High-resolution genome-wide mapping of the primary structure of chromatin.
The genomic organization of chromatin is increasingly recognized as a key regulator of cell behavior, but deciphering its regulation mechanisms requires detailed knowledge of chromatin's primary structure-the assembly of nucleosomes throughout the genome. This Primer explains the principles for mapping and analyzing the primary organization of chromatin on a genomic scale. After introducing chromatin organization and its impact on gene regulation and human health, we then describe methods that detect nucleosome positioning and occupancy levels using chromatin immunoprecipitation in combination with deep sequencing (ChIP-Seq), a strategy that is now straightforward and cost efficient. We then explore current strategies for converting the sequence information into knowledge about chromatin, an exciting challenge for biologists and bioinformaticians.
Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Zhenhai
Z
Zhang
B Franklin
BF
Pugh
D000818:Animals; D002843:Chromatin / Q000737:chemistry*; D042002:Chromatin Assembly and Disassembly; D015894:Genome, Human; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D006801:Humans; D009707:Nucleosomes / Q000737:chemistry*
D002843:Chromatin; D006657:Histones; D009707:Nucleosomes
Nucleic Acids Res. 2011 Jan;39(1):e5
20959287
Methods Enzymol. 2010;470:105-18
20946808
Cell. 2010 Apr 2;141(1):69-80
20371346
Nature. 2007 Mar 29;446(7135):572-6
17392789
Brief Bioinform. 2010 Sep;11(5):473-83
20460430
Nature. 2010 Jul 15;466(7304):383-7
20555324
Science. 2008 Mar 28;319(5871):1791-2
18369138
Nat Genet. 2009 Mar;41(3):376-81
19182803
PLoS Biol. 2008 Mar 18;6(3):e65
18351804
Genome Res. 2008 Jul;18(7):1073-83
18550805
Cell. 2007 Feb 23;128(4):693-705
17320507
Genes Dev. 2000 May 1;14(9):1021-6
10809662
Methods. 1997 Feb;11(2):246-52
8993037
Neuropharmacology. 2009 Jul;57(1):67-74
19393671
Nat Methods. 2009 Apr;6(4):283-9
19305407
Science. 2009 Oct 9;326(5950):289-93
19815776
Dev Cell. 2010 Jun 15;18(6):1030-40
20627084
Science. 2001 Aug 10;293(5532):1074-80
11498575
Nature. 2007 Jun 14;447(7146):799-816
17571346
Nature. 2010 May 13;465(7295):175-81
20418860
Methods. 2009 Jul;48(3):233-9
19303047
Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5
19920125
Genome Biol. 2010;11(8):R86
20738864
Neuron. 2009 Dec 10;64(5):678-91
20005824
J Clin Oncol. 2010 Mar 10;28(8):1358-65
20142597
Bioinformatics. 2008 May 15;24(10):1305-6
18388141
Nature. 2010 Feb 18;463(7283):943-7
20164927
Science. 2005 Jul 22;309(5734):626-30
15961632
Nat Methods. 2010 Aug;7(8):615-8
20622861
Nature. 2009 Aug 13;460(7257):863-8
19587682
Nucleic Acids Res. 2010 Jan;38(3):709-19
19934265
J Biol. 2009;8(11):96
20067596
Genome Res. 2009 Mar;19(3):460-9
19088306
Genome Res. 2010 Jan;20(1):90-100
19846608
Nature. 2009 Jun 11;459(7248):802-7
19516333
Cell. 2007 May 18;129(4):823-37
17512414
Science. 2010 May 7;328(5979):753-6
20448184
BMC Genomics. 2009 Dec 18;10:618
20017957
Genome Biol. 2008;9(9):R137
18798982
Nat Rev Genet. 2007 Nov;8(11):829-33
17909537
Nat Struct Mol Biol. 2009 Aug;16(8):847-52
19620965
Nature. 2009 May 7;459(7243):108-12
19295514
Cell. 2008 Mar 7;132(5):887-98
18329373
Nature. 2009 Mar 19;458(7236):362-6
19092803
Trends Genet. 2009 Aug;25(8):335-43
19596482
PLoS Biol. 2005 Oct;3(10):e328
16122352
Nat Struct Biol. 2003 Nov;10(11):882-91
14583738
Nat Rev Genet. 2009 Mar;10(3):161-72
19204718
Science. 2009 Jan 16;323(5912):401-4
19074313
Cell Stem Cell. 2010 May 7;6(5):479-91
20452322