Absolute nucleosome occupancy map for the
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
12 2019
12 2019
Historique:
received:
07
06
2019
accepted:
31
10
2019
pubmed:
7
11
2019
medline:
16
4
2020
entrez:
8
11
2019
Statut:
ppublish
Résumé
Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation because nucleosomes modulate DNA access by their positioning along the genome. A cell-population nucleosome map requires two observables: nucleosome positions along the DNA ("Where?") and nucleosome occupancies across the population ("In how many cells?"). All available genome-wide nucleosome mapping techniques are yield methods because they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or nonnucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions, but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby cross-validating approaches to measure absolute nucleosome occupancy across the
Identifiants
pubmed: 31694866
pii: gr.253419.119
doi: 10.1101/gr.253419.119
pmc: PMC6886505
doi:
Substances chimiques
DNA, Fungal
0
Nucleosomes
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1996-2009Informations de copyright
© 2019 Oberbeckmann et al.; Published by Cold Spring Harbor Laboratory Press.
Références
Nat Rev Mol Cell Biol. 2018 Oct;19(10):621-637
pubmed: 29946135
J Biol Chem. 2016 Jul 15;291(29):15307-19
pubmed: 27226635
BMC Genomics. 2013 Nov 10;14:774
pubmed: 24206606
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Genome Res. 2019 Dec;29(12):1985-1995
pubmed: 31511305
PLoS Comput Biol. 2013;9(8):e1003118
pubmed: 23950696
Genome Res. 2012 Dec;22(12):2497-506
pubmed: 22960375
Genome Res. 2018 Feb 14;:
pubmed: 29444801
Prog Biophys Mol Biol. 2007 Sep-Nov;95(1-3):23-49
pubmed: 17291569
Genome Biol. 2009;10(3):R25
pubmed: 19261174
Methods Mol Biol. 1999;119:417-25
pubmed: 10804529
Science. 2007 Mar 9;315(5817):1405-8
pubmed: 17347438
Nature. 1974 Sep 20;251(5472):249-51
pubmed: 4422492
Nature. 2009 Feb 19;457(7232):1033-7
pubmed: 19169243
Nat Methods. 2008 Mar;5(3):239-41
pubmed: 18246075
Mol Cell. 2015 Nov 5;60(3):422-34
pubmed: 26545077
Nature. 2007 Mar 29;446(7135):572-6
pubmed: 17392789
Mol Cell Biol. 2013 Dec;33(24):4779-92
pubmed: 24100010
Nucleic Acids Res. 1981 Jun 25;9(12):2643-58
pubmed: 7279658
Mol Cell. 2017 Aug 3;67(3):411-422.e4
pubmed: 28735898
Nucleic Acids Res. 2009 Sep;37(16):5309-21
pubmed: 19596807
Mol Cell. 2017 Feb 16;65(4):604-617.e6
pubmed: 28212748
Mol Cell Biol. 2015 May;35(9):1588-605
pubmed: 25733687
Elife. 2015 Mar 30;4:e06073
pubmed: 25821983
Methods Enzymol. 2012;513:185-204
pubmed: 22929770
Cell. 2016 Apr 21;165(3):580-92
pubmed: 27062929
Nucleic Acids Res. 2014 Apr;42(8):4934-46
pubmed: 24586063
BMC Genomics. 2014 Dec 15;15:1104
pubmed: 25494698
Genome Res. 2013 Feb;23(2):341-51
pubmed: 23193179
Nucleic Acids Res. 2011 Dec;39(22):9521-35
pubmed: 21880600
Cell. 2016 Oct 20;167(3):709-721.e12
pubmed: 27768892
Nat Genet. 2007 Oct;39(10):1235-44
pubmed: 17873876
Cold Spring Harb Perspect Biol. 2016 May 02;8(5):
pubmed: 27141050
Genome Biol. 2018 Feb 9;19(1):19
pubmed: 29426353
Brief Bioinform. 2015 Jul;16(4):576-87
pubmed: 25296770
Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1370-5
pubmed: 8643638
Cell. 2004 Mar 5;116(5):699-709
pubmed: 15006352
EMBO J. 1986 Oct;5(10):2689-96
pubmed: 3536481
Science. 2005 Jul 22;309(5734):626-30
pubmed: 15961632
EMBO J. 2011 Apr 6;30(7):1277-88
pubmed: 21343911
Chromosoma. 2015 Jun;124(2):131-51
pubmed: 25529773
Genes Dev. 2015 Sep 15;29(18):1942-54
pubmed: 26385964
Mol Cell. 2018 Jul 5;71(1):89-102.e5
pubmed: 29979971
Nucleic Acids Res. 2010 Jan;38(3):709-19
pubmed: 19934265
Mol Cell. 2019 Jan 17;73(2):238-249.e3
pubmed: 30554944
J Mol Biol. 1983 Oct 25;170(2):423-46
pubmed: 6631965
J Biol Chem. 1973 Feb 10;248(3):1080-3
pubmed: 4684705
Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):E2462-71
pubmed: 24889621
PLoS Comput Biol. 2013;9(8):e1003181
pubmed: 23990766
Nucleic Acids Res. 2014 Apr;42(7):4270-82
pubmed: 24465003
Genome Res. 2010 Jan;20(1):90-100
pubmed: 19846608
Mol Cell Biol. 2005 Oct;25(20):8985-99
pubmed: 16199876
Nucleic Acids Res. 1992 Mar 11;20(5):1031-8
pubmed: 1567507
Nat Rev Mol Cell Biol. 2015 Mar;16(3):178-89
pubmed: 25650798
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Genome Biol. 2010;11(11):140
pubmed: 21118582
Nat Struct Mol Biol. 2009 Aug;16(8):847-52
pubmed: 19620965
Nat Rev Genet. 2014 Nov;15(11):709-21
pubmed: 25223782
PLoS One. 2010 Nov 16;5(11):e15442
pubmed: 21103382
Nucleic Acids Res. 2016 Sep 6;44(15):7189-203
pubmed: 27106059
Annu Rev Biophys. 2016 Jul 5;45:153-81
pubmed: 27391925
Methods. 2004 May;33(1):68-80
pubmed: 15039089
Mol Cell. 2016 May 5;62(3):453-461
pubmed: 27153540
Nucleic Acids Res. 2011 Nov 1;39(20):8803-19
pubmed: 21785133
BMC Bioinformatics. 2016 Oct 8;17(1):419
pubmed: 27717304
Genes Dev. 2014 Aug 1;28(15):1695-709
pubmed: 25085421
Cell. 2012 Jun 22;149(7):1461-73
pubmed: 22726434
Nature. 2011 Jun 22;475(7354):114-7
pubmed: 21697827
Science. 2011 May 20;332(6032):977-80
pubmed: 21596991
Dev Cell. 2009 Mar;16(3):466-81
pubmed: 19289091
Genome Biol. 2019 Sep 13;20(1):198
pubmed: 31519205
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
Nucleic Acids Res. 2012 Aug;40(15):7176-89
pubmed: 22573177
J Mol Biol. 1998 Feb 13;276(1):19-42
pubmed: 9514715
Annu Rev Biochem. 2014;83:671-96
pubmed: 24606138
Genome Res. 2018 Apr;28(4):497-508
pubmed: 29563167
Transcription. 2013 May-Jun;4(3):97-101
pubmed: 23665541
Methods. 2007 Mar;41(3):320-32
pubmed: 17309843
Science. 2019 Feb 15;363(6428):744-747
pubmed: 30733384
Mol Cell. 2008 Dec 26;32(6):878-87
pubmed: 19111667
Cell Rep. 2016 Sep 6;16(10):2651-2665
pubmed: 27568571
Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20158-63
pubmed: 24277842
Genes Dev. 2017 Nov 1;31(21):2162-2174
pubmed: 29203645
Nat Methods. 2017 Apr;14(4):407-410
pubmed: 28218898
BMC Mol Biol. 2012 May 06;13:15
pubmed: 22559821
Nature. 1997 Sep 18;389(6648):251-60
pubmed: 9305837
Cell. 1996 Dec 27;87(7):1249-60
pubmed: 8980231
J Mol Biol. 1995 Nov 24;254(2):130-49
pubmed: 7490738
Epigenetics. 2013 Jan;8(1):10-5
pubmed: 23257840
Mol Cell. 2017 Feb 2;65(3):565-577.e3
pubmed: 28157509
Nature. 2011 Jan 20;469(7330):368-73
pubmed: 21248844
Mol Cell. 2018 Jun 21;70(6):1054-1066.e4
pubmed: 29932900
Methods Enzymol. 2012;513:233-50
pubmed: 22929772
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Nat Rev Genet. 2009 Mar;10(3):161-72
pubmed: 19204718
Nat Commun. 2018 Dec 21;9(1):5432
pubmed: 30575770
Nature. 2012 Jun 28;486(7404):496-501
pubmed: 22722846
Nucleic Acids Res. 1981 Jun 25;9(12):2659-73
pubmed: 6269057
Cell. 2009 May 1;137(3):445-58
pubmed: 19410542
Nat Commun. 2017 Jun 06;8:15741
pubmed: 28585565
Curr Protoc Mol Biol. 2010 Jul;Chapter 7:Unit 7.9.1-17
pubmed: 20583099
Cell Rep. 2018 Mar 6;22(10):2797-2807
pubmed: 29514105
Methods Enzymol. 2012;513:205-32
pubmed: 22929771
Annu Rev Genet. 2018 Nov 23;52:295-319
pubmed: 30208290
Dev Cell. 2019 Dec 2;51(5):632-644.e6
pubmed: 31630981