Genetic features and genomic targets of human KRAB-zinc finger proteins.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
08 2023
08 2023
Historique:
received:
19
01
2023
accepted:
18
07
2023
medline:
5
10
2023
pubmed:
21
9
2023
entrez:
20
9
2023
Statut:
ppublish
Résumé
Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on close to a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.
Identifiants
pubmed: 37730438
pii: gr.277722.123
doi: 10.1101/gr.277722.123
pmc: PMC10547255
doi:
Substances chimiques
Transcription Factors
0
DNA Transposable Elements
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1409-1423Subventions
Organisme : European Research Council
ID : 268721
Pays : International
Organisme : European Research Council
ID : 694658
Pays : International
Informations de copyright
© 2023 de Tribolet-Hardy et al.; Published by Cold Spring Harbor Laboratory Press.
Références
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Genome Biol Evol. 2014 Mar;6(3):510-25
pubmed: 24534434
Structure. 1998 Apr 15;6(4):451-64
pubmed: 9562555
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432
pubmed: 30357350
Bioinformatics. 2018 Jul 15;34(14):2483-2484
pubmed: 29514181
J Mol Biol. 2005 Dec 9;354(4):994-1007
pubmed: 16288912
PLoS One. 2012;7(1):e29518
pubmed: 22235304
PLoS Genet. 2022 Jun 15;18(6):e1010225
pubmed: 35704668
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Genome Res. 2006 May;16(5):669-77
pubmed: 16606702
Nat Commun. 2022 Jan 24;13(1):463
pubmed: 35075135
Mob DNA. 2016 May 06;7:9
pubmed: 27158268
Int J Mol Med. 2022 Oct;50(4):
pubmed: 36043524
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Nature. 2020 May;581(7809):434-443
pubmed: 32461654
Nature. 2020 Jul;583(7818):720-728
pubmed: 32728244
Nat Commun. 2022 Nov 23;13(1):7178
pubmed: 36418324
Mol Cell. 2011 Nov 4;44(3):361-72
pubmed: 22055183
J Biol Chem. 2010 Jan 8;285(2):1393-403
pubmed: 19887448
Development. 2022 Oct 1;149(19):
pubmed: 36052683
Nucleic Acids Res. 2012 Feb;40(4):e31
pubmed: 22156162
Retrovirology. 2015 May 16;12:41
pubmed: 25980612
Mol Cells. 2021 Dec 31;44(12):861-878
pubmed: 34963103
Cell. 2013 Aug 15;154(4):801-13
pubmed: 23953112
Nature. 2016 Aug 17;536(7616):285-91
pubmed: 27535533
Nat Methods. 2018 May;15(5):330-338
pubmed: 29638227
Annu Rev Genet. 2019 Dec 3;53:393-416
pubmed: 31518518
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Cell. 2014 Sep 11;158(6):1431-1443
pubmed: 25215497
Genome Res. 2021 Sep;31(9):1531-1545
pubmed: 34400477
Nature. 2017 Oct 11;550(7675):204-213
pubmed: 29022597
Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5
pubmed: 23193258
Cold Spring Harb Symp Quant Biol. 2015;80:281-8
pubmed: 26763983
Mob DNA. 2022 Jan 18;13(1):4
pubmed: 35042549
Cell Death Differ. 2014 Mar;21(3):381-7
pubmed: 24162661
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190333
pubmed: 32075554
Genomics Inform. 2016 Sep;14(3):70-77
pubmed: 27729835
RNA. 2022 Sep;28(9):1157-1171
pubmed: 35732404
Bioinformatics. 2015 Sep 1;31(17):2879-81
pubmed: 25953800
Nat Rev Genet. 2019 Feb;20(2):89-108
pubmed: 30446728
Science. 2017 May 19;356(6339):757-759
pubmed: 28522536
Cell Stem Cell. 2019 May 2;24(5):724-735.e5
pubmed: 31006620
Genome Biol. 2017 Sep 6;18(1):167
pubmed: 28877740
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Science. 1969 Jul 25;165(3891):349-57
pubmed: 5789433
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Cell. 2020 Dec 23;183(7):2020-2035.e16
pubmed: 33326746
Nucleic Acids Res. 2019 Jan 8;47(D1):D853-D858
pubmed: 30407534
Genome Res. 2016 Dec;26(12):1742-1752
pubmed: 27852650
Nature. 2022 Jan;601(7893):440-445
pubmed: 34794168
Trends Genet. 2017 Nov;33(11):871-881
pubmed: 28935117
J Biol Chem. 2000 May 26;275(21):15685-90
pubmed: 10748193
Cell Cycle. 2006 Mar;5(6):615-20
pubmed: 16582607
Genes Dev. 2019 Jan 1;33(1-2):49-54
pubmed: 30602440
Dev Cell. 2008 Oct;15(4):547-57
pubmed: 18854139
Cell Stem Cell. 2022 Jan 6;29(1):52-69.e8
pubmed: 34624206
Sci Adv. 2020 Aug 28;6(35):eaba3200
pubmed: 32923624
Genome Biol. 2003;4(10):231
pubmed: 14519192
Nat Commun. 2019 Apr 18;10(1):1809
pubmed: 31000713
Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22358-63
pubmed: 20007773
Brief Funct Genomics. 2010 Jan;9(1):65-78
pubmed: 20081217
Mob DNA. 2018 Jan 4;9:2
pubmed: 29308093
Nature. 2009 Apr 30;458(7242):1201-4
pubmed: 19270682
Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995
pubmed: 34791404
Semin Cancer Biol. 2010 Aug;20(4):234-45
pubmed: 20416380
Nature. 2014 Dec 11;516(7530):242-5
pubmed: 25274305
Nature. 2017 Mar 23;543(7646):550-554
pubmed: 28273063
Structure. 2001 Aug;9(8):717-23
pubmed: 11587646
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nucleic Acids Res. 1987 Nov 11;15(21):8725-37
pubmed: 2825118
EMBO J. 2019 Sep 16;38(18):e101220
pubmed: 31403225
Int J Mol Sci. 2019 Nov 27;20(23):
pubmed: 31783611
PLoS Genet. 2009 Jan;5(1):e1000325
pubmed: 19119423
Genome Res. 2021 Apr;31(4):551-563
pubmed: 33722937