Home LiteratureArticle Details
PMID: 22421062 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Review

Nucleosome positioning: bringing order to the eukaryotic genome.

Trends in cell biology ·Vol. 22 ·No. 5 ·2012-05-00 ·Pages 250-6

Iyer VR

Abstract

Nucleosomes are an essential component of eukaryotic chromosomes. The impact of nucleosomes is seen not just on processes that directly access the genome, such as transcription, but also on an evolutionary timescale. Recent studies in various organisms have provided high-resolution maps of nucleosomes throughout the genome. Computational analysis, in conjunction with many other kinds of data, has shed light on several aspects of nucleosome biology. Nucleosomes are positioned by several means, including intrinsic sequence biases, by stacking against a fixed barrier, by DNA-binding proteins and by chromatin remodelers. These studies underscore the important organizational role of nucleosomes in all eukaryotic genomes. This paper reviews recent genomic studies that have shed light on the determinants of nucleosome positioning and their impact on the genome.

MeSH Terms
Animals Chromatin Eukaryotic Cells/cytology Genome Humans Nucleosomes Sequence Analysis, DNA
Chemicals
Chromatin Nucleosomes
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Iyer Vishwanath R
Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712-0159, USA. [email protected]
References (68)
68 references, click to expand
  1. Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization.
    Nat Genet. 2009 Apr;41(4):438-45 PMID: 19252487
  2. Nucleosome positioning: how is it established, and why does it matter?
    Dev Biol. 2010 Mar 15;339(2):258-66 PMID: 19527704
  3. Genome-scale identification of nucleosome positions in S. cerevisiae.
    Science. 2005 Jul 22;309(5734):626-30 PMID: 15961632
  4. Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?
    Nucleic Acids Res. 2010 Jan;38(3):709-19 PMID: 19934265
  5. High-resolution profiling of histone methylations in the human genome.
    Cell. 2007 May 18;129(4):823-37 PMID: 17512414
  6. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome.
    Science. 2011 May 20;332(6032):977-80 PMID: 21596991
  7. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites.
    Science. 2009 Jan 16;323(5912):401-4 PMID: 19074313
  8. G+C content dominates intrinsic nucleosome occupancy.
    BMC Bioinformatics. 2009 Dec 22;10:442 PMID: 20028554
  9. Chromatin and transcription--how transcription factors battle with a repressive chromatin environment.
    Eur J Biochem. 1998 Jan 15;251(1-2):9-18 PMID: 9492263
  10. Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation.
    Genome Res. 2011 May;21(5):718-24 PMID: 21363969
  11. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes.
    Nature. 2009 Dec 24;462(7276):1016-21 PMID: 20033039
  12. Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output.
    PLoS Biol. 2011 Jun;9(6):e1001086 PMID: 21738444
  13. Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae.
    Nat Struct Mol Biol. 2010 Feb;17(2):251-7 PMID: 20118936
  14. Combinatorial patterns of histone acetylations and methylations in the human genome.
    Nat Genet. 2008 Jul;40(7):897-903 PMID: 18552846
  15. Multiple functions of nucleosomes and regulatory factors in transcription.
    Trends Biochem Sci. 1993 Mar;18(3):90-5 PMID: 8480368
  16. A common topology for bacterial and eukaryotic transcription initiation?
    EMBO Rep. 2007 Feb;8(2):147-51 PMID: 17268506
  17. The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes.
    Nat Struct Mol Biol. 2011 Nov 13;18(12):1394-9 PMID: 22081017
  18. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.
    BMC Genomics. 2008 Nov 13;9:537 PMID: 19014516
  19. Nucleosome-coupled expression differences in closely-related species.
    BMC Genomics. 2011 Sep 26;12:466 PMID: 21942931
  20. Histones: annotating chromatin.
    Annu Rev Genet. 2009;43:559-99 PMID: 19886812
  21. Analysis of primary structure of chromatin with next-generation sequencing.
    Epigenomics. 2010 Apr;2(2):187-197 PMID: 22022339
  22. Nucleosome positioning in Saccharomyces cerevisiae.
    Microbiol Mol Biol Rev. 2011 Jun;75(2):301-20 PMID: 21646431
  23. Impact of chromatin structure on sequence variability in the human genome.
    Nat Struct Mol Biol. 2011 Apr;18(4):510-5 PMID: 21399641
  24. A preoccupied position on nucleosomes.
    Nat Struct Mol Biol. 2010 Aug;17(8):923 PMID: 20683475
  25. The role of nucleosome positioning in the evolution of gene regulation.
    PLoS Biol. 2010 Jul 06;8(7):e1000414 PMID: 20625544
  26. Regulation of gene expression by nucleosomes.
    Curr Opin Genet Dev. 1996 Apr;6(2):164-70 PMID: 8722172
  27. Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences.
    Mol Syst Biol. 2010 May 11;6:365 PMID: 20461072
  28. The biology of chromatin remodeling complexes.
    Annu Rev Biochem. 2009;78:273-304 PMID: 19355820
  29. A high-resolution atlas of nucleosome occupancy in yeast.
    Nat Genet. 2007 Oct;39(10):1235-44 PMID: 17873876
  30. Histone H3K4 and K36 methylation, Chd1 and Rpd3S oppose the functions of Saccharomyces cerevisiae Spt4-Spt5 in transcription.
    Genetics. 2010 Feb;184(2):321-34 PMID: 19948887
  31. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging.
    Genome Res. 2010 Jan;20(1):90-100 PMID: 19846608
  32. Signals and combinatorial functions of histone modifications.
    Annu Rev Biochem. 2011;80:473-99 PMID: 21529160
  33. Widespread signatures of recent selection linked to nucleosome positioning in the human lineage.
    Genome Res. 2011 Nov;21(11):1777-87 PMID: 21903742
  34. Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites.
    PLoS Comput Biol. 2010 Aug 19;6(8): PMID: 20808881
  35. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.
    Nat Struct Mol Biol. 2009 Aug;16(8):847-52 PMID: 19620965
  36. High-resolution genome-wide mapping of the primary structure of chromatin.
    Cell. 2011 Jan 21;144(2):175-86 PMID: 21241889
  37. Nucleosome sequence preferences influence in vivo nucleosome organization.
    Nat Struct Mol Biol. 2010 Aug;17(8):918-20 PMID: 20683473
  38. Dynamic regulation of nucleosome positioning in the human genome.
    Cell. 2008 Mar 7;132(5):887-98 PMID: 18329373
  39. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.
    Genome Res. 2009 Jan;19(1):24-32 PMID: 19056695
  40. Chromatin remodelling at promoters suppresses antisense transcription.
    Nature. 2007 Dec 13;450(7172):1031-5 PMID: 18075583
  41. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast.
    Nature. 1999 Nov 25;402(6760):418-21 PMID: 10586882
  42. Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization.
    Genome Res. 2011 Nov;21(11):1851-62 PMID: 21914852
  43. Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.
    Science. 2009 Jul 31;325(5940):626-8 PMID: 19644123
  44. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
    PLoS Biol. 2008 Mar 18;6(3):e65 PMID: 18351804
  45. Relationship between nucleosome positioning and DNA methylation.
    Nature. 2010 Jul 15;466(7304):388-92 PMID: 20512117
  46. Determinants of nucleosome organization in primary human cells.
    Nature. 2011 May 22;474(7352):516-20 PMID: 21602827
  47. Patterns and mechanisms of ancestral histone protein inheritance in budding yeast.
    PLoS Biol. 2011 Jun;9(6):e1001075 PMID: 21666805
  48. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.
    PLoS Genet. 2008 Jul 25;4(7):e1000138 PMID: 18654629
  49. Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".
    Nat Struct Mol Biol. 2010 Aug;17(8):920-3 PMID: 20683474
  50. An effect of DNA sequence on nucleosome occupancy and removal.
    Nat Struct Mol Biol. 2011 Apr;18(4):507-9 PMID: 21378966
  51. Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns.
    Mol Cell Biol. 2011 Nov;31(21):4348-55 PMID: 21896781
  52. Nucleosomes and the accessibility problem.
    Trends Genet. 2011 Dec;27(12):487-92 PMID: 22019336
  53. Pioneer transcription factors: establishing competence for gene expression.
    Genes Dev. 2011 Nov 1;25(21):2227-41 PMID: 22056668
  54. The DNA-encoded nucleosome organization of a eukaryotic genome.
    Nature. 2009 Mar 19;458(7236):362-6 PMID: 19092803
  55. The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes.
    Crit Rev Biochem Mol Biol. 2008 Nov-Dec;43(6):393-418 PMID: 19037758
  56. Nucleosomes: regulators of transcription.
    Trends Genet. 1990 Dec;6(12):395-400 PMID: 2087781
  57. Nascent transcript sequencing visualizes transcription at nucleotide resolution.
    Nature. 2011 Jan 20;469(7330):368-73 PMID: 21248844
  58. Nucleosome organization in the Drosophila genome.
    Nature. 2008 May 15;453(7193):358-62 PMID: 18408708
  59. High nucleosome occupancy is encoded at human regulatory sequences.
    PLoS One. 2010 Feb 09;5(2):e9129 PMID: 20161746
  60. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome.
    Cell. 1999 Aug 6;98(3):285-94 PMID: 10458604
  61. The nucleosome map of the mammalian liver.
    Nat Struct Mol Biol. 2011 Jun;18(6):742-6 PMID: 21623366
  62. Phylogenomics of the nucleosome.
    Nat Struct Biol. 2003 Nov;10(11):882-91 PMID: 14583738
  63. Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin.
    Cell. 2005 Oct 21;123(2):233-48 PMID: 16239142
  64. Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism.
    Nucleic Acids Res. 1988 Jul 25;16(14A):6677-90 PMID: 3399412
  65. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.
    Genome Res. 2008 Jul;18(7):1073-83 PMID: 18550805
  66. Mechanisms that specify promoter nucleosome location and identity.
    Cell. 2009 May 1;137(3):445-58 PMID: 19410542
  67. A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization.
    Science. 2011 Sep 23;333(6050):1758-60 PMID: 21940898
  68. A genomic code for nucleosome positioning.
    Nature. 2006 Aug 17;442(7104):772-8 PMID: 16862119
Article Info
Journal
Trends in cell biology
Abbr.
Trends Cell Biol
ISSN
1879-3088
DOI
10.1016/j.tcb.2012.02.004
Email
[email protected]
Published
2012-05-00
Epub
2012-00-14
Pages
250-6
Language
English
Region
England
NLM ID
9200566
PMCID
PMC3348441
Subset
IM
Grants
NCI NIH HHS · R01 CA130075 · United States
NHGRI NIH HHS · HG004563 · United States
NCI NIH HHS · R01 CA095548 · United States
NHGRI NIH HHS · U54 HG004563 · United States
NCI NIH HHS · R01 CA130075-05 · United States
NCI NIH HHS · CA130075 · United States
NHGRI NIH HHS · U54 HG004563-04 · United States
NCI NIH HHS · R01 CA095548-08 · United States
NCI NIH HHS · CA095548 · United States
External Links
PubMed source DOI: 10.1016/j.tcb.2012.02.004 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2