), in which it is the females that are heterogametic (ZW), while males are homogametic (ZZ).

Many insects of the order Hymenoptera instead have a system (the haplo-diploid sex-determination system), where the males are haploid individuals (which have just one chromosome of each type), while the females are diploid (with chromosomes appearing in pairs). Some other insects have the X0 sex-determination system, where just one chromosome type appears in pairs for the female but alone in the males, while all other chromosomes appear in pairs in both sexes.

Influences

Genetic

PBB Protein SRY image

It has long been believed that the female form was the default template for the mammalian fetuses of both sexes. After the discovery of the testis-determining gene SRY, many scientists shifted to the theory that the genetic mechanism that causes a fetus to develop into a male form was initiated by the SRY gene, which was thought to be responsible for the production of testosterone and its overall effects on body and brain development. This perspective still shares the classical way of thinking; that in order to produce two sexes, nature has developed a default female pathway and an active pathway by which male genes would initiate the process of determining a male sex, as something that is developed in addition to and based on the default female form. However, In an interview for the Rediscovering Biology website, researcher Eric Vilain described how the paradigm changed since the discovery of the SRY gene:

For a long time we thought that SRY would activate a cascade of male genes. It turns out that the sex determination pathway is probably more complicated and SRY may in fact inhibit some anti-male genes.
The idea is instead of having a simplistic mechanism by which you have pro-male genes going all the way to make a male, in fact there is a solid balance between pro-male genes and anti-male genes and if there is a little too much of anti-male genes, there may be a female born and if there is a little too much of pro-male genes then there will be a male born.
We [are] entering this new era in molecular biology of sex determination where it's a more subtle dosage of genes, some pro-males, some pro-females, some anti-males, some anti-females that all interplay with each other rather than a simple linear pathway of genes going one after the other, which makes it very fascinating but very complicated to study.

In mammals, including humans, the SRY gene is responsible with triggering the development of non-differentiated gonads into testes, rather than ovaries. However, there are cases in which testes can develop in the absence of an SRY gene. In these cases, the SOX9 gene, involved in the development of testes, can induce their development without the aid of SRY. In the absence of SRY and SOX9, no testes can develop and the path is clear for the development of ovaries. Even so, the absence of the SRY gene or the silencing of the SOX9 gene are not enough to trigger sexual differentiation of a fetus in the female direction. A recent finding suggests that ovary development and maintenance is an active process, regulated by the expression of a "pro-female" gene, FOXL2. In an interview for the TimesOnline edition, study co-author Robin Lovell-Badge explained the significance of the discovery:

We take it for granted that we maintain the sex we are born with, including whether we have testes or ovaries. But this work shows that the activity of a single gene, FOXL2, is all that prevents adult ovary cells turning into cells found in testes.

Implications

Looking into the genetic determinants of human sex can have wide-ranging consequences. Scientists have been studying different sex determination systems in fruit flies and animal models to attempt an understanding of how the genetics of sexual differentiation can influence biological processes like reproduction, ageing and disease.

Maternal

In humans and many other species of animals, the father determines the sex of the child. In the XY sex-determination system, the female-provided ovum contributes an X chromosome and the male-provided sperm contributes either an X chromosome or a Y chromosome, resulting in female (XX) or male (XY) offspring, respectively.

Hormone levels in the male parent affect the sex ratio of sperm in humans. Maternal influences also impact which sperm are more likely to achieve conception. 

Human ova, like those of other mammals, are covered with a thick translucent layer called the zona pellucida, which the sperm must penetrate to fertilize the egg. Once viewed simply as an impediment to fertilization, recent research indicates the zona pellucida may instead function as a sophisticated biological security system that chemically controls the entry of the sperm into the egg and protects the fertilized egg from additional sperm.

Recent research indicates that human ova may produce a chemical which appears to attract sperm and influence their swimming motion. However, not all sperm are positively impacted; some appear to remain uninfluenced and some actually move away from the egg.

Maternal influences may also be possible that affect sex determination in such a way as to produce fraternal twins equally weighted between one male and one female.

The time at which insemination occurs during the estrus cycle has been found to affect the sex ratio of the offspring of humans, cattle, hamsters, and other mammals. Hormonal and pH conditions within the female reproductive tract vary with time, and this affects the sex ratio of the sperm that reach the egg.

Sex-specific mortality of embryos also occurs.

History

Ancient ideas on sex determination

Aristotle believed that the sex of an infant is determined by how much heat a man's sperm had during insemination. He wrote:

...the semen of the male differs from the corresponding secretion of the female in that it contains a principle within itself of such a kind as to set up movements also in the embryo and to concoct thoroughly the ultimate nourishment, whereas the secretion of the female contains material alone. If, then, the male element prevails it draws the female element into itself, but if it is prevailed over it changes into the opposite or is destroyed.

Aristotle claimed that the male principle was the driver behind sex determination, such that if the male principle was insufficiently expressed during reproduction, the fetus would develop as a female.

20th century genetics

Nettie Stevens and Edmund Beecher Wilson are credited with independently discovering, in 1905, the chromosomal XY sex-determination system, i.e. the fact that males have XY sex chromosomes and females have XX sex chromosomes.

The first clues to the existence of a factor that determines the development of testis in mammals came from experiments carried out by Alfred Jost, who castrated embryonic rabbits in utero and noticed that they all developed as female.

In 1959, C. E. Ford and his team, in the wake of Jost's experiments, discovered that the Y chromosome was needed for a fetus to develop as male when they examined patients with Turner's syndrome, who grew up as phenotypic females, and found them to be X0 (hemizygous for X and no Y). At the same time, Jacob & Strong described a case of a patient with Klinefelter syndrome (XXY), which implicated the presence of a Y chromosome in development of maleness.

All these observations lead to a consensus that a dominant gene that determines testis development (TDF) must exist on the human Y chromosome. The search for this testis-determining factor (TDF) led a team of scientists in 1990 to discover a region of the Y chromosome that is necessary for the male sex determination, which was named SRY (sex-determining region of the Y chromosome).

Polytene chromosome

From Wikipedia, the free encyclopedia

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

 

Polytene chromosomes in a Chironomus salivary gland cell

 

Polytene chromosome

 

Polytene chromosomes are large chromosomes which have thousands of DNA strands. They provide a high level of function in certain tissues such as salivary glands.

Polytene chromosomes were first reported by E.G.Balbiani in 1881. Polytene chromosomes are found in dipteran flies: the best understood are those of Drosophila, Chironomus and Rhynchosciara. They are present in another group of arthropods of the class Collembola, a protozoan group Ciliophora, mammalian trophoblasts and antipodal, and suspensor cells in plants. In insects, they are commonly found in the salivary glands when the cells are not dividing. 

They are produced when repeated rounds of DNA replication without cell division forms a giant chromosome. Thus polytene chromosomes form when multiple rounds of replication produce many sister chromatids which stay fused together.

Polytene chromosomes, at interphase, are seen to have distinct thick and thin banding patterns. These patterns were originally used to help map chromosomes, identify small chromosome mutations, and in taxonomic identification. They are now used to study the function of genes in transcription.

Function

In addition to increasing the volume of the cells' nuclei and causing cell expansion, polytene cells may also have a metabolic advantage as multiple copies of genes permits a high level of gene expression. In Drosophila melanogaster, for example, the chromosomes of the larval salivary glands undergo many rounds of endoreduplication to produce large quantities of adhesive mucoprotein (“glue”) before pupation. Another example within the fly itself is the tandem duplication of various polytene bands located near the centromere of the X chromosome which results in the Bar phenotype of kidney-shaped eyes.

The interbands are involved in the interaction with the active chromatin proteins, nucleosome remodeling, and origin recognition complexes. Their primary functions are: to act as binding sites for RNA pol II, to initiate replication and, to start nucleosome remodeling of short fragments of DNA.

Structure

In insects, polytene chromosomes are commonly found in the salivary glands; they are also referred to as "salivary gland chromosomes". The large size of the chromosome is due to the presence of many longitudinal strands called chromonemata; hence the name polytene (many stranded). They are about 0.5 mm in length and 20 μm in diameter. The chromosomal strands are formed after repeated division of the chromosome in the absence of cytoplasmic division. This type of division is called endomitosis. The polytene chromosome contains two types of bands, dark bands and interbands. The dark bands are darkly stained and the inter bands are lightly stained with nuclear stains. The dark bands contain more DNA and less RNA. The interbands contain more RNA and less DNA. The amount of DNA in interbands ranges from 0.8 - 25%.

The bands of polytene chromosomes become enlarged at certain times to form swellings called puffs. The formation of puffs is called puffing. In the regions of puffs, the chromonemata uncoil and open out to form many loops. The puffing is caused by the uncoiling of individual chromomeres in a band. The puffs indicate the site of active genes where mRNA synthesis takes place. The chromonemata of puffs give out a series of many loops laterally. As these loops appear as rings, they are called Balbiani rings after the name of the researcher who discovered them. They are formed of DNA, RNA and a few proteins. As they are the site of transcription, transcription mechanisms such as RNA polymerase and ribonucleoproteins are present.

In protozoans, there is no transcription, since the puff consists only of DNA.

History

Polytene chromosomes were originally observed in the larval salivary glands of Chironomus midges by Édouard-Gérard Balbiani in 1881. Balbiani described the chromosomal puffs among the tangled thread inside the nucleus, and named it "permanent spireme". In 1890, he observed similar spireme in a ciliated protozoan Loxophyllum meleagris. The existence of such spireme in Drosophila melanogaster was reported by Bulgarian geneticist Dontcho Kostoff in 1930. Kostoff predicted that the discs (bands) which he observed were "the actual packets in which inherited characters are passed from generation to generation."

The hereditary nature of these structures was not confirmed until they were studied in Drosophila melanogaster in the early 1930s by German biologists Emil Heitz and Hans Bauer. In 1930, Heitz studied different species of Drosophila (D. melanogaster, D. simulans, D. hydei, and D. virilis) and found that all their interphase chromatins in certain cells were swollen and messy. In 1932, he collaborated with Karl Heinrich Bauer with whom he discovered that the tangled chromosomes having distinct bands are unique to the cells of the salivary glands, midgut, Malphigian tubules, and brain of the flies Bibio hurtulunus and Drosophila funebris. The two papers were published in the early 1933. Unaware of these papers, an American geneticist Theophilus Shickel Painter reported in December 1933 the existence of giant chromosome in D. melanogaster (followed by a series of papers the following year). Learning of this, Heitz accused Painter of deliberately ignoring their original publication to claim priority of discovery. In 1935, Henry J. Muller and A.A. Prokofyeva established that the individual band or part of a band corresponds with a gene in Drosophila. The same year, P.C. Koller hesitantly introduced the name "polytene" to describe the giant chromosome, writing:

It seems that we can regard these chromosomes as corresponding with paired pachytene chromosomes at meiosis in which the intercalary parts between chromomeres have been stretched and separated into smaller units, and in which, instead of two threads lying side by side, we have 16 or even more. Hence they are "polytene" rather than pachytene; I do not, however, propose to use this term; I shall refer to them as "multiple threads."

Occurrence

Polytene chromosomes are present in secretory tissues of dipteran insects such as the Malpighian tubules of Sciara and also in protists, plants, mammals, or in cells from other insects. Some of the largest polytene chromosomes described thus far occur in larval salivary gland cells of the chironomid genus Axarus. 

In plants, they are found in only a few species, and are restricted to ovary and immature seed tissues such as in Phaseolus coccineus and P. vulgaris (Nagl, 1981), and the anther tapetum of Vigna unguiculata and of some Phaseolus species.

Polytene chromosomes are also used to identify the species of chironomid larvae that are notoriously difficult to identify. Each morphologically distinct group of larvae consists of a number of morphologically identical (sibling) species that can only be identified by rearing adult males or by cytogenetic analysis of the polytene chromosomes of the larvae. Karyotypes are used to confirm the presence of specific species and to study genetic diversity in species with a wide range of genetic variation.

Non-coding DNA

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Non-coding_DNA

 

Non-coding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAs). Other functions of non-coding DNA include the transcriptional and translational regulation of protein-coding sequences, scaffold attachment regions, origins of DNA replication, centromeres and telomeres.

The amount of non-coding DNA varies greatly among species. Often, only a small percentage of the genome is responsible for coding proteins, but an increasing percentage is being shown to have regulatory functions. When there is much non-coding DNA, a large proportion appears to have no biological function, as predicted in the 1960s. Since that time, this non-functional portion has controversially been called "junk DNA".

The international Encyclopedia of DNA Elements (ENCODE) project uncovered, by direct biochemical approaches, that at least 80% of human genomic DNA has biochemical activity. Though this was not necessarily unexpected due to previous decades of research discovering many functional non-coding regions, some scientists criticized the conclusion for conflating biochemical activity with biological function. Estimates for the biologically functional fraction of the human genome based on comparative genomics range between 8 and 15%. However, others have argued against relying solely on estimates from comparative genomics due to its limited scope. Non-coding DNA has been found to be involved in epigenetic activity and complex networks of genetic interactions and is being explored in evolutionary developmental biology.

Fraction of non-coding genomic DNA

Utricularia gibba has only 3% non-coding DNA.

 

The amount of total genomic DNA varies widely between organisms, and the proportion of coding and non-coding DNA within these genomes varies greatly as well. For example, it was originally suggested that over 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA, while 20% of a typical prokaryote genome is non-coding.

In eukaryotes, genome size, and by extension the amount of non-coding DNA, is not correlated to organism complexity, an observation known as the C-value enigma. For example, the genome of the unicellular Polychaos dubium (formerly known as Amoeba dubia) has been reported to contain more than 200 times the amount of DNA in humans. The pufferfish Takifugu rubripes genome is only about one eighth the size of the human genome, yet seems to have a comparable number of genes; approximately 90% of the Takifugu genome is non-coding DNA. Therefore, most of the difference in genome size is not due to variation in amount of coding DNA, rather, it is due to a difference in the amount of non-coding DNA.

In 2013, a new "record" for the most efficient eukaryotic genome was discovered with Utricularia gibba, a bladderwort plant that has only 3% non-coding DNA and 97% of coding DNA. Parts of the non-coding DNA were being deleted by the plant and this suggested that non-coding DNA may not be as critical for plants, even though non-coding DNA is useful for humans. Other studies on plants have discovered crucial functions in portions of non-coding DNA that were previously thought to be negligible and have added a new layer to the understanding of gene regulation.

Types of non-coding DNA sequences

Cis- and trans-regulatory elements

Cis-regulatory elements are sequences that control the transcription of a nearby gene. Many such elements are involved in the evolution and control of development. Cis-elements may be located in 5' or 3' untranslated regions or within introns. Trans-regulatory elements control the transcription of a distant gene.

Promoters facilitate the transcription of a particular gene and are typically upstream of the coding region. Enhancer sequences may also exert very distant effects on the transcription levels of genes.

Introns

Simple illustration of an unspliced mRNA precursor, with two introns and three exons (top). After the introns have been removed via splicing, the mature mRNA sequence is ready for translation (bottom).

 

Introns are non-coding sections of a gene, transcribed into the precursor mRNA sequence, but ultimately removed by RNA splicing during the processing to mature messenger RNA. Many introns appear to be mobile genetic elements.

Studies of group I introns from Tetrahymena protozoans indicate that some introns appear to be selfish genetic elements, neutral to the host because they remove themselves from flanking exons during RNA processing and do not produce an expression bias between alleles with and without the intron. Some introns appear to have significant biological function, possibly through ribozyme functionality that may regulate tRNA and rRNA activity as well as protein-coding gene expression, evident in hosts that have become dependent on such introns over long periods of time; for example, the trnL-intron is found in all green plants and appears to have been vertically inherited for several billions of years, including more than a billion years within chloroplasts and an additional 2–3 billion years prior in the cyanobacterial ancestors of chloroplasts.

Pseudogenes

Pseudogenes are DNA sequences, related to known genes, that have lost their protein-coding ability or are otherwise no longer expressed in the cell. Pseudogenes arise from retrotransposition or genomic duplication of functional genes, and become "genomic fossils" that are nonfunctional due to mutations that prevent the transcription of the gene, such as within the gene promoter region, or fatally alter the translation of the gene, such as premature stop codons or frameshifts. Pseudogenes resulting from the retrotransposition of an RNA intermediate are known as processed pseudogenes; pseudogenes that arise from the genomic remains of duplicated genes or residues of inactivated genes are nonprocessed pseudogenes. Transpositions of once functional mitochondrial genes from the cytoplasm to the nucleus, also known as NUMTs, also qualify as one type of common pseudogene. Numts occur in many eukaryotic taxa. 

While Dollo's Law suggests that the loss of function in pseudogenes is likely permanent, silenced genes may actually retain function for several million years and can be "reactivated" into protein-coding sequences and a substantial number of pseudogenes are actively transcribed. Because pseudogenes are presumed to change without evolutionary constraint, they can serve as a useful model of the type and frequencies of various spontaneous genetic mutations.

Repeat sequences, transposons and viral elements

Mobile genetic elements in the cell (left) and how they can be acquired (right)

 

Transposons and retrotransposons are mobile genetic elements. Retrotransposon repeated sequences, which include long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), account for a large proportion of the genomic sequences in many species. Alu sequences, classified as a short interspersed nuclear element, are the most abundant mobile elements in the human genome. Some examples have been found of SINEs exerting transcriptional control of some protein-encoding genes.

Endogenous retrovirus sequences are the product of reverse transcription of retrovirus genomes into the genomes of germ cells. Mutation within these retro-transcribed sequences can inactivate the viral genome.

Over 8% of the human genome is made up of (mostly decayed) endogenous retrovirus sequences, as part of the over 42% fraction that is recognizably derived of retrotransposons, while another 3% can be identified to be the remains of DNA transposons. Much of the remaining half of the genome that is currently without an explained origin is expected to have found its origin in transposable elements that were active so long ago (> 200 million years) that random mutations have rendered them unrecognizable. Genome size variation in at least two kinds of plants is mostly the result of retrotransposon sequences.

Telomeres

Telomeres are regions of repetitive DNA at the end of a chromosome, which provide protection from chromosomal deterioration during DNA replication. Recent studies have shown that telomeres function to aid in its own stability. Telomeric repeat-containing RNA (TERRA) are transcripts derived from telomeres. TERRA has been shown to maintain telomerase activity and lengthen the ends of chromosomes.

Junk DNA

The term "junk DNA" became popular in the 1960s. According to T. Ryan Gregory, the nature of junk DNA was first discussed explicitly in 1972 by a genomic biologist, David Comings, who applied the term to all non-coding DNA. The term was formalized that same year by Susumu Ohno, who noted that the mutational load from deleterious mutations placed an upper limit on the number of functional loci that could be expected given a typical mutation rate. Ohno hypothesized that mammal genomes could not have more than 30,000 loci under selection before the "cost" from the mutational load would cause an inescapable decline in fitness, and eventually extinction. This prediction remains robust, with the human genome containing approximately 20,000 genes. Another source for Ohno's theory was the observation that even closely related species can have widely (orders-of-magnitude) different genome sizes, which had been dubbed the C-value paradox in 1971. Though the fruitfulness of the term "junk DNA" has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality and though some have recommended using more neutral terminology such as "non-coding DNA" instead; "junk DNA" remains a label for the portions of a genome sequence for which no discernible function has been identified and that through comparative genomics analysis appear under no functional constraint suggesting that the sequence itself has provided no adaptive advantage. Since the late 70s it has become apparent that the majority of non-coding DNA in large genomes finds its origin in the selfish amplification of transposable elements, of which W. Ford Doolittle and Carmen Sapienza in 1980 wrote in the journal Nature: "When a given DNA, or class of DNAs, of unproven phenotypic function can be shown to have evolved a strategy (such as transposition) which ensures its genomic survival, then no other explanation for its existence is necessary." The amount of junk DNA can be expected to depend on the rate of amplification of these elements and the rate at which non-functional DNA is lost. In the same issue of Nature, Leslie Orgel and Francis Crick wrote that junk DNA has "little specificity and conveys little or no selective advantage to the organism". The term occurs mainly in popular science and in a colloquial way in scientific publications, and it has been suggested that its connotations may have delayed interest in the biological functions of non-coding DNA. Several lines of evidence indicate that some "junk DNA" sequences are likely to have unidentified functional activity and that the process of exaptation of fragments of originally selfish or non-functional DNA has been commonplace throughout evolution.

ENCODE Project

In 2012, the ENCODE project, a research program supported by the National Human Genome Research Institute, reported that 76% of the human genome's non-coding DNA sequences were transcribed and that nearly half of the genome was in some way accessible to genetic regulatory proteins such as transcription factors. However, the suggestion by ENCODE that over 80% of the human genome is biochemically functional has been criticized by other scientists, who argue that neither accessibility of segments of the genome to transcription factors nor their transcription guarantees that those segments have biochemical function and that their transcription is selectively advantageous. Furthermore, the much lower estimates of functionality prior to ENCODE were based on genomic conservation estimates across mammalian lineages. In response to such views, other scientists argue that the wide spread transcription and splicing that is observed in the human genome directly by biochemical testing is a more accurate indicator of genetic function than genomic conservation because conservation estimates are relative due to incredible variations in genome sizes of even closely related species, it is partially tautological, and these estimates are not based on direct testing for functionality on the genome. Conservation estimates may be used to provide clues to identify possible functional elements in the genome, but it does not limit or cap the total amount of functional elements that could possibly exist in the genome since elements that do things at the molecular level can be missed by comparative genomics. Furthermore, much of the apparent junk DNA is involved in epigenetic regulation and appears to be necessary for the development of complex organisms. In a 2014 paper, ENCODE researchers tried to address "the question of whether nonconserved but biochemically active regions are truly functional". They noted that in the literature, functional parts of the genome have been identified differently in previous studies depending on the approaches used. There have been three general approaches used to identify functional parts of the human genome: genetic approaches (which rely on changes in phenotype), evolutionary approaches (which rely on conservation) and biochemical approaches (which rely on biochemical testing and was used by ENCODE). All three have limitations: genetic approaches may miss functional elements that do not manifest physically on the organism, evolutionary approaches have difficulties using accurate multispecies sequence alignments since genomes of even closely related species vary considerably, and with biochemical approaches, though having high reproducibility, the biochemical signatures do not always automatically signify a function. They noted that 70% of the transcription coverage was less than 1 transcript per cell. They noted that this "larger proportion of genome with reproducible but low biochemical signal strength and less evolutionary conservation is challenging to parse between specific functions and biological noise". Furthermore, assay resolution often is much broader than the underlying functional sites so some of the reproducibly "biochemically active but selectively neutral" sequences are unlikely to serve critical functions, especially those with lower-level biochemical signal. To this they added, "However, we also acknowledge substantial limitations in our current detection of constraint, given that some human-specific functions are essential but not conserved and that disease-relevant regions need not be selectively constrained to be functional." On the other hand, they argued that the 12–15% fraction of human DNA under functional constraint, as estimated by a variety of extrapolative evolutionary methods, may still be an underestimate. They concluded that in contrast to evolutionary and genetic evidence, biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act. Ultimately genetic, evolutionary, and biochemical approaches can all be used in a complementary way to identify regions that may be functional in human biology and disease. Some critics have argued that functionality can only be assessed in reference to an appropriate null hypothesis. In this case, the null hypothesis would be that these parts of the genome are non-functional and have properties, be it on the basis of conservation or biochemical activity, that would be expected of such regions based on our general understanding of molecular evolution and biochemistry. According to these critics, until a region in question has been shown to have additional features, beyond what is expected of the null hypothesis, it should provisionally be labelled as non-functional.

Evidence of functionality

Many non-coding DNA sequences must have some important biological function. This is indicated by comparative genomics studies that report highly conserved regions of non-coding DNA, sometimes on time-scales of hundreds of millions of years. This implies that these non-coding regions are under strong evolutionary pressure and positive selection. For example, in the genomes of humans and mice, which diverged from a common ancestor 65–75 million years ago, protein-coding DNA sequences account for only about 20% of conserved DNA, with the remaining 80% of conserved DNA represented in non-coding regions. Linkage mapping often identifies chromosomal regions associated with a disease with no evidence of functional coding variants of genes within the region, suggesting that disease-causing genetic variants lie in the non-coding DNA. The significance of non-coding DNA mutations in cancer was explored in April 2013.

Non-coding genetic polymorphisms play a role in infectious disease susceptibility, such as hepatitis C.^[49] Moreover, non-coding genetic polymorphisms contribute to susceptibility to Ewing sarcoma, an aggressive pediatric bone cancer.

Some specific sequences of non-coding DNA may be features essential to chromosome structure, centromere function and recognition of homologous chromosomes during meiosis.

According to a comparative study of over 300 prokaryotic and over 30 eukaryotic genomes, eukaryotes appear to require a minimum amount of non-coding DNA. The amount can be predicted using a growth model for regulatory genetic networks, implying that it is required for regulatory purposes. In humans the predicted minimum is about 5% of the total genome.

Over 10% of 32 mammalian genomes may function through the formation of specific RNA secondary structures. The study used comparative genomics to identify compensatory DNA mutations that maintain RNA base-pairings, a distinctive feature of RNA molecules. Over 80% of the genomic regions presenting evolutionary evidence of RNA structure conservation do not present strong DNA sequence conservation.

Non-coding DNA separates genes from each other with long gaps, so mutation in one gene or part of a chromosome, for example deletion or insertion, does not have a frameshift effect on the whole chromosome. When genome complexity is relatively high, like in the case of human genome, not only between different genes, but also inside many genes, there are gaps of introns to protect the entire coding segment and minimise the changes caused by mutation. Non-coding DNA may perhaps serve to decrease the probability of gene disruption during chromosomal crossover.

Regulating gene expression

Some non-coding DNA sequences determine the expression levels of various genes, both those that are transcribed to proteins and those that themselves are involved in gene regulation.

Transcription factors

Some non-coding DNA sequences determine where transcription factors attach. A transcription factor is a protein that binds to specific non-coding DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA.

Operators

An operator is a segment of DNA to which a repressor binds. A repressor is a DNA-binding protein that regulates the expression of one or more genes by binding to the operator and blocking the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes. This blocking of expression is called repression.

Enhancers

An enhancer is a short region of DNA that can be bound with proteins (trans-acting factors), much like a set of transcription factors, to enhance transcription levels of genes in a gene cluster.

Silencers

A silencer is a region of DNA that inactivates gene expression when bound by a regulatory protein. It functions in a very similar way as enhancers, only differing in the inactivation of genes.

Promoters

A promoter is a region of DNA that facilitates transcription of a particular gene when a transcription factor binds to it. Promoters are typically located near the genes they regulate and upstream of them.

Insulators

A genetic insulator is a boundary element that plays two distinct roles in gene expression, either as an enhancer-blocking code, or rarely as a barrier against condensed chromatin. An insulator in a DNA sequence is comparable to a linguistic word divider such as a comma in a sentence, because the insulator indicates where an enhanced or repressed sequence ends.

Uses

Evolution

Shared sequences of apparently non-functional DNA are a major line of evidence of common descent.

Pseudogene sequences appear to accumulate mutations more rapidly than coding sequences due to a loss of selective pressure. This allows for the creation of mutant alleles that incorporate new functions that may be favored by natural selection; thus, pseudogenes can serve as raw material for evolution and can be considered "protogenes".

A study published in 2019 shows that new genes (termed de novo gene birth) can be fashioned from non-coding regions. Some studies suggest at least one-tenth of genes could be made in this way.

Long range correlations

A statistical distinction between coding and non-coding DNA sequences has been found. It has been observed that nucleotides in non-coding DNA sequences display long range power law correlations while coding sequences do not.

Forensic anthropology

Police sometimes gather DNA as evidence for purposes of forensic identification. As described in Maryland v. King, a 2013 U.S. Supreme Court decision:

The current standard for forensic DNA testing relies on an analysis of the chromosomes located within the nucleus of all human cells. 'The DNA material in chromosomes is composed of "coding" and "non-coding" regions. The coding regions are known as genes and contain the information necessary for a cell to make proteins. . . . Non-protein coding regions . . . are not related directly to making proteins, [and] have been referred to as "junk" DNA.' The adjective "junk" may mislead the lay person, for in fact this is the DNA region used with near certainty to identify a person.