Sirius

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Sirius

The position of Sirius.
Observation data Epoch J2000.0      Equinox ICRS
Constellation	Canis Major
Sirius (/ˈsɪriəs/) system
Right ascension	06h 45m 08.91728s
Declination	−16° 42′ 58.0171″
Apparent magnitude (V)	−1.46
Sirius A
Right ascension	06h 45m 08.917s
Declination	−16° 42′ 58.02″
Apparent magnitude (V)	−1.47
Sirius B
Right ascension	06h 45m 09.0s
Declination	−16° 43′ 06″
Apparent magnitude (V)	8.44
Characteristics
Sirius A
Evolutionary stage	Main sequence
Spectral type	A0mA1 Va
U−B color index	−0.05
B−V color index	+0.00
Sirius B
Evolutionary stage	White dwarf
Spectral type	DA2
U−B color index	−1.04
B−V color index	−0.03
Astrometry
Radial velocity (Rv)	−5.50 km/s
Proper motion (μ)	RA: −546.01 mas/yr Dec.: −1223.07 mas/yr
Parallax (π)	379.21 ± 1.58 mas
Distance	8.60 ± 0.04 ly (2.64 ± 0.01 pc)
Sirius A
Absolute magnitude (MV)	+1.42
Sirius B
Orbit
Companion	α CMa B
Period (P)	50.1284 ± 0.0043 yr
Semi-major axis (a)	7.4957 ± 0.0025″
Eccentricity (e)	0.59142 ± 0.00037
Inclination (i)	136.336 ± 0.040°
Longitude of the node (Ω)	45.400 ± 0.071°
Periastron epoch (T)	1994.5715 ± 0.0058
Argument of periastron (ω) (secondary)	149.161 ± 0.075°
Details
α CMa A
Mass	2.063 ± 0.023 M☉
Radius	1.711 R☉
Luminosity	25.4 L☉
Surface gravity (log g)	4.33 cgs
Temperature	9,940 K
Metallicity [Fe/H]	0.50 dex
Rotation	16 km/s
Age	237–247 Myr
α CMa B
Mass	1.018 ± 0.011 M☉
Radius	0.0084 ± 3% R☉
Luminosity	0.056 L☉
Surface gravity (log g)	8.57 cgs
Temperature	25,000 ± 200 K
Age	228+10 −8 Myr
Other designations
Dog Star, Aschere, Canicula, Al Shira, Sothis, Alhabor, Mrgavyadha, Lubdhaka, Tenrōsei, α Canis Majoris (α CMa), 9 Canis Majoris (9 CMa), HD 48915, HR 2491, BD−16°1591, GJ 244, LHS 219, ADS 5423, LTT 2638, HIP 32349
Sirius B: EGGR 49, WD 0642-166, GCTP 1577.00
Database references
SIMBAD	The system
	A
	B

Sirius (/ˈsɪriəs/, a latinisation of Greek Σείριος, Seirios, lit. "glowing" or "scorching") is a binary star and the brightest star in the night sky. With a visual apparent magnitude of −1.46, it is almost twice as bright as Canopus, the next brightest star. The system has the Bayer designation α (Alpha) Canis Majoris. The binary system consists of a main-sequence star of spectral type A0 or A1, termed Sirius A, and a faint white dwarf companion of spectral type DA2, designated Sirius B. The distance between the two varies between 8.2 and 31.5 astronomical units as they orbit every 50 years.

Sirius appears bright because of its intrinsic luminosity and its proximity to Earth. At a distance of 2.6 parsecs (8.6 ly), as determined by the Hipparcos astrometry satellite, the Sirius system is one of Earth's near neighbors. Sirius is gradually moving closer to the Solar System, so it will slightly increase in brightness over the next 60,000 years. After that time its distance will begin to increase and it will become fainter, but it will continue to be the brightest star in the Earth's night sky for the next 210,000 years.

Sirius A is about twice as massive as the Sun (M_☉) and has an absolute visual magnitude of +1.42. It is 25 times more luminous than the Sun but has a significantly lower luminosity than other bright stars such as Canopus or Rigel. The system is between 200 and 300 million years old. It was originally composed of two bright bluish stars. The more massive of these, Sirius B, consumed its resources and became a red giant before shedding its outer layers and collapsing into its current state as a white dwarf around 120 million years ago.

Sirius is also known colloquially as the "Dog Star", reflecting its prominence in its constellation, Canis Major (Greater Dog). The heliacal rising of Sirius marked the flooding of the Nile in Ancient Egypt and the "dog days" of summer for the ancient Greeks, while to the Polynesians in the Southern Hemisphere the star marked winter and was an important reference for their navigation around the Pacific Ocean.

Sirius in space.

Observational history

The brightest star in the night sky, Sirius is recorded in the earliest astronomical records. Its displacement from the ecliptic causes this heliacal rising to be remarkably regular compared to other stars, with a period of almost exactly 365.25 days holding it constant relative to the solar year. This occurs at Cairo on 19 July (Julian), placing it just prior to the summer solstice and the onset of the annual flooding of the Nile during antiquity.

Owing to the flood's own irregularity, the extreme precision of the star's return made it important to the ancient Egyptians, who worshipped it as the goddess Sopdet (Ancient Egyptian: Spdt, "Triangle"; Greek: Σῶθις, Sō̂this), guarantor of the fertility of their land. The Egyptian civil calendar was apparently initiated to have its New Year "Mesori" coincide with the appearance of Sirius, although its lack of leap years meant that this congruence only held for four years until its date began to wander backwards through the months. The Egyptians continued to note the times of Sirius's annual return, which may have led them to the discovery of the 1460-year Sothic cycle and influenced the development of the Julian and Alexandrian calendars. 

The ancient Greeks observed that the appearance of Sirius heralded the hot and dry summer and feared that it caused plants to wilt, men to weaken, and women to become aroused. Due to its brightness, Sirius would have been noted to twinkle more in the unsettled weather conditions of early summer. To Greek observers, this signified certain emanations which caused its malignant influence. Anyone suffering its effects was said to be "star-struck" (ἀστροβόλητος, astrobólētos). It was described as "burning" or "flaming" in literature. The season following the star's reappearance came to be known as the "dog days". The inhabitants of the island of Ceos in the Aegean Sea would offer sacrifices to Sirius and Zeus to bring cooling breezes, and would await the reappearance of the star in summer. If it rose clear, it would portend good fortune; if it was misty or faint then it foretold (or emanated) pestilence. Coins retrieved from the island from the 3rd century BC feature dogs or stars with emanating rays, highlighting Sirius's importance. The Romans celebrated the heliacal setting of Sirius around April 25, sacrificing a dog, along with incense, wine, and a sheep, to the goddess Robigo so that the star's emanations would not cause wheat rust on wheat crops that year.

Ptolemy of Alexandria mapped the stars in Books VII and VIII of his Almagest, in which he used Sirius as the location for the globe's central meridian. He depicted it as one of six red-colored stars (see the Color controversy section below). The other five are class M and K stars, such as Arcturus and Betelgeuse.

Bright stars were important to the ancient Polynesians for navigation between the many islands and atolls of the Pacific Ocean. Low on the horizon, they acted as stellar compasses. They also served as latitude markers; the declination of Sirius matches the latitude of the archipelago of Fiji at 17°S and thus passes directly over the islands each night. Sirius served as the body of a "Great Bird" constellation called Manu, with Canopus as the southern wingtip and Procyon the northern wingtip, which divided the Polynesian night sky into two hemispheres. Just as the appearance of Sirius in the morning sky marked summer in Greece, it marked the onset of winter for the Māori, whose name Takurua described both the star and the season. Its culmination at the winter solstice was marked by celebration in Hawaii, where it was known as Ka'ulua, "Queen of Heaven". Many other Polynesian names have been recorded, including Tau-ua in the Marquesas Islands, Rehua in New Zealand, and Ta'urua-fau-papa "Festivity of original high chiefs" and Ta'urua-e-hiti-i-te-tara-te-feiai "Festivity who rises with prayers and religious ceremonies" in Tahiti. The Hawaiian people had many names for Sirius, including Aa ("glowing"), Hoku-kauopae, Kau-ano-meha (also Kaulanomeha), "Standing-alone-and-sacred", Hiki-kauelia or Hiki-kauilia (the navigational name), Hiki-kau-lono-meha ("star of solitary Lono", the astrological name), Kaulua (also Kaulua-ihai-mohai, "flower of the heavens"), Hiki-kauelia, Hoku-hoo-kele-waa ("star which causes the canoe to sail", a marine navigation name), and Kaulua-lena ("yellow star"). The people of the Society Islands called Sirius variously Taurua-fau-papa, Taurua-nui-te-amo-aha, and Taurua-e-hiti-i-tara-te-feiai. Other names for Sirius included Palolo-mua (Futuna), Mere (Mangaia), Apura (Manihiki), Taku-ua (Marquesas Islands), and Tokiva (Pukapuka). In the cosmology of the Tuamotus, Sirius had various names, including Takurua-te-upuupu, Te Kaha ("coconut fiber"), Te Upuupu, Taranga, and Vero-ma-torutoru ("flaming and diminishing").

The indigenous Boorong people of northwestern Victoria named Sirius as Warepil.

Kinematics

In 1717, Edmond Halley discovered the proper motion of the hitherto presumed "fixed" stars after comparing contemporary astrometric measurements with those from the second century AD given in Ptolemy's Almagest. The bright stars Aldebaran, Arcturus and Sirius were noted to have moved significantly; Sirius had progressed about 30 arc-minutes (about the diameter of the Moon) to the southwest.

In 1868, Sirius became the first star to have its velocity measured, the beginning of the study of celestial radial velocities. Sir William Huggins examined the spectrum of the star and observed a red shift. He concluded that Sirius was receding from the Solar System at about 40 km/s. Compared to the modern value of −5.5 km/s, this was an overestimate and had the wrong sign; the minus means it is approaching the Sun. It's possible that Huggins did not account for the Earth's orbital velocity, which would cause an error of up to 30 km/s.

Distance

In his 1698 book, Cosmotheoros, Christiaan Huygens estimated the distance to Sirius at 27664 times the distance from the Earth to the Sun (about 0.437 light years, translating to a parallax of roughly 7.5 arcseconds). There were several unsuccessful attempts to measure the parallax of Sirius: by Jacques Cassini (6 seconds); by some astronomers (including Nevil Maskelyne) using Lacaille's observations made at the Cape of Good Hope (4 seconds); by Piazzi (the same amount); using Lacaille's observations made at Paris, more numerous and certain than those made at the Cape (no sensible parallax); by Bessel (no sensible parallax).

Scottish astronomer Thomas Henderson was the first to gain some meaningful value using his observations made in 1832–1833 and South African astronomer Thomas Maclear's observations made in 1836–1837, and was published in 1839. The value of the parallax was 0.23 arcseconds, and error of the parallax was estimated not to exceed a quarter of a second, or in Henderson's words, "On the whole we may conclude that the parallax of Sirius is not greater than half a second in space; and that it is probably much less." Astronomers adopted a value of 0.25 arc-seconds for much of the 19th century. It is now known to have a parallax of 0.3792 ± 0.0016 arc-seconds and therefore a distance of 1/0.3792 ≅ 2.637 parsecs, showing Henderson's measurement to be accurate.

Discovery of Sirius B

Hubble Space Telescope image of Sirius A and Sirius B. The white dwarf can be seen to the lower left. The diffraction spikes and concentric rings are instrumental effects.

 

In 1844, the German astronomer Friedrich Bessel deduced from changes in the proper motion of Sirius that it had an unseen companion. On January 31, 1862, American telescope-maker and astronomer Alvan Graham Clark first observed the faint companion, which is now called Sirius B, or affectionately "the Pup". This happened during testing of an 18.5-inch (470 mm) aperture great refractor telescope for Dearborn Observatory, which was the largest refracting telescope lens in existence at the time, and the largest telescope in the United States. Sirius B's sighting was confirmed on March 8 with smaller telescopes.

The visible star is now sometimes known as Sirius A. Since 1894, some apparent orbital irregularities in the Sirius system have been observed, suggesting a third very small companion star, but this has never been confirmed. The best fit to the data indicates a six-year orbit around Sirius A and a mass of 0.06 M_☉. This star would be five to ten magnitudes fainter than the white dwarf Sirius B, which would make it difficult to observe. Observations published in 2008 were unable to detect either a third star or a planet. An apparent "third star" observed in the 1920s is now believed to be a background object.

In 1915, Walter Sydney Adams, using a 60-inch (1.5 m) reflector at Mount Wilson Observatory, observed the spectrum of Sirius B and determined that it was a faint whitish star. This led astronomers to conclude that it was a white dwarf, the second to be discovered. The diameter of Sirius A was first measured by Robert Hanbury Brown and Richard Q. Twiss in 1959 at Jodrell Bank using their stellar intensity interferometer. In 2005, using the Hubble Space Telescope, astronomers determined that Sirius B has nearly the diameter of the Earth, 12,000 kilometers (7,500 mi), with a mass 102% of the Sun's.

Color controversy

Around the year 150 CE, the Greek astronomer of the Roman period Claudius Ptolemy described Sirius as reddish, along with five other stars, Betelgeuse, Antares, Aldebaran, Arcturus and Pollux, all of which are of orange or red hue. The discrepancy was first noted by amateur astronomer Thomas Barker, squire of Lyndon Hall in Rutland, who prepared a paper and spoke at a meeting of the Royal Society in London in 1760. The existence of other stars changing in brightness gave credibility to the idea that some may change in color too; Sir John Herschel noted this in 1839, possibly influenced by witnessing Eta Carinae two years earlier. Thomas Jefferson Jackson See resurrected discussion on red Sirius with the publication of several papers in 1892, and a final summary in 1926. He cited not only Ptolemy but also the poet Aratus, the orator Cicero, and general Germanicus as calling the star red, though acknowledging that none of the latter three authors were astronomers, the last two merely translating Aratus' poem Phaenomena. Seneca had described Sirius as being of a deeper red than Mars. Not all ancient observers saw Sirius as red. The 1st-century poet Marcus Manilius described it as "sea-blue", as did the 4th century Avienus. It was the standard white star in ancient China, and multiple records from the 2nd century BCE up to the 7th century CE all describe Sirius as white.

In 1985, German astronomers Wolfhard Schlosser and Werner Bergmann published an account of an 8th-century Lombardic manuscript, which contains De cursu stellarum ratio by St. Gregory of Tours. The Latin text taught readers how to determine the times of nighttime prayers from positions of the stars, and Sirius is described within as rubeola – "reddish". The authors proposed this was further evidence Sirius B had been a red giant at the time. Other scholars replied that it was likely St. Gregory had been referring to Arcturus.

The possibility that stellar evolution of either Sirius A or Sirius B could be responsible for this discrepancy has been rejected by astronomers on the grounds that the timescale of thousands of years is too short and that there is no sign of the nebulosity in the system that would be expected had such a change taken place. An interaction with a third star, to date undiscovered, has also been proposed as a possibility for a red appearance. Alternative explanations are either that the description as red is a poetic metaphor for ill fortune, or that the dramatic scintillations of the star when rising left the viewer with the impression that it was red. To the naked eye, it often appears to be flashing with red, white and blue hues when near the horizon.

Observation

Sirius (bottom) and the constellation Orion (right). The three brightest stars in this image – Sirius, Betelgeuse (top right), and Procyon (top left) – form the Winter Triangle.

 

With an apparent magnitude of −1.46, Sirius is the brightest star in the night sky, almost twice as bright as the second-brightest star, Canopus. From Earth, Sirius always appears dimmer than Jupiter and Venus, as well as Mercury and Mars at certain times. Sirius is visible from almost everywhere on Earth, except latitudes north of 73° N, and it does not rise very high when viewed from some northern cities (reaching only 13° above the horizon from Saint Petersburg). Due to its declination of roughly −17°, Sirius is a circumpolar star from latitudes south of 73° S. From the Southern Hemisphere in early July, Sirius can be seen in both the evening where it sets after the Sun, and in the morning where it rises before the Sun.

Sirius, along with Procyon and Betelgeuse, forms one of the three vertices of the Winter Triangle to observers in the Northern Hemisphere.

Due to precession (and slight proper motion), Sirius will move further south in the future. Starting around the year 9000, Sirius will no longer be visible from northern and central Europe, and in 14000 its declination will be −67° and thus it will be circumpolar throughout South Africa and in most parts of Australia. 

Sirius can be observed in daylight with the naked eye under the right conditions. Ideally, the sky should be very clear, with the observer at a high altitude, the star passing overhead, and the Sun low on the horizon. These observing conditions are more easily met in the Southern Hemisphere, due to the southerly declination of Sirius.

The orbital motion of the Sirius binary system brings the two stars to a minimum angular separation of 3 arc-seconds and a maximum of 11 arc-seconds. At the closest approach, it is an observational challenge to distinguish the white dwarf from its more luminous companion, requiring a telescope with at least 300 mm (12 in) aperture and excellent seeing conditions. A periastron occurred in 1994 and the pair have since been moving apart, making them easier to separate with a telescope.

At a distance of 2.6 parsecs (8.6 ly), the Sirius system contains two of the eight nearest stars to the Solar System (not including the Sun), and is the fifth closest stellar system to ours (again not including the Sun). This proximity is the main reason for its brightness, as with other near stars such as α Centauri and in contrast to distant, highly luminous supergiants such as Canopus, Rigel or Betelgeuse. It is still around 25 times more luminous than the Sun. The closest large neighboring star to Sirius is Procyon, 1.61 parsecs (5.24 ly) away. The Voyager 2 spacecraft, launched in 1977 to study the four Jovian planets in the Solar System, is expected to pass within 4.3 light-years (1.3 pc) of Sirius in approximately 296,000 years.

Stellar system

The orbit of Sirius B around A as seen from Earth (slanted ellipse). The wide horizontal ellipse shows the true shape of the orbit (with an arbitrary orientation) as it would appear if viewed straight on.

 

Artist's impression of Sirius A and Sirius B. Sirius A is the larger of the two stars.

 

A Chandra X-ray Observatory image of the Sirius star system, where the spike-like pattern is due to the support structure for the transmission grating. The bright source is Sirius B. Credit: NASA/SAO/CXC.

 

Sirius is a binary star system consisting of two white stars orbiting each other with a separation of about 20 AU (roughly the distance between the Sun and Uranus) and a period of 50.1 years. The brighter component, termed Sirius A, is a main-sequence star of spectral type early A, with an estimated surface temperature of 9,940 K. Its companion, Sirius B, is a star that has already evolved off the main sequence and become a white dwarf. Currently 10,000 times less luminous in the visual spectrum, Sirius B was once the more massive of the two. The age of the system has been estimated at around 230 million years. Early in its lifespan it was thought to have been two bluish white stars orbiting each other in an elliptical orbit every 9.1 years. The system emits a higher than expected level of infrared radiation, as measured by IRAS space-based observatory. This may be an indication of dust in the system, and is considered somewhat unusual for a binary star. The Chandra X-ray Observatory image shows Sirius B outshining its bright partner as it is a brighter X-ray source.

In 2015, Vigan and colleagues used the VLT Survey Telescope to search for evidence of sub-stellar companions, and were able to rule out the presence of giant planets 11 times more massive than Jupiter at 0.5 au distance from Sirius A, 6–7 times the mass of Jupiter at 1–2 au distance, and down to around 4 times the mass of Jupiter at 10 au distance.

Sirius A

Comparison of Sirius A and Sun, to scale and relative surface brightness.

 

Sirius A has a mass of 2 M_☉. The radius of this star has been measured by an astronomical interferometer, giving an estimated angular diameter of 5.936±0.016 mas. The projected rotational velocity is a relatively low 16 km/s, which does not produce any significant flattening of its disk. This is at marked variance with the similar-sized Vega, which rotates at a much faster 274 km/s and bulges prominently around its equator. A weak magnetic field has been detected on the surface of Sirius A.

Stellar models suggest that the star formed during the collapsing of a molecular cloud, and that after 10 million years, its internal energy generation was derived entirely from nuclear reactions. The core became convective and used the CNO cycle for energy generation. It is predicted that Sirius A will have completely exhausted the store of hydrogen at its core within a billion (10⁹) years of its formation. At this point it will pass through a red giant stage, then settle down to become a white dwarf. 

Sirius A is classed as an Am star because the spectrum shows deep metallic absorption lines, indicating an enhancement in elements heavier than helium, such as iron. The spectral type has been reported as A0mA1 Va, which indicates that it would be classified as A1 from hydrogen and helium lines, but A0 from the metallic lines that cause it to be grouped with the Am stars. When compared to the Sun, the proportion of iron in the atmosphere of Sirius A relative to hydrogen is given by ${\displaystyle \textstyle \left[{\frac {{\ce {Fe}}}{{\ce {H}}}}\right]=0.5}$, meaning iron is 316% as abundant as in the Sun's atmosphere. The high surface content of metallic elements is unlikely to be true of the entire star; rather the iron-peak and heavy metals are radiatively levitated towards the surface.

Sirius B

Comparison of Sirius B to earth

 

Sirius B is one of the more massive white dwarfs known. With a mass of 1.02 M_☉ it is almost double the 0.5–0.6 M_☉ average. This mass is packed into a volume roughly equal to the Earth's. The current surface temperature is 25,200 K. Because there is no internal heat source, Sirius B will steadily cool as the remaining heat is radiated into space over more than two billion years.

A white dwarf forms only after the star has evolved from the main sequence and then passed through a red giant stage. This occurred when Sirius B was less than half its current age, around 120 million years ago. The original star had an estimated 5 M_☉ and was a B-type star (roughly B4–5) when it was still on the main sequence. While it passed through the red giant stage, Sirius B may have enriched the metallicity of its companion. 

This star is primarily composed of a carbon–oxygen mixture that was generated by helium fusion in the progenitor star. This is overlaid by an envelope of lighter elements, with the materials segregated by mass because of the high surface gravity. The outer atmosphere of Sirius B is now almost pure hydrogen—the element with the lowest mass—and no other elements are seen in its spectrum.

Potential third star

Since 1894, there have been observed irregularities in the orbits of Sirius A and B with an apparent periodicity of 6–6.4 years. A 1995 study found such a companion to likely exist, with a mass of roughly 0.05 solar masses- a small red dwarf or large brown dwarf, with an apparent magnitude of g.t. 15, and less than 3 arcseconds from Sirius A.

More recent (and accurate) astrometric observations by the Hubble Space Telescope ruled out the possibility of such an object entirely. The 1995 study predicted an astrometric movement of roughly 90 mas (0.09 arc-seconds), although Hubble was unable to detect any location anomaly to an accuracy of 5 mas (0.005 arc-sec). This ruled out any objects orbiting Sirius A with more than 0.033 solar masses orbiting in 0.5 years, and 0.014 in 2 years. They were additionally able to rule out any companions to Sirius B with more than 0.024 solar masses orbiting in 0.5 years, and 0.0095 orbiting in 1.8 years. Effectively, there are almost certainly no additional bodies in the Sirius system larger than a small brown dwarf or large exoplanet.

Sirius star cluster

In 1909, Ejnar Hertzsprung was the first to suggest that Sirius was a member of the Ursa Major Moving Group, based on his observations of the system's movements across the sky. The Ursa Major Group is a set of 220 stars that share a common motion through space and were once formed as members of an open cluster, which has since become gravitationally unbound. Analyses in 2003 and 2005 found Sirius's membership in the group to be questionable: the Ursa Major Group has an estimated age of 500 ± 100 million years, whereas Sirius, with metallicity similar to the Sun's, has an age that is only half this, making it too young to belong to the group. Sirius may instead be a member of the proposed Sirius Supercluster, along with other scattered stars such as Beta Aurigae, Alpha Coronae Borealis, Beta Crateris, Beta Eridani and Beta Serpentis. This is one of three large clusters located within 500 light-years (150 pc) of the Sun. The other two are the Hyades and the Pleiades, and each of these clusters consists of hundreds of stars.

A bust of Sopdet, Egyptian goddess of Sirius and the fertility of the Nile, syncretized with Isis and Demeter

Gaia 1

In 2017, a massive star cluster was discovered only 10' from Sirius. It was discovered during a statistical analysis of Gaia data. The cluster is over a thousand times further away from us than the star system.

Etymology and cultural significance

The most commonly used proper name of this star comes from the Latin Sīrius, from the Ancient Greek Σείριος (Seirios, "glowing" or "scorcher"), although the Greek word itself may have been imported from elsewhere before the Archaic period, one authority suggesting a link with the Egyptian god Osiris. The name's earliest recorded use dates from the 7th century BC in Hesiod's poetic work Works and Days. In 2016, the International Astronomical Union organized a Working Group on Star Names (WGSN) to catalog and standardize proper names for stars. The WGSN's first bulletin of July 2016 included a table of the first two batches of names approved by the WGSN; which included Sirius for the star α Canis Majoris A. It is now so entered in the IAU Catalog of Star Names.

Sirius has over 50 other designations and names attached to it. In Geoffrey Chaucer's essay Treatise on the Astrolabe, it bears the name Alhabor and is depicted by a hound's head. This name is widely used on medieval astrolabes from Western Europe. In Sanskrit it is known as Mrgavyadha "deer hunter", or Lubdhaka "hunter". As Mrgavyadha, the star represents Rudra (Shiva). The star is referred as Makarajyoti in Malayalam and has religious significance to the pilgrim center Sabarimala. In Scandinavia, the star has been known as Lokabrenna ("burning done by Loki", or "Loki's torch"). In the astrology of the Middle Ages, Sirius was a Behenian fixed star, associated with beryl and juniper. Its astrological symbol was listed by Heinrich Cornelius Agrippa.

Many cultures have historically attached special significance to Sirius, particularly in relation to dogs. It is often colloquially called the "Dog Star" as the brightest star of Canis Major, the "Great Dog" constellation.

It was classically depicted as Orion's dog. The Ancient Greeks thought that Sirius's emanations could affect dogs adversely, making them behave abnormally during the "dog days", the hottest days of the summer. The Romans knew these days as dies caniculares, and the star Sirius was called Canicula, "little dog". The excessive panting of dogs in hot weather was thought to place them at risk of desiccation and disease. In extreme cases, a foaming dog might have rabies, which could infect and kill humans they had bitten. Homer, in the Iliad, describes the approach of Achilles toward Troy in these words:

Sirius rises late in the dark, liquid sky
On summer nights, star of stars,
Orion's Dog they call it, brightest
Of all, but an evil portent, bringing heat
And fevers to suffering humanity.

In Iranian mythology, especially in Persian mythology and in Zoroastrianism, the ancient religion of Persia, Sirius appears as Tishtrya and is revered as the rain-maker divinity (Tishtar of New Persian poetry). Beside passages in the sacred texts of the Avesta, the Avestan language Tishtrya followed by the version Tir in Middle and New Persian is also depicted in the Persian epic Shahnameh of Ferdowsi. Due to the concept of the yazatas, powers which are "worthy of worship", Tishtrya is a divinity of rain and fertility and an antagonist of apaosha, the demon of drought. In this struggle, Tishtrya is depicted as a white horse.

In Chinese astronomy Sirius is known as the star of the "celestial wolf" (Chinese and Japanese: 天狼 Chinese romanization: Tiānláng; Japanese romanization: Tenrō;) in the Mansion of Jǐng (井宿). Many nations among the indigenous peoples of North America also associated Sirius with canines; the Seri and Tohono O'odham of the southwest note the star as a dog that follows mountain sheep, while the Blackfoot called it "Dog-face". The Cherokee paired Sirius with Antares as a dog-star guardian of either end of the "Path of Souls". The Pawnee of Nebraska had several associations; the Wolf (Skidi) tribe knew it as the "Wolf Star", while other branches knew it as the "Coyote Star". Further north, the Alaskan Inuit of the Bering Strait called it "Moon Dog".

Several cultures also associated the star with a bow and arrows. The ancient Chinese visualized a large bow and arrow across the southern sky, formed by the constellations of Puppis and Canis Major. In this, the arrow tip is pointed at the wolf Sirius. A similar association is depicted at the Temple of Hathor in Dendera, where the goddess Satet has drawn her arrow at Hathor (Sirius). Known as "Tir", the star was portrayed as the arrow itself in later Persian culture.

Sirius is mentioned in Surah, An-Najm ("The Star"), of the Qur'an, where it is given the name الشِّعْرَى (transliteration: aš-ši‘rā or ash-shira; the leader). The verse is: "وأنَّهُ هُوَ رَبُّ الشِّعْرَى", "That He is the Lord of Sirius (the Mighty Star)." (An-Najm:49) Ibn Kathir said in his commentary "that it is the bright star, named Mirzam Al-Jawza' (Sirius), which a group of Arabs used to worship". The alternate name Aschere, used by Johann Bayer, is derived from this.

In theosophy, it is believed the Seven Stars of the Pleiades transmit the spiritual energy of the Seven Rays from the Galactic Logos to the Seven Stars of the Great Bear, then to Sirius. From there is it sent via the Sun to the god of Earth (Sanat Kumara), and finally through the seven Masters of the Seven Rays to the human race.

Dogon

The Dogon people are an ethnic group in Mali, West Africa, reported by some researchers to have traditional astronomical knowledge about Sirius that would normally be considered impossible without the use of telescopes. In 1938 Marcel Griaule produced his dissertation and received his doctorate degree from the École pratique des hautes études (EPHE) based on his research work with the Dogon. According to Griaule's books Conversations with Ogotemmêli 1965 and The Pale Fox 1972 they knew about the fifty-year orbital period of Sirius and its companion prior to western astronomers. They also refer to a third star accompanying Sirius A and B. Robert Temple's 1976 book The Sirius Mystery credits them with knowledge of the four Galilean moons of Jupiter and the rings of Saturn. This has been the subject of controversy and speculation. 

Yoonir, symbol of the universe in Serer religion.

 

Doubts have been raised about the validity of Griaule and Dieterlein's work. In a 1991 article in Current Anthropology anthropologist Walter van Beek concluded after his research among the Dogon that, "Though they do speak about sigu tolo [which is what Griaule claimed the Dogon called Sirius] they disagree completely with each other as to which star is meant; for some it is an invisible star that should rise to announce the sigu [festival], for another it is Venus that, through a different position, appears as sigu tolo. All agree, however, that they learned about the star from Griaule."

Noah Brosch explained in his book Sirius Matters that the cultural transfer of relatively modern astronomical information could have taken place in 1893, when a French expedition arrived in Central West Africa to observe the total eclipse on April 16.

Serer religion

In the religion of the Serer people of Senegal, the Gambia and Mauritania, Sirius is called Yoonir from the Serer language (and some of the Cangin language speakers, who are all ethnically Serers). The star Sirius is one of the most important and sacred stars in Serer religious cosmology and symbolism. The Serer high priests and priestesses (Saltigues, the hereditary "rain priests") chart Yoonir in order to forecast rainfall and enable Serer farmers to start planting seeds. In Serer religious cosmology, it is the symbol of the universe.

Modern significance

Sirius is a frequent subject of science fiction, and has been the subject of poetry. Dante and John Milton reference the star, while Tennyson's poem The Princess describes the star's scintillation:

...the fiery Sirius alters hue
And bickers into red and emerald.

Other modern references:

• Plans for using solar sail propulsion for interstellar travel have targeted Sirius as the star system fastest to arrive at from Earth. While Alpha Centauri and others are closer, the brightness of Sirius provides the best braking power to arrive with the least travel time.
• Sirius is featured on the coat of arms of Macquarie University and is the name of its alumnae journal.
• The name of the North American satellite radio company Satellite CD Radio, Inc. was changed to Sirius Satellite Radio in November 1999, being named after "the brightest star in the night sky".
• Composer Karlheinz Stockhausen, who wrote a piece called Sirius, has been claimed to have said on several occasions that he came from a planet in the Sirius system. To Stockhausen, Sirius stood for "the place where music is the highest of vibrations" and where music had been developed in the most perfect way.
• Astronomer Noah Brosch has speculated that the name of the character Sirius Black from the Harry Potter stories, who has a unique ability to transform into a black dog, might have been inspired by "Sirius B".
• Sirius is one of the 27 stars on the flag of Brazil, where it represents the state of Mato Grosso.
• The Swedish football team IK Sirius from Uppsala, who currently plays in the top tier Allsvenskan, is named after the star system.

Vehicles:

• Seven ships of Great Britain's Royal Navy have been called HMS Sirius since the 18th century, with the first being the flagship of the First Fleet to Australia in 1788.
• The Royal Australian Navy subsequently named a vessel HMAS Sirius in honor of the flagship.
• American vessels include the USNS Sirius and a monoplane Lockheed Model 8 Sirius, the first of which was flown by Charles Lindbergh. The name was also adopted by Mitsubishi Motors for the Mitsubishi Sirius engine in 1980.

Renewables and Climate Policy Are On A Collision Course

• Date: 09/12/18
• Original link:  https://www.thegwpf.com/renewables-and-climate-policy-are-on-a-collision-course/
• Dr John Constable: GWPF Energy Editor

Those advocating climate change mitigation policy have hitherto wagered everything on the success of renewable energy technologies. The steadily accumulating data on energy and emissions over the period of intense policy commitment suggests that this gamble has not been successful. Pragmatic environmentalists will be asking whether sentimental attachment to wind and solar is standing in the way of an effective emissions reduction trajectory.

For almost as long as there has been a climate policy, emissions reduction has been seen as dependent on the replacement of fossil fuels with renewable energy sources. Policies supporting this outcome are ubiquitous in the developed and developing world; markets have been coerced globally, with varying degrees of severity it is true, but with extraordinary force in the OECD states, and particularly in the European Union. The net result of several decades of such measures has been negligible. Consider, for example the global total primary energy mix since 1971, as recorded in the International Energy Agency datasets, the most recent discussion of which has just been published in the World Energy Outlook (2018):

Figure 1: Global Total Primary Energy Supply: 1971–2015. Source: Redrawn by the author from International Energy Agency, Key World Energy Statistics 2017 and 2018. IEA Notes: 1. World includes international aviation and international marine bunkers. 2. Peat and oil shale are aggregated with coal. 3. “Other” Includes geothermal, solar, wind, tide/wave/ocean, heat and other.

It is perfectly true that the proportional increase in modern renewables, the “Other” category represented by the thin red line at the top of the chart is a significant multiple of the starting base, but even this increase is disappointing given the subsidies involved, and in any case it is almost completely swamped by the increase in overall energy consumption, and that of fossil fuels in particular. Renewables in total, modern renewables plus biofuels and waste and hydro, amounted to about 13% of Total Primary Energy in 1971, and in 2016 are almost unchanged at somewhat under 14%. Thirty years of deployment, almost half of that time under increasingly strong post-Kyoto policies, has seen the proportion of renewable energy in the world’s primary energy input creep up by about one percentage point.

Furthermore, what is true at a global level is also true in every national jurisdiction of importance, with the exception that in the less economically vibrant parts of the developed world, including the EU and the UK, energy consumption is actually declining, largely due the transfer of much manufacturing to other parts of the world, principally China.

It should therefore come as no surprise to anybody that emissions not only continue to rise, but have recently started to increase at the highest rate for several years, a point that is revealed in the latest release of the Global Carbon Budget, 2018, and can be conveniently illustrated in the chart derived from this paper’s data and published in the coverage of the Financial Times:

Figure 2: Global Emissions 1960 to 2018. Source: Financial Times, 6 December 2018, drawn from Global Carbon Budget Report 2018.

These dismal facts are producing the obtuse reaction that the current renewables dependent policies are insufficiently aggressive, or, to use the accepted jargon, ambitious, and that the world must try harder. The reaction of the BBC’s Matt McGrath may be typical. He asks: “Why are governments taking so long to take action?”.

But this is a misplaced question. The plain reality is that the global market coercions, and related policy pressures favouring renewables are already intense and incessant, and have been so with growing intensity for over fifteen years. Many economies, large and small, have tried very hard indeed, but the global energy markets have barely moved. Why? Because the effort is wasted; the picked winners, the renewable technologies, remain stubbornly uneconomic, with the consequence that spontaneous, uncoerced and rapid adoption remains a dream.

This is what policy failure looks like. At what point do those sincerely concerned to see prompt and sustainable emissions reductions begin to wonder whether the renewables industry is a liability and an obstacle to the aim of climate change mitigation?

Instead of blaming lazy governments, or the irrational consumer, now rioting in the streets of Paris in protest at climate policy impositions on transport fuels, environmentalists and campaigning analysts might spend their time more fruitfully by reviewing the wisdom of the policies that they have pressed on decision-makers. In doing so they could reflect that climate change mitigation is in certain important respects no different from other insurance policies, and must therefore pass the same tests: Is the policy providing real cover and is the premium affordable and proportional to the risk?

Since the rising trend in emissions leaves no doubt that the current policies have as yet provided no real insurance, discussion of affordability becomes in a sense academic, though we can note in passing that it is also true that the emissions abatement cost of renewables is so great that it exceeds even high end estimates of Social Cost of Carbon, meaning that the policies are more harmful than the climate change they set out to mitigate. – This is not only wasted effort, it is counterproductive to human welfare.

It will take time for this evidence and reasoning to change minds. Many environmentalists have a sentimental attachment to renewable energy flows in spite of their evident thermodynamic inferiority as fuels. They see them as Goop energy, pure heavenly gifts, handed down, naturally, from a benevolent sun, as opposed to the dirty and artificial earthly products of the soil that are fossil fuels and nuclear. But such feelings must be set aside in the interest of practicality. Climate campaigners must now ask themselves which they prefer, renewables or the stable and long-term reduction of greenhouse gas emissions, for it is increasingly clear that they cannot have both. The renewables industry, the vested interests of Big Green, and the widely endorsed imperative for climate change mitigation cannot co-exist for much longer. One or the other, or perhaps both, has to give way.

Epigenomics

From Wikipedia, the free encyclopedia

Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. The field is analogous to genomics and proteomics, which are the study of the genome and proteome of a cell. Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence. Epigenomic maintenance is a continuous process and plays an important role in stability of eukaryotic genomes by taking part in crucial biological mechanisms like DNA repair. Plant flavones are said to be inhibiting epigenomic marks that cause cancers. Two of the most characterized epigenetic modifications are DNA methylation and histone modification. Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development  and tumorigenesis. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.

Introduction to epigenetics

The mechanisms governing phenotypic plasticity, or the capacity of a cell to change its state in response to stimuli, have long been the subject of research (Phenotypic plasticity 1). The traditional central dogma of biology states that the DNA of a cell is transcribed to RNA, which is translated to proteins, which perform cellular processes and functions. A paradox exists, however, in that cells exhibit diverse responses to varying stimuli and that cells sharing identical sets of DNA such as in multicellular organisms can have a variety of distinct functions and phenotypes. Classical views have attributed phenotypic variation to differences in primary DNA structure, be it through aberrant mutation or an inherited sequence allele. However, while this did explain some aspects of variation, it does not explain how tightly coordinated and regulated cellular responses, such as differentiation, are carried out. 

A more likely source of cellular plasticity is through the Regulation of gene expression, such that while two cells may have near identical DNA, the differential expression of certain genes results in variation. Research has shown that cells are capable of regulating gene expression at several stages: mRNA transcription, processing and transportation as well as in protein translation, post-translational processing and degradation. Regulatory proteins that bind to DNA, RNA, and/or proteins are key effectors in these processes and function by positively or negatively regulating specific protein level and function in a cell. And, while DNA binding transcription factors provide a mechanism for specific control of cellular responses, a model where DNA binding transcription factors are the sole regulators of gene activity is also unlikely. For example, in a study of Somatic-cell nuclear transfer, it was demonstrated that stable features of differentiation remain after the nucleus is transferred to a new cellular environment, suggesting that a stable and heritable mechanism of gene regulation was involved in the maintenance of the differentiated state in the absence of the DNA binding transcription factors.

With the finding that DNA methylation and histone modifications are stable, heritable, and also reversible processes that influence gene expression without altering DNA primary structure, a mechanism for the observed variability in cell gene expression was provided. These modifications were termed epigenetic, from epi “on top of” the genetic material “DNA” (Epigenetics 1). The mechanisms governing epigenetic modifications are complex, but through the advent of high-throughput sequencing technology they are now becoming better understood.

Epigenetics

Genomic modifications that alter gene expression that cannot be attributed to modification of the primary DNA sequence and that are heritable mitotically and meiotically are classified as epigenetic modifications. DNA methylation and histone modification are among the best characterized epigenetic processes.

DNA methylation

The first epigenetic modification to be characterized in depth was DNA methylation. As its name implies, DNA methylation is the process by which a methyl group is added to DNA. The enzymes responsible for catalyzing this reaction are the DNA methyltransferases (DNMTs). While DNA methylation is stable and heritable, it can be reversed by an antagonistic group of enzymes known as DNA de-methylases. In eukaryotes, methylation is most commonly found on the carbon 5 position of cytosine residues (5mC) adjacent to guanine, termed CpG dinucleotides.

DNA methylation patterns vary greatly between species and even within the same organism. The usage of methylation among animals is quite different; with vertebrates exhibiting the highest levels of 5mC and invertebrates more moderate levels of 5mC. Some organisms like Caenorhabditis elegans have not been demonstrated to have 5mC nor a conventional DNA methyltransferase; this would suggest that other mechanisms other than DNA methylation are also involved.

Within an organism, DNA methylation levels can also vary throughout development and by region. For example, in mouse primordial germ cells, a genome wide de-methylation even occurs; by implantation stage, methylation levels return to their prior somatic levels. When DNA methylation occurs at promoter regions, the sites of transcription initiation, it has the effect of repressing gene expression. This is in contrast to unmethylated promoter regions which are associated with actively expressed genes.

The mechanism by which DNA methylation represses gene expression is a multi-step process. The distinction between methylated and unmethylated cytosine residues is carried out by specific DNA-binding proteins. Binding of these proteins recruit histone deacetylases (HDACs) enzyme which initiate chromatin remodeling such that the DNA becoming less accessible to transcriptional machinery, such as RNA polymerase, effectively repressing gene expression.

Histone modification

In eukaryotes, genomic DNA is coiled into protein-DNA complexes called chromatin. Histones, which are the most prevalent type of protein found in chromatin, function to condense the DNA; the net positive charge on histones facilitates their bonding with DNA, which is negatively charged. The basic and repeating units of chromatin, nucleosomes, consist of an octamer of histone proteins (H2A, H2B, H3 and H4) and a 146 bp length of DNA wrapped around it. Nucleosomes and the DNA connecting form a 10 nm diameter chromatin fiber, which can be further condensed.

Chromatin packaging of DNA varies depending on the cell cycle stage and by local DNA region. The degree to which chromatin is condensed is associated with a certain transcriptional state. Unpackaged or loose chromatin is more transcriptionally active than tightly packaged chromatin because it is more accessible to transcriptional machinery. By remodeling chromatin structure and changing the density of DNA packaging, gene expression can thus be modulated.

Chromatin remodeling occurs via post-translational modifications of the N-terminal tails of core histone proteins. The collective set of histone modifications in a given cell is known as the histone code. Many different types of histone modification are known, including: acetylation, methylation, phosphorylation, ubiquitination, SUMOylation, ADP-ribosylation, deamination and proline isomerization; acetylation, methylation, phosphorylation and ubiquitination have been implicated in gene activation whereas methylation, ubiquitination, SUMOylation, deamination and proline isomerization have been implicated in gene repression. Note that several modification types including methylation, phosphorylation and ubiquitination can be associated with different transcriptional states depending on the specific amino acid on the histone being modified. Furthermore, the DNA region where histone modification occurs can also elicit different effects; an example being methylation of the 3rd core histone at lysine residue 36 (H3K36). When H3K36 occurs in the coding sections of a gene, it is associated with gene activation but the opposite is found when it is within the promoter region.

Histone modifications regulate gene expression by two mechanisms: by disruption of the contact between nucleosomes and by recruiting chromatin remodeling ATPases. An example of the first mechanism occurs during the acetylation of lysine terminal tail amino acids, which is catalyzed by histone acetyltransferases (HATs). HATs are part of a multiprotein complex that is recruited to chromatin when activators bind to DNA binding sites. Acetylation effectively neutralizes the basic charge on lysine, which was involved in stabilizing chromatin through its affinity for negatively charged DNA. Acetylated histones therefore favor the dissociation of nucleosomes and thus unwinding of chromatin can occur. Under a loose chromatin state, DNA is more accessible to transcriptional machinery and thus expression is activated. The process can be reversed through removal of histone acetyl groups by deacetylases.

The second process involves the recruitment of chromatin remodeling complexes by the binding of activator molecules to corresponding enhancer regions. The nucleosome remodeling complexes reposition nucleosomes by several mechanisms, enabling or disabling accessibility of transcriptional machinery to DNA. The SWI/SNF protein complex in yeast is one example of a chromatin remodeling complex that regulates the expression of many genes through chromatin remodeling.

Relation to other genomic fields

Epigenomics shares many commonalities with other genomics fields, in both methodology and in its abstract purpose. Epigenomics seeks to identify and characterize epigenetic modifications on a global level, similar to the study of the complete set of DNA in genomics or the complete set of proteins in a cell in proteomics. The logic behind performing epigenetic analysis on a global level is that inferences can be made about epigenetic modifications, which might not otherwise be possible through analysis of specific loci. As in the other genomics fields, epigenomics relies heavily on bioinformatics, which combines the disciplines of biology, mathematics and computer science. However while epigenetic modifications had been known and studied for decades, it is through these advancements in bioinformatics technology that have allowed analyses on a global scale. Many current techniques still draw on older methods, often adapting them to genomic assays as is described in the next section.

Methods

Histone modification assays

The cellular processes of transcription, DNA replication and DNA repair involve the interaction between genomic DNA and nuclear proteins. It had been known that certain regions within chromatin were extremely susceptible to DNAse I digestion, which cleaves DNA in a low sequence specificity manner. Such hypersensitive sites were thought to be transcriptionally active regions, as evidenced by their association with RNA polymerase and topoisomerases I and II.

It is now known that sensitivity to DNAse I regions correspond to regions of chromatin with loose DNA-histone association. Hypersensitive sites most often represent promoters regions, which require for DNA to be accessible for DNA binding transcriptional machinery to function.

ChIP-Chip and ChIP-Seq

Histone modification was first detected on a genome wide level through the coupling of chromatin immunoprecipitation (ChIP) technology with DNA microarrays, termed ChIP-Chip. However instead of isolating a DNA-binding transcription factor or enhancer protein through chromatin immunoprecipitation, the proteins of interest are the modified histones themselves. First, histones are cross-linked to DNA in vivo through light chemical treatment (e.g., formaldehyde). The cells are next lysed, allowing for the chromatin to be extracted and fragmented, either by sonication or treatment with a non-specific restriction enzyme (e.g., micrococcal nuclease). Modification-specific antibodies in turn, are used to immunoprecipitate the DNA-histone complexes. Following immunoprecipitation, the DNA is purified from the histones, amplified via PCR and labeled with a fluorescent tag (e.g., Cy5, Cy3). The final step involves hybridization of labeled DNA, both immunoprecipitated DNA and non-immunoprecipitated onto a microarray containing immobilized gDNA. Analysis of the relative signal intensity allows the sites of histone modification to be determined.

ChIP-chip was used extensively to characterize the global histone modification patterns of yeast. From these studies, inferences on the function of histone modifications were made; that transcriptional activation or repression was associated with certain histone modifications and by region. While this method was effective providing near full coverage of the yeast epigenome, its use in larger genomes such as humans is limited.

In order to study histone modifications on a truly genome level, other high-throughput methods were coupled with the chromatin immunoprecipitation, namely: SAGE: serial analysis of gene expression (ChIP-SAGE), PET: paired end ditag sequencing (ChIP-PET) and more recently, next-generation sequencing (ChIP-Seq). ChIP-seq follows the same protocol for chromatin immunoprecipitation but instead of amplification of purified DNA and hybridization to a microarray, the DNA fragments are directly sequenced using next generation parallel re-sequencing. It has proven to be an effective method for analyzing the global histone modification patterns and protein target sites, providing higher resolution than previous methods.

DNA methylation assays

Techniques for characterizing primary DNA sequences could not be directly applied to methylation assays. For example, when DNA was amplified in PCR or bacterial cloning techniques, the methylation pattern was not copied and thus the information lost. The DNA hybridization technique used in DNA assays, in which radioactive probes were used to map and identify DNA sequences, could not be used to distinguish between methylated and non-methylated DNA.

Restriction endonuclease based methods

Non genome-wide approaches

The earliest methylation detection assays used methylation modification sensitive restriction endonucleases. Genomic DNA was digested with both methylation-sensitive and insensitive restriction enzymes recognizing the same restriction site. The idea being that whenever the site was methylated, only the methylation insensitive enzyme could cleave at that position. By comparing restriction fragment sizes generated from the methylation-sensitive enzyme to those of the methylation-insensitive enzyme, it was possible to determine the methylation pattern of the region. This analysis step was done by amplifying the restriction fragments via PCR, separating them through gel electrophoresis and analyzing them via southern blot with probes for the region of interest.

This technique was used to compare the DNA methylation modification patterns in the human adult and hemoglobin gene loci. Different regions of the gene (gamma delta beta globin) were known to be expressed at different stages of development. Consistent with a role of DNA methylation in gene repression, regions that were associated with high levels of DNA methylation were not actively expressed.

This method was limited not suitable for studies on the global methylation pattern, or ‘methylome’. Even within specific loci it was not fully representative of the true methylation pattern as only those restriction sites with corresponding methylation sensitive and insensitive restriction assays could provide useful information. Further complications could arise when incomplete digestion of DNA by restriction enzymes generated false negative results.

Genome wide approaches

DNA methylation profiling on a large scale was first made possible through the Restriction Landmark Genome Scanning (RLGS) technique. Like the locus-specific DNA methylation assay, the technique identified methylated DNA via its digestion methylation sensitive enzymes. However it was the use of two-dimensional gel electrophoresis that allowed be characterized on a broader scale.

However it was not until the advent of microarray and next generation sequencing technology when truly high resolution and genome-wide DNA methylation became possible. As with RLGS, the endonuclease component is retained in the method but it is coupled to new technologies. One such approach is the differential methylation hybridization (DMH), in which one set of genomic DNA is digested with methylation-sensitive restriction enzymes and a parallel set of DNA is not digested. Both sets of DNA are subsequently amplified and each labelled with fluorescent dyes and used in two-colour array hybridization. The level of DNA methylation at a given loci is determined by the relative intensity ratios of the two dyes. Adaptation of next generation sequencing to DNA methylation assay provides several advantages over array hybridization. Sequence-based technology provides higher resolution to allele specific DNA methylation, can be performed on larger genomes, and does not require creation of DNA microarrays which require adjustments based on CpG density to properly function.

Bisulfite sequencing

Bisulfite sequencing relies on chemical conversion of unmethylated cytosines exclusively, such that they can be identified through standard DNA sequencing techniques. Sodium bisulfate and alkaline treatment does this by converting unmethylated cytosine residues into uracil while leaving methylated cytosine unaltered. Subsequent amplification and sequencing of untreated DNA and sodium bisulphite treated DNA allows for methylated sites to be identified. Bisulfite sequencing, like the traditional restriction based methods, was historically limited to methylation patterns of specific gene loci, until whole genome sequencing technologies became available. However, unlike traditional restriction based methods, bisulfite sequencing provided resolution on a nucleotide level.

Limitations of the bisulfite technique include the incomplete conversion of cytosine to uracil, which is a source of false positives. Further, bisulfite treatment also causes DNA degradation and requires an additional purification step to remove the sodium bisulfite.

Next-generation sequencing is well suited in complementing bisulfite sequencing in genome-wide methylation analysis. While this now allows for methylation pattern to be determined on the highest resolution possible, on the single nucleotide level, challenges still remain in the assembly step because of reduced sequence complexity in bisulphite treated DNA. Increases in read length seek to address this challenge, allowing for whole genome shotgun bisulphite sequencing (WGBS) to be performed. The WGBS approach using an Illumina Genome Analyzer platform and has already been implemented in Arabidopsis thaliana.

Chromatin accessibility assays

Chromatin accessibility is the measure of how "accessible" or "open" a region of genome is to transcription or binding of transcription factors. The regions which are inaccessible (i.e. because they're bound by nucleosomes) are not actively transcribed by the cell while open and accessible regions are actively transcribed. Changes in chromatin accessibility are important epigenetic regulatory processes that govern cell- or context-specific expression of genes. Assays such as MNase-seq, DNase-seq, ATAC-seq or FAIRE-seq are routinely used to understand the accessible chromatin landscape of cells. The main feature of all these methods is that they're able to selectively isolate either the DNA sequences that are bounded to the histones, or those that are not. These sequences are then compared to a reference genome that allows to identify their relative position.

MNase-seq and DNase-seq both follow the same principles, as they employ lytic enzymes that target nucleic acids to cut the DNA strands unbounded by nucleosomes or other proteic factors, while the bounded pieces are sheltered, and can be retrieved and analyzed. Since active, unbound regions are destroyed, their detection can only be indirect, by sequencing with a Next Generation Sequencing technique and comparison with a reference. MNase-seq utilizes a micrococcal nuclease that produces a single strand cleavage on the opposite strand of the target sequence. DNase-seq employs DNase I, a non-specific double strand-cleaving endonuclease. This technique has been used to such an extent that nucleosome-free regions have been labelled as DHSs, DNase I hypersensitive sites, and has been ENCODE consortium's election method for genome wide chromatin accessibility analyses. The main issue of this technique is that the cleavage distribution can be biased, lowering the quality of the results. 

FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements) requires as its first step crosslinking of the DNA with nucleosomes, then DNA shearing by sonication. The free and linked fragments are separated with a traditional phenol-chloroform extraction, since the proteic fraction is stuck in the interphase while the unlinked DNA shifts to the aqueous phase and can be analyzed with various methods. Sonication produces random breaks, and therefore is not subject to any kind of bias, and is also the bigger length of the fragments (200-700 nt) makes this technique suitable for wider regions, while it's unable to resolve the single nucleosome. Unlike the nuclease-based methods, FAIRE-seq allows the direct identification of the transcriptionally active sites, and a less laborious sample preparation.

ATAC-seq is based on the activity of Tn5 transposase. The transposase is used to insert tags in the genome, with higher frequency on regions not covered by proteic factors. The tags are then used as adapters for PRC or other analytical tools.

Direct detection

Polymerase sensitivity in single-molecule real-time sequencing made it possible for scientists to directly detect epigenetic marks such as methylation as the polymerase moves along the DNA molecule being sequenced. Several projects have demonstrated the ability to collect genome-wide epigenetic data in bacteria.

Nanopore sequencing is based on changes of electrolytic current signals according to base modifications (e.g. Methylation). A polymerase mediates the entrance of ssDNA in the pore: the ion-current variation is modulated by a section of the pore and the consequently generated difference is recorded revealing the position of CpG. Discrimination between hydroxymethylation and methylation is possible thanks to solid-state nanopores even if the current while passing through the high-field region of the pore may be slightly influenced in it. As a reference amplified DNA is used which will not present copied methylated sites after the PCR process. The Oxford Nanopore Technologies MinION sequencer is a technology where, according to a hidden Markov model, it is possible to distinguish unmethylated cytosine from the methylated one even without chemical treatment that acts to enhance the signal of that modification. The data are registered commonly in picoamperes during established time. Other devices are the Nanopolish and the SignaAlign: the former expresses the frequency of a methylation in a read while the latter gives a probability of it derived from the sum of all the reads.

Single-molecule real-time sequencing (SMRT) is a single-molecule DNA sequencing method. Single-molecule real-time sequencing utilizes a zero-mode waveguide (ZMW). A single DNA polymerase enzyme is bound to the bottom of a ZMW with a single molecule of DNA as a template. Each of the four DNA bases is attached to one of four different fluorescent dyes. When a nucleotide is incorporated by the DNA polymerase, the fluorescent tag is cleaved off and the detector detects the fluorescent signal of the nucleotide incorporation. As the sequencing occurs, the polymerase enzyme kinetics shift when it encounters a region of methylation or any other base modification. When the enzyme encounters chemically modified bases, it will slow down or speed up in a uniquely identifiable way. Fluorescence pulses in SMRT sequencing are characterized not only by their emission spectra but also by their duration and by the interval between successive pulses. These metrics, defined as pulse width and interpulse duration (IPD), add valuable information about DNA polymerase kinetics. Pulse width is a function of all kinetic steps after nucleotide binding and up to fluorophore release, and IPD is determined by the kinetics of nucleotide binding and polymerase translocation. 

In 2010 a team of scientists demonstrated the use of single-molecule real-time sequencing for direct detection of modified nucleotide in the DNA template including N6-methyladenosine, 5-methylcytosine and 5-hydroxylcytosine. These various modifications affect polymerase kinetics differently, allowing discrimination between them.

In 2017, another team proposed a combined bisulfite conversion with third-generation single-molecule real-time sequencing, it is called single-molecule real-time bisulfite sequencing (SMRT-BS), which is an accurate targeted CpG methylation analysis method capable of a high degree of multiplying and long read lengths (1.5 kb) without the need for PCR amplicon sub-cloning.

Theoretical modeling approaches

First mathematical models for different nucleosome states affecting gene expression were introduced in 1980s [ref]. Later, this idea was almost forgotten, until the experimental evidence has indicated a possible role of covalent histone modifications as an epigenetic code. In the next several years, high-throughput data have indeed uncovered the abundance of epigenetic modifications and their relation to chromatin functioning which has motivated new theoretical models for the appearance, maintaining and changing these patterns. These models are usually formulated in the frame of one-dimensional lattice approaches.