OpenLB
Open Library of Bioscience
Advanced Search
Nature structural & molecular biology
Nov, 2012;19 (11): 1185-92.

Genome-wide nucleosome positioning during embryonic stem cell development.

Vladimir B Teif, Yevhen Vainshtein, Maïwen Caudron-Herger, Jan-Philipp Mallm, Caroline Marth, Thomas Höfer, Karsten Rippe
Author Information
  1. Vladimir B Teif: Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum, Heidelberg, Germany. v.teif@dkfz.de
PMID: 23085715 DOI: 10.1038/nsmb.2419

Abstract

We determined genome-wide nucleosome occupancies in mouse embryonic stem cells and their neural progenitor and embryonic fibroblast counterparts to assess features associated with nucleosome positioning during lineage commitment. Cell-type- and protein-specific binding preferences of transcription factors to sites with either low (Myc, Klf4 and Zfx) or high (Nanog, Oct4 and Sox2) nucleosome occupancy as well as complex patterns for CTCF were identified. Nucleosome-depleted regions around transcription start and transcription termination sites were broad and more pronounced for active genes, with distinct patterns for promoters classified according to CpG content or histone methylation marks. Throughout the genome, nucleosome occupancy was correlated with certain histone methylation or acetylation modifications. In addition, the average nucleosome repeat length increased during differentiation by 5-7 base pairs, with local variations for specific regions. Our results reveal regulatory mechanisms of cell differentiation that involve nucleosome repositioning.

Associated Data

GEO | GSE40896

References

  1. Genome Biol. 2009;10(3):R25 [PMID: 19261174]
  2. Nat Protoc. 2009;4(1):44-57 [PMID: 19131956]
  3. Nucleic Acids Res. 2012 Jan;40(2):553-68 [PMID: 21926158]
  4. Nature. 2007 Aug 2;448(7153):553-60 [PMID: 17603471]
  5. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5187-91 [PMID: 19279218]
  6. Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17945-50 [PMID: 20921369]
  7. Genome Res. 2011 Oct;21(10):1650-8 [PMID: 21795385]
  8. Biochem Biophys Res Commun. 2010 Jan 1;391(1):884-9 [PMID: 19948147]
  9. PLoS Genet. 2008 Jul 25;4(7):e1000138 [PMID: 18654629]
  10. Brief Bioinform. 2010 Sep;11(5):499-511 [PMID: 20501549]
  11. Genome Res. 2011 May;21(5):718-24 [PMID: 21363969]
  12. Nature. 2012 Aug 23;488(7412):504-7 [PMID: 22820252]
  13. Cell. 2005 Dec 29;123(7):1199-212 [PMID: 16377562]
  14. Mol Cell Biol. 2002 May;22(10):3339-44 [PMID: 11971967]
  15. Genome Res. 2011 Jun;21(6):875-84 [PMID: 21515815]
  16. Mol Cell Biol. 2012 Feb;32(3):675-88 [PMID: 22124157]
  17. Microbiol Mol Biol Rev. 1999 Jun;63(2):405-45 [PMID: 10357856]
  18. Mol Cell Biol. 2003 Jul;23(13):4559-72 [PMID: 12808097]
  19. Nat Protoc. 2012 Mar 01;7(3):562-78 [PMID: 22383036]
  20. Genome Res. 2008 Jul;18(7):1051-63 [PMID: 18477713]
  21. PLoS Genet. 2008 Oct;4(10):e1000242 [PMID: 18974828]
  22. Nature. 2011 Oct 30;480(7375):123-7 [PMID: 22037307]
  23. Nat Rev Genet. 2012 Mar 06;13(4):233-45 [PMID: 22392219]
  24. Science. 2005 Jul 22;309(5734):626-30 [PMID: 15961632]
  25. Nucleic Acids Res. 2012 Jan;40(2):625-37 [PMID: 21948798]
  26. Nat Genet. 2011 Jun 19;43(7):630-8 [PMID: 21685913]
  27. Genome Res. 2010 Jan;20(1):90-100 [PMID: 19846608]
  28. Genome Biol. 2010;11(10):R106 [PMID: 20979621]
  29. Nature. 2012 Aug 2;488(7409):116-20 [PMID: 22763441]
  30. Nat Struct Mol Biol. 2009 Aug;16(8):847-52 [PMID: 19620965]
  31. Genome Biol. 2008;9(9):R137 [PMID: 18798982]
  32. Genome Biol. 2010;11(5):R49 [PMID: 20459718]
  33. Cell. 2011 Jan 21;144(2):175-86 [PMID: 21241889]
  34. Nucleic Acids Res. 2009 Sep;37(17):5641-55 [PMID: 19625488]
  35. Genome Res. 2009 Jan;19(1):24-32 [PMID: 19056695]
  36. Cell. 2008 Mar 7;132(5):887-98 [PMID: 18329373]
  37. Cell. 2008 Jun 13;133(6):1106-17 [PMID: 18555785]
  38. PLoS Genet. 2010 Jul 15;6(7):e1001023 [PMID: 20657823]
  39. Curr Opin Struct Biol. 2009 Feb;19(1):65-71 [PMID: 19208466]
  40. Nucleus. 2011 Sep-Oct;2(5):410-24 [PMID: 21983088]
  41. Nat Genet. 2006 Oct;38(10):1210-5 [PMID: 16964265]
  42. J Mol Biol. 2012 Mar 30;417(3):152-64 [PMID: 22310051]
  43. Chromosome Res. 2006;14(1):17-25 [PMID: 16506093]
  44. Genesis. 2010 Mar;48(3):200-6 [PMID: 20140888]
  45. Methods Mol Biol. 2012;833:413-9 [PMID: 22183607]
  46. Nature. 2011 May 22;474(7352):516-20 [PMID: 21602827]
  47. Nature. 2009 Mar 19;458(7236):362-6 [PMID: 19092803]
  48. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 May;83(5 Pt 1):050903 [PMID: 21728479]
  49. Nature. 2008 May 15;453(7193):358-62 [PMID: 18408708]
  50. Genes Dev. 2011 Apr 1;25(7):742-54 [PMID: 21460038]
  51. Nat Struct Mol Biol. 2011 Jun;18(6):708-14 [PMID: 21602820]
  52. Nat Struct Mol Biol. 2011 Jun;18(6):742-6 [PMID: 21623366]
  53. Genetics. 2012 Feb;190(2):351-87 [PMID: 22345607]
  54. PLoS One. 2010 Dec 29;5(12):e15754 [PMID: 21206756]
  55. Biochim Biophys Acta. 2011 Sep;1809(9):497-508 [PMID: 21704204]
  56. Cell. 2011 Oct 14;147(2):263-6 [PMID: 22000006]
  57. Nature. 2006 Aug 17;442(7104):772-8 [PMID: 16862119]
  58. PLoS One. 2011;6(8):e23490 [PMID: 21853138]
  59. EMBO J. 2012 May 16;31(10):2416-26 [PMID: 22473209]

MeSH Term

Animals
Base Sequence
Cell Differentiation
Cell Lineage
Chromatin Immunoprecipitation
DNA Methylation
Electrophoresis, Agar Gel
Embryonic Stem Cells
Gene Expression Profiling
Gene Expression Regulation, Developmental
High-Throughput Nucleotide Sequencing
Histones
Kruppel-Like Factor 4
Mice
Molecular Sequence Data
Nucleosomes
Sequence Alignment
Transcription Factors

Chemicals

Histones
Klf4 protein, mouse
Kruppel-Like Factor 4
Nucleosomes
Transcription Factors
Comparative Study Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 11

Word Cloud

Created with Highcharts 10.0.0nucleosomeembryonictranscriptionstempositioningsitesoccupancypatternsregionshistonemethylationdifferentiationcelldeterminedgenome-wideoccupanciesmousecellsneuralprogenitorfibroblastcounterpartsassessfeaturesassociatedlineagecommitmentCell-type-protein-specificbindingpreferencesfactorseitherlowMycKlf4ZfxhighNanogOct4Sox2wellcomplexCTCFidentifiedNucleosome-depletedaroundstartterminationbroadpronouncedactivegenesdistinctpromotersclassifiedaccordingCpGcontentmarksThroughoutgenomecorrelatedcertainacetylationmodificationsadditionaveragerepeatlengthincreased5-7basepairslocalvariationsspecificresultsrevealregulatorymechanismsinvolverepositioningGenome-widedevelopment

Similar Articles

Cited By (158)