Absolute quantification of cohesin, CTCF and their regulators in human cells.

CCCTC-Binding Factor / genetics Carrier Proteins / genetics Cell Cycle Proteins / genetics Cell Line Chromatids / genetics Chromatin / genetics Chromosomal Proteins, Non-Histone / genetics Chromosome Segregation / genetics Fluorescence Recovery After Photobleaching / methods G1 Phase / genetics Gene Dosage Gene Expression Genome, Human / genetics HeLa Cells Humans Mass Spectrometry / methods Nuclear Proteins / genetics Proto-Oncogene Proteins / genetics Cohesins
CTCF cell biology chromosomes cohesin fluorescence-correlation spectroscopy gene expression genome organization human mass spectrometry sister chromatid cohesion

Journal

eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614

Informations de publication

Date de publication:
17 06 2019
Historique:
received: 20 02 2019
accepted: 13 06 2019
pubmed: 18 6 2019
medline: 26 2 2020
entrez: 18 6 2019
Statut: epublish

Résumé

The organisation of mammalian genomes into loops and topologically associating domains (TADs) contributes to chromatin structure, gene expression and recombination. TADs and many loops are formed by cohesin and positioned by CTCF. In proliferating cells, cohesin also mediates sister chromatid cohesion, which is essential for chromosome segregation. Current models of chromatin folding and cohesion are based on assumptions of how many cohesin and CTCF molecules organise the genome. Here we have measured absolute copy numbers and dynamics of cohesin, CTCF, NIPBL, WAPL and sororin by mass spectrometry, fluorescence-correlation spectroscopy and fluorescence recovery after photobleaching in HeLa cells. In G1-phase, there are ~250,000 nuclear cohesin complexes, of which ~ 160,000 are chromatin-bound. Comparison with chromatin immunoprecipitation-sequencing data implies that some genomic cohesin and CTCF enrichment sites are unoccupied in single cells at any one time. We discuss the implications of these findings for how cohesin can contribute to genome organisation and cohesion.

Identifiants

DOI: 10.7554/eLife.46269 PMID: 31204999 PMC: PMC6606026
pubmed: 31204999
doi: 10.7554/eLife.46269
pii: 46269
pmc: PMC6606026
doi:
pii:

Substances chimiques

CCCTC-Binding Factor 0
Carrier Proteins 0
Cell Cycle Proteins 0
Chromatin 0
Chromosomal Proteins, Non-Histone 0
NIPBL protein, human 0
Nuclear Proteins 0
Proto-Oncogene Proteins 0
WAPL protein, human 0

Banques de données

GEO
['GSE126990']

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : Vienna Science and Technology Fund
ID : WWTF LS09-13
Pays : International
Organisme : European Molecular Biology Laboratory
ID : International PhD Programme
Pays : International
Organisme : NIDA NIH HHS
ID : U01 DA047728
Pays : United States
Organisme : Austrian Research Promotion Agency
ID : Laura Bassi Centre for Optimized Structural Studies grant FFG-840283
Pays : International
Organisme : NIH HHS
ID : Common Fund 4D Nucleome Program (U01 DA047728)
Pays : United States
Organisme : Paul G. Allen Frontiers Group
ID : Allen Distinguished Investigator Program
Pays : International
Organisme : NIH HHS
ID : Common Fund 4D Nucleome Program (U01 EB021223)
Pays : United States
Organisme : European Molecular Biology Organization
ID : ALTF 1335-2016
Pays : International
Organisme : NIH HHS
ID : Common Fund 4D Nucleome Program (U01 EB021223 / U01 DA047728)
Pays : United States
Organisme : Horizon 2020 Framework Programme
ID : 693949
Pays : International
Organisme : Human Frontier Science Program
ID : LT001527/2017
Pays : International
Organisme : Austrian Science Fund
ID : I 3686-B25 MEIOREC - ERA-CAPS
Pays : International
Organisme : Horizon 2020 Framework Programme
ID : 823839
Pays : International
Organisme : Sixth Framework Programme
ID : 503464 (MitoCheck)
Pays : International
Organisme : Horizon 2020 Framework Programme
ID : 653706
Pays : International
Organisme : NIBIB NIH HHS
ID : U01 EB021223
Pays : United States
Organisme : Austrian Science Fund
ID : Wittgenstein award Z196-B20
Pays : International
Organisme : Seventh Framework Programme
ID : 241548 (MitoSys)
Pays : International
Organisme : Austrian Research Promotion Agency
ID : FFG-834223
Pays : International
Organisme : Austrian Science Fund
ID : FWF special research program SFB F34
Pays : International
Organisme : Austrian Research Promotion Agency
ID : FFG-852936
Pays : International

Commentaires et corrections

Type : CommentIn

Informations de copyright

© 2019, Holzmann et al.

Déclaration de conflit d'intérêts

JH, AP, KN, MH, NW, BK, JF, GD, WT, RL, RS, GB, BN, KM, ID, JE, JP No competing interests declared

Références

Curr Biol. 2003 Nov 11;13(22):1941-53
pubmed: 14614819
Nat Cell Biol. 2011 Oct 03;13(10):1170-7
pubmed: 21968990
Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450
pubmed: 30395289
Elife. 2019 Jun 17;8:
pubmed: 31204999
G3 (Bethesda). 2013 Aug 07;3(8):1213-24
pubmed: 23550136
EMBO J. 2016 Dec 15;35(24):2686-2698
pubmed: 27872142
Cell. 2008 Feb 8;132(3):422-33
pubmed: 18237772
Mol Cell. 2004 Jan 30;13(2):291-8
pubmed: 14759373
Science. 2017 Feb 3;355(6324):524-527
pubmed: 28154080
J Cell Biol. 2008 Dec 15;183(6):1019-31
pubmed: 19075111
Curr Opin Cell Biol. 2018 Jun;52:51-57
pubmed: 29433064
Cell. 2017 Oct 5;171(2):305-320.e24
pubmed: 28985562
Mol Cell. 2005 Apr 15;18(2):185-200
pubmed: 15837422
Science. 2018 Feb 9;359(6376):
pubmed: 29348367
Cell. 2000 Oct 27;103(3):399-410
pubmed: 11081627
Cell Cycle. 2009 Feb 1;8(3):399-402
pubmed: 19177018
BMC Biol. 2015 Aug 07;13:63
pubmed: 26248466
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Science. 2014 Nov 21;346(6212):968-72
pubmed: 25414306
Curr Biol. 2011 Jan 11;21(1):12-24
pubmed: 21185190
Cell. 2015 Aug 13;162(4):900-10
pubmed: 26276636
Nature. 2017 Apr 6;544(7648):59-64
pubmed: 28289288
Elife. 2017 Sep 15;6:
pubmed: 28914604
Nature. 2014 Jan 16;505(7483):367-71
pubmed: 24291789
Curr Biol. 2004 Jul 13;14(13):1187-93
pubmed: 15242616
Nat Cell Biol. 2004 Oct;6(10):991-6
pubmed: 15448702
Cell Rep. 2016 May 31;15(9):2038-49
pubmed: 27210764
J Proteome Res. 2011 Feb 4;10(2):780-9
pubmed: 21043528
Cell Rep. 2016 May 3;15(5):988-998
pubmed: 27117417
Cell. 2012 Aug 31;150(5):961-74
pubmed: 22901742
Nature. 2010 Apr 1;464(7289):721-7
pubmed: 20360735
Elife. 2019 Jun 17;8:
pubmed: 31205001
EMBO J. 2017 Dec 15;36(24):3600-3618
pubmed: 29217590
Curr Biol. 2006 Aug 8;16(15):1571-8
pubmed: 16890534
Curr Biol. 2004 Sep 7;14(17):1598-603
pubmed: 15341749
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65
pubmed: 26499245
Cell. 2018 May 31;173(6):1508-1519.e18
pubmed: 29754816
Nature. 2017 Jul 5;547(7661):61-67
pubmed: 28682332
Mol Cell. 2015 Nov 19;60(4):676-84
pubmed: 26527277
EMBO J. 2017 Dec 15;36(24):3573-3599
pubmed: 29217591
Cell. 2017 May 4;169(4):693-707.e14
pubmed: 28475897
Elife. 2017 May 03;6:
pubmed: 28467304
Mol Cell Biol. 2004 Apr;24(8):3497-504
pubmed: 15060168
Mol Cell. 2018 Jun 21;70(6):1134-1148.e7
pubmed: 29932904
Nat Methods. 2007 Nov;4(11):923-5
pubmed: 17952086
Curr Biol. 2006 Dec 19;16(24):2406-17
pubmed: 17112726
Cell. 2005 Sep 23;122(6):849-60
pubmed: 16179255
Nature. 2008 Jul 17;454(7202):297-301
pubmed: 18596691
Cell. 2017 May 18;169(5):930-944.e22
pubmed: 28525758
Annu Rev Genet. 2001;35:673-745
pubmed: 11700297
J Cell Biol. 2000 Nov 13;151(4):749-62
pubmed: 11076961
Cell. 2006 Dec 1;127(5):955-67
pubmed: 17113138
Nature. 2012 Apr 11;485(7398):381-5
pubmed: 22495304
J Cell Biol. 2018 Jun 4;217(6):1985-2004
pubmed: 29695489
Nat Protoc. 2018 Jun;13(6):1445-1464
pubmed: 29844523
Sci Adv. 2018 Feb 28;4(2):eaar8082
pubmed: 29503869
Nature. 2017 Apr 6;544(7648):110-114
pubmed: 28355183
EMBO J. 2016 Dec 15;35(24):2671-2685
pubmed: 27799150
Nat Biotechnol. 2015 Apr;33(4):384-9
pubmed: 25774713
EMBO J. 2016 Mar 15;35(6):635-53
pubmed: 26903600
Science. 2018 Oct 26;362(6413):
pubmed: 30361340
Nature. 2018 Sep;561(7723):411-415
pubmed: 30202089
J Cell Biol. 2018 Jul 2;217(7):2309-2328
pubmed: 29632028
Curr Biol. 2018 Nov 5;28(21):R1266-R1281
pubmed: 30399354
Nucleic Acids Res. 2015 Nov 16;43(20):e132
pubmed: 26130708
J Cell Biol. 2000 Aug 7;150(3):405-16
pubmed: 10931856
Nature. 2004 Jul 29;430(6999):573-8
pubmed: 15229615
Curr Biol. 2006 May 9;16(9):863-74
pubmed: 16682347
Nature. 2008 Feb 14;451(7180):796-801
pubmed: 18235444
Cell. 2003 Mar 21;112(6):765-77
pubmed: 12654244
Science. 2017 Nov 3;358(6363):672-676
pubmed: 28882993
Science. 2018 Apr 6;360(6384):102-105
pubmed: 29472443
Nature. 2013 Oct 3;502(7469):59-64
pubmed: 24067610
Nature. 2012 Apr 11;485(7398):376-80
pubmed: 22495300
J Proteome Res. 2014 Aug 1;13(8):3679-84
pubmed: 24909410
Mol Cell. 2000 Feb;5(2):243-54
pubmed: 10882066
EMBO J. 2013 Mar 6;32(5):666-76
pubmed: 23361318
Cell Rep. 2015 Mar 3;10(8):1297-309
pubmed: 25732821
Curr Biol. 2003 Nov 11;13(22):1930-40
pubmed: 14614818
Nat Methods. 2012 May 30;9(6):555-66
pubmed: 22669653
Curr Biol. 2014 Oct 6;24(19):2228-37
pubmed: 25220052
EMBO J. 2013 Mar 6;32(5):656-65
pubmed: 23340528
Curr Biol. 2007 Apr 3;17(7):630-6
pubmed: 17349791
Nature. 2013 Sep 26;501(7468):564-8
pubmed: 23975099
Anal Chem. 2009 Dec 15;81(24):10254-61
pubmed: 19924867
Nature. 2017 Nov 2;551(7678):51-56
pubmed: 29094699
Nature. 2017 Apr 27;544(7651):503-507
pubmed: 28424523
Open Biol. 2016 Jun;6(6):
pubmed: 27278645
Cell. 2013 Sep 12;154(6):1380-9
pubmed: 23992846
Nature. 2016 Jan 21;529(7586):418-22
pubmed: 26760202
Cell. 2010 Nov 24;143(5):737-49
pubmed: 21111234
Mol Cell. 2018 Sep 6;71(5):841-847.e5
pubmed: 30100265
Nat Commun. 2015 Oct 01;6:8497
pubmed: 26423723

Auteurs

Johann Holzmann (J)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.

Antonio Z Politi (AZ)

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
ORCID: 0000-0003-4788-0933

Kota Nagasaka (K)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
ORCID: 0000-0003-0765-638X

Merle Hantsche-Grininger (M)

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
ORCID: 0000-0002-5137-1616

Nike Walther (N)

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
ORCID: 0000-0002-7591-5251

Birgit Koch (B)

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

Johannes Fuchs (J)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.

Gerhard Dürnberger (G)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.

Wen Tang (W)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

Rene Ladurner (R)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

Roman R Stocsits (RR)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

Georg A Busslinger (GA)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

Béla Novák (B)

Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
ORCID: 0000-0002-6961-1366

Karl Mechtler (K)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.

Iain Finley Davidson (IF)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
ORCID: 0000-0003-4945-6415

Jan Ellenberg (J)

Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
ORCID: 0000-0001-5909-701X

Jan-Michael Peters (JM)

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
Medical University of Vienna, Vienna, Austria.
ORCID: 0000-0003-2820-3195

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Classifications MeSH

Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Protéines de répression › Facteur de liaison à la séquence CCCTC › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines de transport › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines du cycle cellulaire › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Cellules › Cellules cultivées › Lignée cellulaire › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatides › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Nucléoprotéines › Protéines chromosomiques nonhistones › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Phénomènes génétiques › Division du noyau cellulaire › Ségrégation des chromosomes › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Techniques d'investigation › Techniques de chimie analytique › Photométrie › Mesures de luminescence › Fluorimétrie › Redistribution de fluorescence après photoblanchiment › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Phénomènes physiologiques cellulaires › Cycle cellulaire › Interphase › Phase G1 › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Phénomènes génétiques › Génotype › Dosage génique › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Phénomènes génétiques › Expression des gènes › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Génome › Génome humain › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Cellules › Cellules épithéliales › Cellules HeLa › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Techniques d'investigation › Techniques de chimie analytique › Spectrométrie de masse › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines nucléaires › Absolute quantification of cohesin, CTCF and...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines tumorales › Protéines oncogènes › Protéines proto-oncogènes › Absolute quantification of cohesin, CTCF and...