The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification.
KAP1
KRAB zinc finger proteins
coelacanth
evolution
mass spectrometry
Journal
The EMBO journal
ISSN: 1460-2075
Titre abrégé: EMBO J
Pays: England
ID NLM: 8208664
Informations de publication
Date de publication:
16 09 2019
16 09 2019
Historique:
received:
23
11
2018
revised:
03
07
2019
accepted:
10
07
2019
pubmed:
14
8
2019
medline:
27
12
2019
entrez:
13
8
2019
Statut:
ppublish
Résumé
Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) are encoded in the hundreds by the genomes of higher vertebrates, and many act with the heterochromatin-inducing KAP1 as repressors of transposable elements (TEs) during early embryogenesis. Yet, their widespread expression in adult tissues and enrichment at other genetic loci indicate additional roles. Here, we characterized the protein interactome of 101 of the ~350 human KZFPs. Consistent with their targeting of TEs, most KZFPs conserved up to placental mammals essentially recruit KAP1 and associated effectors. In contrast, a subset of more ancient KZFPs rather interacts with factors related to functions such as genome architecture or RNA processing. Nevertheless, KZFPs from coelacanth, our most distant KZFP-encoding relative, bind the cognate KAP1. These results support a hypothetical model whereby KZFPs first emerged as TE-controlling repressors, were continuously renewed by turnover of their hosts' TE loads, and occasionally produced derivatives that escaped this evolutionary flushing by development and exaptation of novel functions.
Identifiants
pubmed: 31403225
doi: 10.15252/embj.2018101220
pmc: PMC6745500
doi:
Substances chimiques
DNA Transposable Elements
0
Fish Proteins
0
Repressor Proteins
0
TRIM28 protein, human
EC 2.3.2.27
Tripartite Motif-Containing Protein 28
EC 2.3.2.27
Banques de données
GEO
['GSE120539']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e101220Subventions
Organisme : EC|FP7|FP7 Ideas: European Research Council (FP7 Ideas)
ID : 268721
Pays : International
Organisme : EC|H2020|H2020 Priority Excellent Science|H2020 European Research Council (ERC)
ID : 694658
Pays : International
Organisme : EC|H2020|H2020 Priority Excellent Science|H2020 European Research Council (ERC)
ID : 2014-AdG 670821
Pays : International
Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)
ID : 310030_152879
Pays : International
Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)
ID : 310030B_173337
Pays : International
Informations de copyright
© 2019 The Authors. Published under the terms of the CC BY 4.0 license.
Références
FEBS Lett. 1995 Aug 7;369(2-3):153-7
pubmed: 7649249
Mol Syst Biol. 2011 Oct 11;7:539
pubmed: 21988835
Genes Dev. 2002 Apr 15;16(8):919-32
pubmed: 11959841
J Biol Chem. 2010 Jan 8;285(2):1393-403
pubmed: 19887448
Genome Biol Evol. 2014 Mar;6(3):510-25
pubmed: 24534434
Nat Methods. 2013 Aug;10(8):730-6
pubmed: 23921808
Neurobiol Dis. 2015 Jan;73:220-8
pubmed: 25315684
Nature. 2009 Apr 30;458(7242):1201-4
pubmed: 19270682
Microbiol Spectr. 2015 Feb;3(1):MDNA3-0009-2014
pubmed: 26104559
Genes Dev. 2016 Feb 1;30(3):257-65
pubmed: 26833727
J Biol Chem. 2001 Apr 13;276(15):12427-33
pubmed: 11279031
PLoS One. 2010 Jul 06;5(7):e11425
pubmed: 20625510
PLoS One. 2012;7(1):e29518
pubmed: 22235304
Genome Res. 2011 Nov;21(11):1800-12
pubmed: 21784874
Genes Dev. 1996 Aug 15;10(16):2067-78
pubmed: 8769649
Mol Cell Biol. 1999 Dec;19(12):8526-35
pubmed: 10567577
Bioinformatics. 2006 Dec 1;22(23):2841-5
pubmed: 17032681
Genome Res. 2008 Nov;18(11):1752-62
pubmed: 18682548
Cell. 2011 Mar 4;144(5):689-702
pubmed: 21376232
Nucleic Acids Res. 1997 Dec 15;25(24):5025-32
pubmed: 9396811
Mol Cell Biol. 1999 Jun;19(6):4366-78
pubmed: 10330177
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
pubmed: 16381927
Mol Cell. 2011 Nov 4;44(3):361-72
pubmed: 22055183
Science. 2017 May 26;356(6340):
pubmed: 28495876
Cell. 2015 Jul 16;162(2):425-440
pubmed: 26186194
Science. 2016 Mar 4;351(6277):1083-7
pubmed: 26941318
Nature. 2016 Aug 17;536(7616):285-91
pubmed: 27535533
Blood. 2013 Jan 24;121(4):707-15
pubmed: 23212515
Nature. 2010 Apr 8;464(7290):927-31
pubmed: 20164836
Genes Dev. 2001 Feb 15;15(4):428-43
pubmed: 11230151
Genes Dev. 2014 Jul 1;28(13):1397-409
pubmed: 24939876
Nat Genet. 2013 Jun;45(6):580-5
pubmed: 23715323
Cell Rep. 2013 Apr 25;3(4):1105-16
pubmed: 23545495
Science. 2017 May 19;356(6339):757-759
pubmed: 28522536
Cell Stem Cell. 2019 May 2;24(5):724-735.e5
pubmed: 31006620
J Clin Invest. 2008 Sep;118(9):3098-108
pubmed: 18677406
Development. 2017 Aug 1;144(15):2719-2729
pubmed: 28765213
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Mol Biol Evol. 2001 Dec;18(12):2186-94
pubmed: 11719568
J Biol Chem. 2000 Jun 2;275(22):17173-9
pubmed: 10747874
Mol Cell. 2011 May 6;42(3):285-96
pubmed: 21549307
Biochem Biophys Res Commun. 2009 Oct 30;388(4):689-94
pubmed: 19695231
PLoS One. 2010 Dec 08;5(12):e15082
pubmed: 21170338
Genome Res. 2016 Dec;26(12):1742-1752
pubmed: 27852650
Genome Res. 2014 Dec;24(12):1963-76
pubmed: 25319995
Cell. 2012 Jan 20;148(1-2):335-48
pubmed: 22244452
Cell Rep. 2018 Jan 2;22(1):44-58
pubmed: 29298432
J Biol Chem. 2000 May 26;275(21):15685-90
pubmed: 10748193
Genome Res. 2006 Jan;16(1):78-87
pubmed: 16344559
Cell Cycle. 2006 Mar;5(6):615-20
pubmed: 16582607
Genes Dev. 2019 Jan 1;33(1-2):49-54
pubmed: 30602440
Nature. 2010 Jan 14;463(7278):237-40
pubmed: 20075919
Curr Genomics. 2013 Jun;14(4):268-78
pubmed: 24294107
Proc Natl Acad Sci U S A. 1994 May 10;91(10):4509-13
pubmed: 8183939
Nature. 2015 Jun 11;522(7555):221-5
pubmed: 25896322
Nat Struct Mol Biol. 2010 May;17(5):635-40
pubmed: 20418883
Genome Biol. 2003;4(10):231
pubmed: 14519192
PLoS One. 2015 Apr 23;10(4):e0123935
pubmed: 25905708
Mol Cell. 2013 Apr 11;50(1):16-28
pubmed: 23434374
BMC Bioinformatics. 2014 Jan 13;15:7
pubmed: 24410852
PLoS One. 2017 Mar 23;12(3):e0173746
pubmed: 28334004
Chromosoma. 2017 Dec;126(6):681-695
pubmed: 28527011
Nature. 2017 Mar 23;543(7646):550-554
pubmed: 28273063
PLoS One. 2014 Jun 10;9(6):e98679
pubmed: 24914678
Nucleic Acids Res. 2014 Jun;42(11):7305-18
pubmed: 24782531
Nature. 2014 Dec 11;516(7530):242-5
pubmed: 25274305
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600
pubmed: 23671338
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nature. 2017 May 25;545(7655):505-509
pubmed: 28514442
Cell Rep. 2013 Apr 25;3(4):1306-20
pubmed: 23602568
EMBO J. 2019 Sep 16;38(18):e101220
pubmed: 31403225
Nat Methods. 2011 Jan;8(1):70-3
pubmed: 21131968
Genomics. 2008 Apr;91(4):347-55
pubmed: 18255255