euchromatin

Summary

Summary: Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.

Top Publications

  1. Karagiannis T, Harikrishnan K, Kn H, El Osta A. Disparity of histone deacetylase inhibition on repair of radiation-induced DNA damage on euchromatin and constitutive heterochromatin compartments. Oncogene. 2007;26:3963-71 pubmed
  2. Rudolph T, Yonezawa M, Lein S, Heidrich K, Kubicek S, Schafer C, et al. Heterochromatin formation in Drosophila is initiated through active removal of H3K4 methylation by the LSD1 homolog SU(VAR)3-3. Mol Cell. 2007;26:103-15 pubmed
  3. Seum C, Reo E, Peng H, Rauscher F, Spierer P, Bontron S. Drosophila SETDB1 is required for chromosome 4 silencing. PLoS Genet. 2007;3:e76 pubmed
    ..It also shows that DmSETDB1 is responsible for some of the H3K9 mono- and dimethyl marks in euchromatin and for H3K9 dimethylation on Chromosome 4...
  4. Hughes J, Skaletsky H, Pyntikova T, Minx P, Graves T, Rozen S, et al. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature. 2005;437:100-3 pubmed
    ..Gene decay in the chimpanzee lineage might be a consequence of positive selection focused elsewhere on the Y chromosome and driven by sperm competition...
  5. Peters S, Datema E, Szinay D, van Staveren M, Schijlen E, van Haarst J, et al. Solanum lycopersicum cv. Heinz 1706 chromosome 6: distribution and abundance of genes and retrotransposable elements. Plant J. 2009;58:857-69 pubmed publisher
    ..We assembled 25 BAC contigs and eight singleton BACs spanning 2.0 Mb of the short-arm euchromatin, 1.8 Mb of the pericentromeric heterochromatin and 6.9 Mb of the long-arm euchromatin...
  6. Evans Molina C, ROBBINS R, Kono T, Tersey S, Vestermark G, Nunemaker C, et al. Peroxisome proliferator-activated receptor gamma activation restores islet function in diabetic mice through reduction of endoplasmic reticulum stress and maintenance of euchromatin structure. Mol Cell Biol. 2009;29:2053-67 pubmed publisher
    ..The restoration of the Ins1/2 and Glut2 genes corresponded to a two- to threefold increase in the euchromatin marker histone H3 dimethyl-Lys4 at their respective promoters and was coincident with increased nuclear ..
  7. Tate C, Lee J, Skalnik D. CXXC finger protein 1 restricts the Setd1A histone H3K4 methyltransferase complex to euchromatin. FEBS J. 2010;277:210-23 pubmed publisher
    ..of full-length Cfp1 in CXXC1(-/-) ES cells is required to restrict Setd1A and histone H3K4 trimethylation to euchromatin, indicating that both Cfp1 DNA-binding activity and interaction with the Setd1A complex are required for ..
  8. Filion G, van Bemmel J, Braunschweig U, Talhout W, Kind J, Ward L, et al. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell. 2010;143:212-24 pubmed publisher
    ..Furthermore, transcriptionally active euchromatin consists of two types that differ in molecular organization and H3K36 methylation and regulate distinct classes ..
  9. Sharakhova M, George P, Brusentsova I, Leman S, Bailey J, Smith C, et al. Genome mapping and characterization of the Anopheles gambiae heterochromatin. BMC Genomics. 2010;11:459 pubmed publisher
    ..Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles gambiae has not been mapped and characterized...

More Information

Publications62

  1. Leung W, Shaffer C, Cordonnier T, Wong J, Itano M, Slawson Tempel E, et al. Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis. Genetics. 2010;185:1519-34 pubmed publisher
    ..Collectively, despite the heterochromatin-like properties of this domain, genes on the dot evolve to maintain function while being responsive to changes in their local environment...
  2. Sharakhova M, Hammond M, Lobo N, Krzywinski J, Unger M, Hillenmeyer M, et al. Update of the Anopheles gambiae PEST genome assembly. Genome Biol. 2007;8:R5 pubmed
  3. van Dijk K, Marley K, Jeong B, Xu J, Hesson J, Cerny R, et al. Monomethyl histone H3 lysine 4 as an epigenetic mark for silenced euchromatin in Chlamydomonas. Plant Cell. 2005;17:2439-53 pubmed
    ..Together, our results suggest functional differentiation between dimethyl H3K4 and monomethyl H3K4, with the latter operating as an epigenetic mark for repressed euchromatin.
  4. Gill N, Hans C, Jackson S. An overview of plant chromosome structure. Cytogenet Genome Res. 2008;120:194-201 pubmed publisher
  5. Kirsch S, Weiss B, Miner T, Waterston R, Clark R, Eichler E, et al. Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome. Genome Res. 2005;15:195-204 pubmed
    ..known to exist in the human genome: those associated with heterochromatic sequences and those embedded within euchromatin. We identified and analyzed a euchromatic island within the pericentromeric repeats of the human Y chromosome...
  6. Santos Rosa H, Bannister A, Dehe P, Geli V, Kouzarides T. Methylation of H3 lysine 4 at euchromatin promotes Sir3p association with heterochromatin. J Biol Chem. 2004;279:47506-12 pubmed
    ..The inability of Sir3p to bind methylated H3 Lys-4 tails suggests a model whereby H3 Lys-4 methylation prevents Sir3p association at euchromatic sites and therefore concentrates Sir3p at unmodified, heterochromatic regions of the genome...
  7. Dernburg A, Sedat J, Hawley R. Direct evidence of a role for heterochromatin in meiotic chromosome segregation. Cell. 1996;86:135-46 pubmed
  8. Riddle N, Minoda A, Kharchenko P, Alekseyenko A, Schwartz Y, Tolstorukov M, et al. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011;21:147-63 pubmed publisher
    Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin...
  9. Migliori V, Müller J, Phalke S, Low D, Bezzi M, Mok W, et al. Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. Nat Struct Mol Biol. 2012;19:136-44 pubmed publisher
    ..Our findings identify H3R2me2s as a previously unknown mark that keeps genes poised in euchromatin for transcriptional activation upon cell-cycle withdrawal and differentiation in human cells.
  10. Fanti L, Berloco M, Piacentini L, Pimpinelli S. Chromosomal distribution of heterochromatin protein 1 (HP1) in Drosophila: a cytological map of euchromatic HP1 binding sites. Genetica. 2003;117:135-47 pubmed
    ..In addition to its role in heterochromatin assembly and telomere stability, we propose that HP1 plays an important role in regulating the expression of many different euchromatic regions...
  11. Bowen N, McDonald J. Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 2001;11:1527-40 pubmed
    ..melanogaster genome have transposed well after this species diverged from its closest relative Drosophila simulans, 2.3 +/-.3 million years ago...
  12. Horsley D, Hutchings A, Butcher G, Singh P. M32, a murine homologue of Drosophila heterochromatin protein 1 (HP1), localises to euchromatin within interphase nuclei and is largely excluded from constitutive heterochromatin. Cytogenet Cell Genet. 1996;73:308-11 pubmed
    ..M32 is also largely excluded from the large masses of constitutive heterochromatin that are labelled by MAC 353...
  13. Sugiyama T, Cam H, Sugiyama R, Noma K, Zofall M, Kobayashi R, et al. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell. 2007;128:491-504 pubmed
    ..Our analyses suggest that SHREC regulates nucleosome positioning to assemble higher-order chromatin structures critical for heterochromatin functions...
  14. Kubiura M, Okano M, Kimura H, Kawamura F, Tada M. Chromosome-wide regulation of euchromatin-specific 5mC to 5hmC conversion in mouse ES cells and female human somatic cells. Chromosome Res. 2012;20:837-48 pubmed publisher
    ..Therefore, enzymes that hydroxylate the methyl group of 5mC belonging to the Tet family might be excluded from inactive chromatin, which may restrict 5mC to 5hmC conversion in euchromatin to prevent nonselective de novo DNA methylation.
  15. Sun F, Cuaycong M, Craig C, Wallrath L, Locke J, Elgin S. The fourth chromosome of Drosophila melanogaster: interspersed euchromatic and heterochromatic domains. Proc Natl Acad Sci U S A. 2000;97:5340-5 pubmed
    ..former case, the hsp26-pt gene shows an accessibility and heat-shock-inducible activity similar to that seen in euchromatin, whereas in the latter case, accessibility and inducible expression are reduced to levels typical of ..
  16. Bowers J, Arias M, Asher R, Avise J, Ball R, Brewer G, et al. Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci U S A. 2005;102:13206-11 pubmed
    ..The two genomic components correspond to cytologically discernible "euchromatin" and "heterochromatin." Gene and repetitive DNA distributions support this classification...
  17. Kirsch S, Münch C, Jiang Z, Cheng Z, Chen L, Batz C, et al. Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions. Genome Res. 2008;18:1030-42 pubmed publisher
    ..We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchromatin/heterochromatin transition regions (Yp11.2/Yp11.1, Yq11.1/Yq11.21, Yq11.23/Yq12, and Yq12/PAR2)...
  18. Strålfors A, Walfridsson J, Bhuiyan H, Ekwall K. The FUN30 chromatin remodeler, Fft3, protects centromeric and subtelomeric domains from euchromatin formation. PLoS Genet. 2011;7:e1001334 pubmed publisher
    ..Fft3 is localized to insulator elements and inhibits euchromatin assembly in silent chromatin domains...
  19. Vasireddy R, Karagiannis T, El Osta A. gamma-radiation-induced gammaH2AX formation occurs preferentially in actively transcribing euchromatic loci. Cell Mol Life Sci. 2010;67:291-4 pubmed publisher
    ..question by recent findings indicating a disparity in gamma-irradiation-induced gammaH2AX foci formation in euchromatin and heterochromatin...
  20. Tubio J, Naveira H, Costas J. Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae. Mol Biol Evol. 2005;22:29-39 pubmed
    ..gambiae than in D. melanogaster. Finally, we have detected significant overrepresentations of insertions on the X chromosome versus autosomes and of putatively active insertions on euchromatin versus heterochromatin.
  21. Misra S, Crosby M, Mungall C, Matthews B, Campbell K, Hradecky P, et al. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002;3:RESEARCH0083 pubmed
  22. Meneghini M, Wu M, Madhani H. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell. 2003;112:725-36 pubmed
    ..hinder the spread of heterochromatin, yet these sites do not fully account for the preservation of adjacent euchromatin. Histone variant H2A.Z (Htz1 in yeast) replaces conventional H2A in many nucleosomes...
  23. Ficz G, Branco M, Seisenberger S, Santos F, Krueger F, Hore T, et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature. 2011;473:398-402 pubmed publisher
    ..We find that 5hmC is mostly associated with euchromatin and that whereas 5mC is under-represented at gene promoters and CpG islands, 5hmC is enriched and is associated ..
  24. Schuster Böckler B, Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature. 2012;488:504-7 pubmed publisher
    ..This suggests that the arrangement of the genome into heterochromatin- and euchromatin-like domains is a dominant influence on regional mutation-rate variation in human somatic cells.
  25. Wen B, Wu H, Loh Y, Briem E, Daley G, Feinberg A. Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions. BMC Genomics. 2012;13:566 pubmed publisher
    ..The microstructure of these regions has not previously been explored...
  26. Kim C, Lee T, Compton R, Robertson J, Pierce G, Paterson A. A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin. Plant Mol Biol. 2013;81:139-47 pubmed publisher
    ..were placed to 1,503 locations, covering ~198 Mb of the sorghum genome or about 78 % of the estimated 252 Mb of euchromatin. BESs and their analyses presented here may provide an early profile of the sugarcane genome as well as a basis ..
  27. Jung C, Makunin I, Mattick J. Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs. Genomics. 2010;96:154-66 pubmed publisher
    ..This work reports the existence of Drosophila genus-specific sequence motifs, and suggests that many more novel functional elements may be discovered in genomes using the general approach outlined herein...
  28. Shopland L, Johnson C, Byron M, McNeil J, Lawrence J. Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. J Cell Biol. 2003;162:981-90 pubmed
    ..quot;..
  29. Tachibana M, Sugimoto K, Nozaki M, Ueda J, Ohta T, Ohki M, et al. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev. 2002;16:1779-91 pubmed
    ..Our results indicate that euchromatic H3-K9 methylation regulated by G9a is essential for early embryogenesis and is involved in the transcriptional repression of developmental genes...
  30. Strausbaugh L, Williams S. High density of an SAR-associated motif differentiates heterochromatin from euchromatin. J Theor Biol. 1996;183:159-67 pubmed
    ..This high density of SAR-associated sequences not only serves as a molecular tag for heterochromatin but also suggests a hypothesis for its special properties...
  31. Kim J, Islam Faridi M, Klein P, Stelly D, Price H, Klein R, et al. Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics. 2005;171:1963-76 pubmed
    ..Distal regions of euchromatin and pericentromeric regions of heterochromatin were delimited for all 10 sorghum chromosomes and their DNA ..
  32. McKee B, Hong C, Das S. On the roles of heterochromatin and euchromatin in meiosis in drosophila: mapping chromosomal pairing sites and testing candidate mutations for effects on X-Y nondisjunction and meiotic drive in male meiosis. Genetica. 2000;109:77-93 pubmed
    ..In male meiosis, autosomal pairing sites appear to be distributed broadly within euchromatin but to be absent from heterochromatin, whereas the X-pairing site maps in the centric heterochromatin...
  33. Noma K -, Allis C, Grewal S. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science. 2001;293:1150-5 pubmed
    ..repeats flanking the silent interval serve as boundary elements to mark the borders between heterochromatin and euchromatin. Deletions of these boundary elements lead to spreading of H3 Lys9 methylation and Swi6 into neighboring ..
  34. Yasuhara J, DeCrease C, Wakimoto B. Evolution of heterochromatic genes of Drosophila. Proc Natl Acad Sci U S A. 2005;102:10958-63 pubmed
    ..Here we document a recent evolutionary transition of a gene cluster from euchromatin to heterochromatin, which occurred <20 million years ago in the drosophilid lineage...
  35. Miao F, Natarajan R. Mapping global histone methylation patterns in the coding regions of human genes. Mol Cell Biol. 2005;25:4650-61 pubmed
    Histone methylation patterns in the human genome, especially in euchromatin regions, have not been systematically characterized...
  36. Barbi G, Spaich C, Adolph S, Rossier E, Kehrer Sawatzki H. Supernumerary der(1) marker chromosome derived from a ring chromosome 1 which has retained the original centromere and euchromatin from 1q21.1 --> q21.3 with substantial loss of 1q12 heterochromatin in a female with dysmorphic features and psychom. Am J Med Genet A. 2005;132A:419-24 pubmed
    ..The marker has retained its original centromere and euchromatin from 1q21.1-q21.3 but only small remnants of the 1q12 heterochromatin...
  37. Wen B, Wu H, Bjornsson H, Green R, Irizarry R, Feinberg A. Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification. Genome Res. 2008;18:1806-13 pubmed publisher
    ..We have explored this problem by looking for overlapping marks in the genome related to both euchromatin (histone H3 dimethyl lysine-4 [H3K4Me2]) and heterochromatin (DNA methylation [DNAm])...
  38. Mathieu O, Picard G, Tourmente S. Methylation of a euchromatin-heterochromatin transition region in Arabidopsis thaliana chromosome 5 left arm. Chromosome Res. 2002;10:455-66 pubmed
    Cytosine methylation was studied at the level of the euchromatin/heterochromatin transition genomic region of the Arabidopsis chromosome 5 left arm...
  39. Zink D, Amaral M, Englmann A, Lang S, Clarke L, Rudolph C, et al. Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol. 2004;166:815-25 pubmed publisher
    ..heterochromatin, whereas in their actively transcribed states the gene loci preferentially associated with euchromatin in the nuclear interior...
  40. Millar C, Kurdistani S, Grunstein M. Acetylation of yeast histone H4 lysine 16: a switch for protein interactions in heterochromatin and euchromatin. Cold Spring Harb Symp Quant Biol. 2004;69:193-200 pubmed
  41. Raisner R, Hartley P, Meneghini M, Bao M, Liu C, Schreiber S, et al. Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. Cell. 2005;123:233-48 pubmed
    In S. cerevisiae, histone variant H2A.Z is deposited in euchromatin at the flanks of silent heterochromatin to prevent its ectopic spread. We show that H2A.Z nucleosomes are found at promoter regions of nearly all genes in euchromatin...
  42. Yamamoto M, Mitchelson A, Tudor M, O Hare K, Davies J, Miklos G. Molecular and cytogenetic analysis of the heterochromatin-euchromatin junction region of the Drosophila melanogaster X chromosome using cloned DNA sequences. Genetics. 1990;125:821-32 pubmed
    ..The data have implications for the structure of beta-heterochromatin-alpha-heterochromatin junction zones in both mitotic and polytene chromosomes, and are discussed with reference to models of chromosome structure...
  43. Stabell M, Eskeland R, Bjørkmo M, Larsson J, Aalen R, Imhof A, et al. The Drosophila G9a gene encodes a multi-catalytic histone methyltransferase required for normal development. Nucleic Acids Res. 2006;34:4609-21 pubmed
    Mammalian G9a is a histone H3 Lys-9 (H3-K9) methyltransferase localized in euchromatin and acts as a co-regulator for specific transcription factors...
  44. Lomberk G, Bensi D, Fernandez Zapico M, Urrutia R. Evidence for the existence of an HP1-mediated subcode within the histone code. Nat Cell Biol. 2006;8:407-15 pubmed
  45. Fransz P, de Jong J, Lysak M, Castiglione M, Schubert I. Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc Natl Acad Sci U S A. 2002;99:14584-9 pubmed
    ..In contrast, euchromatin contains less methylated DNA and emanates from CCs as loops spanning 0.2-2 Mbp...
  46. Kimura A, Horikoshi M. Partition of distinct chromosomal regions: negotiable border and fixed border. Genes Cells. 2004;9:499-508 pubmed
    ..heterochromatin regions consist of condensed chromatin and contain few transcriptionally active genes, whereas euchromatin regions are less condensed and majority of active genes reside in the euchromatin regions...
  47. Li X, Wang X, He K, Ma Y, Su N, He H, et al. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell. 2008;20:259-76 pubmed publisher
    ..stained heterochromatin had less H3K4me2 and H3K4me3 and more methylated DNA than the less densely stained euchromatin, whereas centromeres had a unique epigenetic composition...
  48. Chosed R, Dent S. A two-way street: LSD1 regulates chromatin boundary formation in S. pombe and Drosophila. Mol Cell. 2007;26:160-2 pubmed
    ..2007; Rudolph et al., 2007) implicate histone demethylation by LSD1 in the regulation of boundaries between silenced and active chromatin domains in both fission yeast and flies, but by distinct mechanisms...
  49. Kobor M, Venkatasubrahmanyam S, Meneghini M, Gin J, Jennings J, Link A, et al. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004;2:E131 pubmed
    The conserved histone variant H2A.Z functions in euchromatin to antagonize the spread of heterochromatin. The mechanism by which histone H2A is replaced by H2A.Z in the nucleosome is unknown...
  50. Suka N, Suka Y, Carmen A, Wu J, Grunstein M. Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol Cell. 2001;8:473-9 pubmed
    ..These data uncover the in vivo usage of acetylation sites in heterochromatin and euchromatin.
  51. She X, Horvath J, Jiang Z, Liu G, Furey T, Christ L, et al. The structure and evolution of centromeric transition regions within the human genome. Nature. 2004;430:857-64 pubmed
    ..The distribution of these duplicated segments is nonrandom among pericentromeric regions, suggesting that some regions have served as preferential acceptors of euchromatic DNA...
  52. Libault M, Tessadori F, Germann S, Snijder B, Fransz P, Gaudin V. The Arabidopsis LHP1 protein is a component of euchromatin. Planta. 2005;222:910-25 pubmed
    ..These data indicate that LHP1 is mainly involved in euchromatin organization in A. thaliana...
  53. Deuring R, Fanti L, Armstrong J, Sarte M, Papoulas O, Prestel M, et al. The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo. Mol Cell. 2000;5:355-65 pubmed
    ..These findings reveal novel functions for the ISWI ATPase and underscore its importance in chromatin remodeling in vivo...