Linking the dynamics of chromatin occupancy and transcription with predictive models.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
06 2021
06 2021
Historique:
received:
03
07
2020
accepted:
19
04
2021
pubmed:
25
4
2021
medline:
11
3
2022
entrez:
24
4
2021
Statut:
ppublish
Résumé
Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within a complex and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins-including histones, transcription factors (TFs), and polymerases-interact with one another, the genome, and other molecules to allow the chromatin to adopt one of exceedingly many possible configurations. Understanding how changing chromatin configurations associate with transcription remains a fundamental research problem. We sought to characterize at high spatiotemporal resolution the dynamic interplay between transcription and chromatin in response to cadmium stress. Whereas gene regulatory responses to environmental stress in yeast have been studied, how the chromatin state changes and how those changes connect to gene regulation remain unexplored. By combining MNase-seq and RNA-seq data, we found chromatin signatures of transcriptional activation and repression involving both nucleosomal and TF-sized DNA-binding factors. Using these signatures, we identified associations between chromatin dynamics and transcriptional regulation, not only for known cadmium response genes, but across the entire genome, including antisense transcripts. Those associations allowed us to develop generalizable models that predict dynamic transcriptional responses on the basis of dynamic chromatin signatures.
Identifiants
pubmed: 33893157
pii: gr.267237.120
doi: 10.1101/gr.267237.120
pmc: PMC8168580
doi:
Substances chimiques
Chromatin
0
Histones
0
Nucleosomes
0
Transcription Factors
0
DNA
9007-49-2
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
1035-1046Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM118551
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM127062
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM141795
Pays : United States
Informations de copyright
© 2021 Tran et al.; Published by Cold Spring Harbor Laboratory Press.
Références
Genome Res. 2018 Feb 14;:
pubmed: 29444801
Appl Microbiol Biotechnol. 2018 Sep;102(17):7319-7331
pubmed: 29974182
Biochim Biophys Acta. 2005 Jan 7;1706(1-2):158-64
pubmed: 15620376
Mol Cell Biol. 1990 Dec;10(12):6362-73
pubmed: 2123293
Mol Biol Cell. 2012 May;23(10):1928-42
pubmed: 22438580
EMBO J. 2005 Feb 9;24(3):521-32
pubmed: 15660125
Genome Biol. 2010;11(7):R75
pubmed: 20637075
PLoS One. 2014 Jan 09;9(1):e83330
pubmed: 24416162
Biometals. 2000 Mar;13(1):65-72
pubmed: 10831226
Mol Cell. 2011 May 20;42(4):536-49
pubmed: 21596317
EMBO J. 1996 May 15;15(10):2519-29
pubmed: 8665859
BMC Biol. 2013 May 30;11:59
pubmed: 23721193
Bioinformatics. 2011 Apr 1;27(7):1017-8
pubmed: 21330290
BMC Bioinformatics. 2006 Mar 07;7:113
pubmed: 16522208
Plant J. 2019 Jan;97(2):306-320
pubmed: 30288820
Theory Biosci. 2012 Dec;131(4):281-5
pubmed: 22872506
Mol Cell Biol. 1997 Jul;17(7):3640-8
pubmed: 9199298
BMC Genomics. 2014 Jun 25;15:521
pubmed: 24965678
Mol Cell. 2017 Feb 2;65(3):578-580
pubmed: 28157510
Mol Cell Proteomics. 2009 Feb;8(2):380-92
pubmed: 19001347
Genes Dev. 2016 Mar 15;30(6):660-72
pubmed: 26966245
Nat Genet. 2007 May;39(5):683-7
pubmed: 17417638
Nat Genet. 2004 Aug;36(8):900-5
pubmed: 15247917
EMBO J. 1998 Nov 2;17(21):6327-36
pubmed: 9799240
Genome Res. 2013 Feb;23(2):341-51
pubmed: 23193179
Mol Biol Cell. 2012 Aug;23(15):3008-24
pubmed: 22696679
Nature. 2008 Jun 26;453(7199):1239-43
pubmed: 18488015
Mol Cell. 2017 Dec 21;68(6):1038-1053.e4
pubmed: 29225036
Trends Genet. 2014 Aug;30(8):348-55
pubmed: 24974018
Mol Cell. 2014 Feb 20;53(4):549-61
pubmed: 24508389
FEMS Yeast Res. 2006 Sep;6(6):924-36
pubmed: 16911514
Cell. 2015 Mar 12;160(6):1111-24
pubmed: 25768907
Genes Dev. 2011 Nov 15;25(22):2387-97
pubmed: 22085965
Mol Cell. 2015 Apr 16;58(2):371-86
pubmed: 25801168
Cell. 2014 Feb 13;156(4):812-24
pubmed: 24529382
Mol Cell. 2002 Jul;10(1):69-80
pubmed: 12150908
Mol Microbiol. 1999 Jul;33(2):274-83
pubmed: 10411744
Nature. 2006 Mar 30;440(7084):637-43
pubmed: 16554755
Mol Cell. 2008 Feb 1;29(2):207-16
pubmed: 18243115
Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11325-30
pubmed: 20534568
Genes Dev. 2015 Sep 15;29(18):1942-54
pubmed: 26385964
J Biol Chem. 1998 Oct 9;273(41):26875-9
pubmed: 9756934
Mol Cell. 2019 Jan 17;73(2):238-249.e3
pubmed: 30554944
Mol Cell. 2002 Apr;9(4):713-23
pubmed: 11983164
Genome Res. 2003 Aug;13(8):1863-72
pubmed: 12902380
Genes Dev. 2015 Jan 15;29(2):212-24
pubmed: 25593310
Genome Res. 2021 May;31(5):775-788
pubmed: 33811083
Mol Cell. 2011 Feb 18;41(4):480-92
pubmed: 21329885
Mol Cell. 2010 Dec 22;40(6):954-64
pubmed: 21172660
Chem Biol. 2010 Sep 24;17(9):1008-17
pubmed: 20851350
Annu Rev Biochem. 2003;72:449-79
pubmed: 12651739
Cell. 2000 Aug 4;102(3):303-14
pubmed: 10975521
Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18318-23
pubmed: 22025700
Mol Syst Biol. 2011 Jan 4;7:458
pubmed: 21206491
EMBO J. 2000 Apr 3;19(7):1613-24
pubmed: 10747029
Nature. 2012 Jan 18;483(7389):295-301
pubmed: 22258509
J Biol Chem. 1993 Apr 5;268(10):7442-8
pubmed: 8463277
Cell. 2007 Nov 16;131(4):706-17
pubmed: 18022365
PLoS Biol. 2012;10(7):e1001369
pubmed: 22912562
J Biol Chem. 2005 Jun 24;280(25):23869-75
pubmed: 15845535
PLoS Genet. 2011 Jun;7(6):e1002163
pubmed: 21738494
Mol Cell Biol. 2008 Apr;28(7):2221-34
pubmed: 18212068
Mol Cell. 2004 Feb 27;13(4):573-85
pubmed: 14992726
Environ Toxicol Chem. 2001 Oct;20(10):2353-60
pubmed: 11596770
Mol Cell. 2017 Feb 2;65(3):565-577.e3
pubmed: 28157509
Antioxid Redox Signal. 2001 Aug;3(4):625-34
pubmed: 11554449
Nat Biotechnol. 2011 May;29(5):436-42
pubmed: 21516085
J Biol Chem. 2003 Mar 21;278(12):10264-72
pubmed: 12525494
Genome Res. 2008 Jul;18(7):1073-83
pubmed: 18550805
Mol Biol Cell. 2012 Aug;23(15):2993-3007
pubmed: 22696683
Nature. 2012 Jun 28;486(7404):496-501
pubmed: 22722846
Toxicol Sci. 2008 Dec;106(2):400-12
pubmed: 18794233
Mol Cell Biol. 2004 Dec;24(23):10111-7
pubmed: 15542822
Nucleic Acids Res. 2013 Jun;41(11):5569-81
pubmed: 23599004
Eukaryot Cell. 2010 Nov;9(11):1669-79
pubmed: 20833895