Hyperacetylated Chromatin Domains: Lessons from Heterochromatin*

A small but growing number of loci that exhibit covalent histone modifications, such as hyperacetylation, over broad regions of 10 kb or more have been characterized. These hyperacetylated domains occur exclusively at loci containing highly expressed, tissue-specific genes, and the available evidence suggests that they are involved in the activation of these genes. Although to date little is known concerning the formation or function of these domains, rather more is known concerning repressive, heterochromatic domains, and the example provided by heterochromatin may be instructive in considering mechanisms of active domain formation.

[1]  J. Broach,et al.  Silencers are required for inheritance of the repressed state in yeast. , 1996, Genes & development.

[2]  Michael Grunstein,et al.  Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin , 2002, Nature Genetics.

[3]  L. Tora,et al.  Formation of an Active Tissue-Specific Chromatin Domain Initiated by Epigenetic Marking at the Embryonic Stem Cell Stage , 2005, Molecular and Cellular Biology.

[4]  B. Panning,et al.  Epigenetic gene regulation by noncoding RNAs. , 2003, Current opinion in cell biology.

[5]  S. Liebhaber,et al.  Targeted Recruitment of Histone Acetyltransferase Activity to a Locus Control Region* , 2000, The Journal of Biological Chemistry.

[6]  S. Liebhaber,et al.  Epigenetic modifications at the human growth hormone locus predict distinct roles for histone acetylation and methylation in placental gene activation. , 2004, Molecular endocrinology.

[7]  R. Sen,et al.  Stepwise activation of the immunoglobulin μ heavy chain gene locus , 2001, The EMBO journal.

[8]  W. Reith,et al.  Chromatin remodeling and extragenic transcription at the MHC class II locus control region , 2003, Nature Immunology.

[9]  Y. Chua,et al.  Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones. , 2004, The Plant journal : for cell and molecular biology.

[10]  S. Liebhaber,et al.  A defined locus control region determinant links chromatin domain acetylation with long-range gene activation. , 2002, Molecular cell.

[11]  C. Allis,et al.  Correlation Between Histone Lysine Methylation and Developmental Changes at the Chicken β-Globin Locus , 2001, Science.

[12]  Hiten D. Madhani,et al.  Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin , 2003, Cell.

[13]  T. R. Hebbes,et al.  Core histone hyperacetylation co‐maps with generalized DNase I sensitivity in the chicken beta‐globin chromosomal domain. , 1994, The EMBO journal.

[14]  Florence Hediger,et al.  The function of nuclear architecture: a genetic approach. , 2004, Annual review of genetics.

[15]  B M Turner,et al.  Identification of a conserved erythroid specific domain of histone acetylation across the α-globin gene cluster , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[16]  T. Aune,et al.  Long-range histone acetylation of the Ifng gene is an essential feature of T cell differentiation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[17]  B. S. Baker,et al.  X Chromosome Sites Autonomously Recruit the Dosage Compensation Complex in Drosophila Males , 2004, PLoS biology.

[18]  L. Wallrath,et al.  Heterochromatin, position effects, and the genetic dissection of chromatin. , 2003, Progress in nucleic acid research and molecular biology.

[19]  S. Grewal,et al.  Heterochromatin: new possibilities for the inheritance of structure. , 2002, Current opinion in genetics & development.

[20]  Michael Grunstein,et al.  Histone acetylation and deacetylation in yeast , 2003, Nature Reviews Molecular Cell Biology.

[21]  H. Ashe,et al.  Intergenic transcription and transinduction of the human beta-globin locus. , 1997, Genes & development.

[22]  M. Groudine,et al.  A Complex Chromatin Landscape Revealed by Patterns of Nuclease Sensitivity and Histone Modification within the Mouse β-Globin Locus , 2003, Molecular and Cellular Biology.

[23]  Alan P. Wolffe,et al.  Disruption of Higher-Order Folding by Core Histone Acetylation Dramatically Enhances Transcription of Nucleosomal Arrays by RNA Polymerase III , 1998, Molecular and Cellular Biology.

[24]  J. Broach,et al.  Chromosomal boundaries in S. cerevisiae. , 2001, Current opinion in genetics & development.

[25]  Charles Kooperberg,et al.  The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. , 2004, Genes & development.

[26]  R. Kelley Path to equality strewn with roX. , 2004, Developmental biology.

[27]  Xin Bi,et al.  Formation of Boundaries of Transcriptionally Silent Chromatin by Nucleosome-Excluding Structures , 2004, Molecular and Cellular Biology.

[28]  Keji Zhao,et al.  Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. , 2005, Genes & development.

[29]  S. Henikoff,et al.  A reexamination of spreading of position-effect variegation in the white-roughest region of Drosophila melanogaster. , 2000, Genetics.

[30]  P. Fraser,et al.  Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. , 2000, Molecular cell.

[31]  A. Wutz RNAs templating chromatin structure for dosage compensation in animals. , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[32]  Philip R. Gafken,et al.  Dot1p Modulates Silencing in Yeast by Methylation of the Nucleosome Core , 2002, Cell.

[33]  G. Felsenfeld,et al.  Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci , 2001, The EMBO journal.

[34]  Craig L. Peterson,et al.  Chromatin Higher Order Folding--Wrapping up Transcription , 2002, Science.

[35]  S. Gygi,et al.  Two RNAi Complexes, RITS and RDRC, Physically Interact and Localize to Noncoding Centromeric RNAs , 2004, Cell.

[36]  C. Allis,et al.  Histone and chromatin cross-talk. , 2003, Current opinion in cell biology.

[37]  M. Groudine,et al.  The murine β-globin locus control region regulates the rate of transcription but not the hyperacetylation of histones at the active genes , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Eric S. Lander,et al.  Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse , 2005, Cell.

[39]  Peter A. Jones,et al.  Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[40]  N. Dhillon,et al.  Breaking through to the other side: silencers and barriers. , 2002, Current opinion in genetics & development.

[41]  C. Crane-Robinson,et al.  Targeted and Extended Acetylation of Histones H4 and H3 at Active and Inactive Genes in Chicken Embryo Erythrocytes* , 2001, The Journal of Biological Chemistry.

[42]  S. Grewal,et al.  Regulation of heterochromatin by histone methylation and small RNAs. , 2004, Current opinion in cell biology.

[43]  P. Fraser,et al.  Antisense intergenic transcription in V(D)J recombination , 2004, Nature Immunology.

[44]  Jasper Rine,et al.  The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. , 2003, Annual review of biochemistry.

[45]  Lei Zeng,et al.  Structure and ligand of a histone acetyltransferase bromodomain , 1999, Nature.

[46]  J. Hansen,et al.  Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. , 2002, Annual review of biophysics and biomolecular structure.

[47]  J. Widom,et al.  Mechanism of Transcriptional Silencing in Yeast , 2005, Cell.

[48]  E. Bresnick,et al.  Developmentally dynamic histone acetylation pattern of a tissue-specific chromatin domain. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[49]  A. Fisher,et al.  Dynamic assembly of silent chromatin during thymocyte maturation , 2004, Nature Genetics.

[50]  Ken-ichi Noma,et al.  Transitions in Distinct Histone H3 Methylation Patterns at the Heterochromatin Domain Boundaries , 2001, Science.

[51]  G. Fourel,et al.  Protosilencers as building blocks for heterochromatin. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[52]  Dmitri A. Nusinow,et al.  Xist RNA and the mechanism of X chromosome inactivation. , 2002, Annual review of genetics.

[53]  J. Workman,et al.  Function and Selectivity of Bromodomains in Anchoring Chromatin-Modifying Complexes to Promoter Nucleosomes , 2002, Cell.