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Heterochromatin

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The regions of DNA packaged in facultative heterochromatin will not be consistent between the cell types within a species, and thus a sequence in one cell that is packaged in facultative heterochromatin (and the genes within are poorly expressed) may be packaged in euchromatin in another cell (and
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An up-to-date account of the current understanding of repetitive DNA, which usually doesn't contain genetic information. If evolution makes sense only in the context of the regulatory control of genes, we propose that heterochromatin, which is the main form of chromatin in higher eukaryotes, is
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and heterochromatin. Originally, the two forms were distinguished cytologically by how intensely they get stained – the euchromatin is less intense, while heterochromatin stains intensely, indicating tighter packing. Heterochromatin was given its name for this reason by botanist Emil Heitz who
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Heterochromatin has been associated with several functions, from gene regulation to the protection of chromosome integrity; some of these roles can be attributed to the dense packing of DNA, which makes it less accessible to protein factors that usually bind DNA or its associated factors. For
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synthesizes a transcript that serves as a platform to recruit RITS, RDRC and possibly other complexes required for heterochromatin assembly. Both RNAi and an exosome-dependent RNA degradation process contribute to heterochromatic gene silencing. These mechanisms of
48:. Because it is tightly packed, it was thought to be inaccessible to polymerases and therefore not transcribed; however, according to Volpe et al. (2002), and many other papers since, much of this DNA is in fact transcribed, but it is continuously 160:. Despite this early dichotomy, recent evidence in both animals and plants has suggested that there are more than two distinct heterochromatin states, and it may in fact exist in four or five 'states', each marked by different combinations of 437:, two RNAi complexes, the RITS complex and the RNA-directed RNA polymerase complex (RDRC), are part of an RNAi machinery involved in the initiation, propagation and maintenance of heterochromatin assembly. These two complexes localize in a 105:. It is not repetitive and shares the compact structure of constitutive heterochromatin. However, under specific developmental or environmental signaling cues, it can lose its condensed structure and become transcriptionally active. 1113:
positioned to be a deeply effective target for evolutionary change. Future investigations into assembly, maintenance and the many other functions of heterochromatin will shed light on the processes of gene and chromosome regulation.
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discovered that heterochromatin remained darkly stained throughout the entire cell cycle, unlike euchromatin whose stain disappeared during interphase. Heterochromatin is usually localized to the periphery of the
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has regions of DNA that are transcribed very poorly. These loci are the so-called silent mating type loci (HML and HMR), the rDNA (encoding ribosomal RNA), and the sub-telomeric regions. Fission yeast (
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sequences may act as a barrier in rare cases where constitutive heterochromatin and highly active genes are juxtaposed (e.g. the 5'HS4 insulator upstream of the chicken β-globin locus, and loci in two
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contain large regions of constitutive heterochromatin. In most organisms, constitutive heterochromatin occurs around the chromosome centromere and near telomeres.
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Kato H, Goto DB, Martienssen RA, Urano T, Furukawa K, Murakami Y (July 2005). "RNA polymerase II is required for RNAi-dependent heterochromatin assembly".
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the genes within are no longer silenced). However, the formation of facultative heterochromatin is regulated, and is often associated with
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Allis CD, Grewal SI (August 2001). "Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries".
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is packaged as facultative heterochromatin and silenced, while the other X chromosome is packaged as euchromatin and expressed.
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Some regions of chromatin are very densely packed with fibers that display a condition comparable to that of the chromosome at
1163:; et al. (December 1986). "Cytogenetic and molecular aspects of position effect variegation in Drosophila melanogaster". 767: 243:) at these boundary domains. This gives rise to expression levels that vary from cell to cell, which may be demonstrated by 1555:"Heterochromatin Assembly and Transcriptional Gene Silencing under the Control of Nuclear RNAi: Lessons from Fission Yeast" 2292: 1882: 368: 1753: 272: 266: 34: 2287: 1312:"RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae" 416:
and its heterochromatin has been defined thoroughly. Although most of its genome can be characterized as euchromatin,
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example, naked double-stranded DNA ends would usually be interpreted by the cell as damaged or viral DNA, triggering
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has also been implicated in the production of siRNAs to mediate heterochromatin formation in some fission yeast.
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Burgess-Beusse B, Farrell C, Gaszner M, Litt M, Mutskov V, Recillas-Targa F, et al. (December 2002).
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pathway. Double-stranded RNA is believed to result in silencing of the region through a series of steps.
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Djupedal I, Kos-Braun IC, Mosher RA, Söderholm N, Simmer F, Hardcastle TJ, et al. (December 2009).
367:. The mechanism for such spreading is still a matter of controversy. The polycomb repressive complexes 288: 2244: 2169: 2154: 1984: 1932: 1907: 1847: 1696: 1462: 1221: 722: 495: 379:
compaction and gene expression and have a fundamental role in developmental processes. PRC-mediated
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appear to have a pivotal role in modifying heterochromatin during lineage commitment at the onset of
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Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, et al. (February 2001).
140: 57: 1506:"RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing" 711:"H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification" 1486: 1384: 1292: 1190: 1103: 640: 521: 384: 1504:
Djupedal I, Portoso M, Spåhr H, Bonilla C, Gustafsson CM, Allshire RC, Ekwall K (October 2005).
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Talbert PB, Henikoff S (October 2006). "Spreading of silent chromatin: inaction at a distance".
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Fisher AG, Merkenschlager M (April 2002). "Gene silencing, cell fate and nuclear organisation".
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Among the molecular components that appear to regulate the spreading of heterochromatin are the
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Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S, et al. (May 2011).
396: 276: 45: 86:, in addition to acting as an attractor for other gene-expression or repression signals. 1700: 1466: 1225: 726: 499: 1947: 1871: 1666: 1641: 1608: 1583: 1530: 1505: 1430: 1403: 1051: 1002: 953: 928: 904: 879: 855: 820: 743: 710: 686: 659: 588: 563: 349: 90: 1336: 1311: 1244: 1209: 1138: 977: 789: 2281: 1927: 1026: 978:"Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster" 709:
Nicetto D, Donahue G, Jain T, Peng T, Sidoli S, Sheng L, et al. (January 2019).
484:"Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi" 341: 253: 168: 129: 49: 1490: 1296: 1194: 1107: 644: 1902: 1776: 1388: 525: 353: 326: 318: 292: 225: 184: 157: 117: 993: 929:"Integrative epigenomic mapping defines four main chromatin states in Arabidopsis" 208: 1042: 482:
Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA (September 2002).
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Proceedings of the National Academy of Sciences of the United States of America
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Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ (March 2009).
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Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O'Shea CC (July 2017).
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RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity
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General model for duplication of heterochromatin during cell division
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Constitutive heterochromatin can affect the genes near itself (e.g.
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staining reveal that the dense packing is not due to the chromatin.
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Lu BY, Emtage PC, Duyf BJ, Hilliker AJ, Eissenberg JC (June 2000).
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All cells of a given species package the same regions of DNA in
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may occur in other eukaryotes. A large RNA structure called
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Facultative heterochromatin is the result of genes that are
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Penagos-Puig, Andrés; Furlan-Magaril, Mayra (2020-09-18).
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Microscopy of heterochromatic versus euchromatic nuclei (
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Cha, Ariana Eunjung; Bernstein, Lenny (April 30, 2015).
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Heterochromatin mainly consists of genetically inactive
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International System for Human Cytogenetic Nomenclature
1728:"Scientists discover an important new driver of aging" 1636: – Histology Learning System at Boston University 2237: 2140: 2102: 2072: 2000: 1856: 1787: 1402:Veneti Z, Gkouskou KK, Eliopoulos AG (July 2017). 976:Lohe AR, Hilliker AJ, Roberts PA (August 1993). 348:. An example of facultative heterochromatin is 611:Oberdoerffer P, Sinclair DA (September 2007). 16:Compact and highly condensed form of chromatin 1761: 1127:Current Opinion in Genetics & Development 777:Current Opinion in Genetics & Development 108:Heterochromatin has been associated with the 8: 1408:International Journal of Molecular Sciences 825:Frontiers in Cell and Developmental Biology 224:or destruction of the fragment, such as by 2099: 1768: 1754: 1746: 120:in certain portions of the human genome. 1708: 1665: 1607: 1529: 1429: 1419: 1335: 1243: 1233: 1050: 1001: 952: 903: 880:"Chromatin: constructing the big picture" 854: 836: 742: 685: 675: 587: 507: 768:"Heterochromatin and gene regulation in 474: 78:and forms structural functions such as 1310:Donze D, Kamakaka RT (February 2001). 617:Nature Reviews. Molecular Cell Biology 387:and malignancy and play a role in the 2257:List of organisms by chromosome count 279:. For example, all human chromosomes 132:and in maintaining lineage fidelity. 54:RNA-induced transcriptional silencing 7: 325:, which is a method that includes 14: 1074:Grewal SI, Jia S (January 2007). 1878:Macrochromosome/Microchromosome 1553:Vavasseur; et al. (2008). 412:, or budding yeast, is a model 179:are heterochromatic, as is the 144:Heterochromatin vs. euchromatin 1: 1139:10.1016/S0959-437X(02)00286-1 790:10.1016/S0959-437X(96)80050-5 363:and non-coding genes such as 317:, showing an overview of the 273:constitutive heterochromatin 267:Constitutive heterochromatin 261:Constitutive heterochromatin 93:through a mechanism such as 56:(RITS). Recent studies with 35:constitutive heterochromatin 22:is a tightly packed form of 1076:"Heterochromatin revisited" 994:10.1093/genetics/134.4.1149 878:van Steensel B (May 2011). 301:Facultative heterochromatin 245:position-effect variegation 183:of the second, inactivated 151:is found in two varieties: 72:position-effect variegation 41:facultative heterochromatin 2309: 1918:Dinoflagellate chromosomes 1561:. Caister Academic Press. 1043:10.1093/genetics/155.2.699 383:aberrations are linked to 330: 264: 44:. Both play a role in the 2262:List of sequenced genomes 2030:Chromosomal translocation 1903:A chromosome/B chromosome 1894:(or accessory chromosome) 1634:Histology image: 20102loa 838:10.3389/fcell.2020.579137 448:Schizosaccharomyces pombe 435:Schizosaccharomyces pombe 423:Schizosaccharomyces pombe 350:X chromosome inactivation 2084:Telomere-binding protein 1898:Supernumerary chromosome 1640:Avramova ZV (May 2002). 1361:Nature Reviews. Genetics 1080:Nature Reviews. Genetics 677:10.1186/1471-2164-10-143 409:Saccharomyces cerevisiae 1710:10.1126/science.1056794 1510:Genes & Development 1475:10.1126/science.1114955 1281:10.1126/science.1064150 735:10.1126/science.aau0583 580:10.1126/science.aag0025 509:10.1126/science.1074973 464:Centric heterochromatin 395:and in the fidelity of 361:Polycomb-group proteins 352:in female mammals: one 2020:Structural alterations 1600:10.1038/emboj.2009.351 1328:10.1093/emboj/20.3.520 1235:10.1073/pnas.162342499 945:10.1038/emboj.2011.103 896:10.1038/emboj.2011.135 336: 237:epigenetic inheritance 212: 200: 145: 2037:Numerical alterations 2025:Chromosomal inversion 1923:Homologous chromosome 433:In the fission yeast 403:Yeast heterochromatin 331:Further information: 308: 206: 198: 143: 95:histone deacetylation 2293:Nuclear organization 2245:Extrachromosomal DNA 1933:Satellite chromosome 1908:Lampbrush chromosome 1848:Nuclear organization 1421:10.3390/ijms18081657 1220:(Suppl 4): 16433–7. 766:Elgin, S.C. (1996). 543:www.researchgate.net 99:Piwi-interacting RNA 1938:Centromere position 1913:Polytene chromosome 1883:Circular chromosome 1701:2001Sci...291.1289C 1467:2005Sci...309..467K 1226:2002PNAS...9916433B 727:2019Sci...363..294N 500:2002Sci...297.1833V 169:satellite sequences 58:electron microscopy 46:expression of genes 2288:Molecular genetics 1522:10.1101/gad.344205 1179:10.1007/BF00292759 574:(6349): eaag0025. 385:genome instability 337: 213: 201: 146: 126:methyltransferases 2275: 2274: 2233: 2232: 1970:Centromere number 1887:Linear chromosome 1695:(5507): 1289–92. 1658:10.1104/pp.010981 1568:978-1-904455-25-7 721:(6424): 294–297. 443:RNA polymerase II 74:). It is usually 2300: 2100: 2064:Polyploidization 1892:Extra chromosome 1807:Genetic material 1770: 1763: 1756: 1747: 1742: 1740: 1738: 1722: 1712: 1679: 1669: 1646:Plant Physiology 1622: 1621: 1611: 1588:The EMBO Journal 1579: 1573: 1572: 1550: 1544: 1543: 1533: 1501: 1495: 1494: 1450: 1444: 1443: 1433: 1423: 1399: 1393: 1392: 1356: 1350: 1349: 1339: 1316:The EMBO Journal 1307: 1301: 1300: 1275:(5532): 1150–5. 1264: 1258: 1257: 1247: 1237: 1205: 1199: 1198: 1157: 1151: 1150: 1122: 1116: 1115: 1071: 1065: 1064: 1054: 1022: 1016: 1015: 1005: 973: 967: 966: 956: 933:The EMBO Journal 924: 918: 917: 907: 884:The EMBO Journal 875: 869: 868: 858: 840: 816: 810: 809: 763: 757: 756: 746: 706: 700: 699: 689: 679: 655: 649: 648: 608: 602: 601: 591: 559: 553: 552: 550: 549: 536: 530: 529: 511: 494:(5588): 1833–7. 479: 116:-methylation of 101:(piRNA) through 2308: 2307: 2303: 2302: 2301: 2299: 2298: 2297: 2278: 2277: 2276: 2271: 2229: 2136: 2098: 2068: 2057:Paleopolyploidy 2002: 1996: 1852: 1826:Heterochromatin 1789: 1783: 1774: 1736: 1734: 1725: 1682: 1639: 1630: 1625: 1594:(24): 3832–44. 1581: 1580: 1576: 1569: 1552: 1551: 1547: 1503: 1502: 1498: 1461:(5733): 467–9. 1452: 1451: 1447: 1401: 1400: 1396: 1373:10.1038/nrg1920 1367:(10): 793–803. 1358: 1357: 1353: 1309: 1308: 1304: 1266: 1265: 1261: 1207: 1206: 1202: 1159: 1158: 1154: 1124: 1123: 1119: 1092:10.1038/nrg2008 1073: 1072: 1068: 1024: 1023: 1019: 975: 974: 970: 939:(10): 1928–38. 926: 925: 921: 890:(10): 1885–95. 877: 876: 872: 818: 817: 813: 765: 764: 760: 708: 707: 703: 657: 656: 652: 629:10.1038/nrm2238 610: 609: 605: 561: 560: 556: 547: 545: 538: 537: 533: 481: 480: 476: 472: 460: 405: 346:differentiation 335: 327:Giemsa staining 303: 269: 263: 193: 138: 65: 20:Heterochromatin 17: 12: 11: 5: 2306: 2304: 2296: 2295: 2290: 2280: 2279: 2273: 2272: 2270: 2269: 2264: 2259: 2254: 2253: 2252: 2241: 2239: 2235: 2234: 2231: 2230: 2228: 2227: 2222: 2217: 2212: 2207: 2202: 2197: 2192: 2187: 2182: 2177: 2172: 2167: 2162: 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Index

DNA
condensed DNA
constitutive heterochromatin
facultative heterochromatin
expression of genes
turned over
RNA-induced transcriptional silencing
electron microscopy
OsO4
position-effect variegation
repetitive
centromeres
telomeres
silenced
histone deacetylation
Piwi-interacting RNA
RNAi
di-
tri
H3K9
H3K9me3
methyltransferases
organogenesis

Chromatin
euchromatin
nucleus
epigenetic
satellite sequences
centromeres

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