The impact of whole genome duplications on the human gene regulatory networks.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
12 2021
12 2021
Historique:
received:
19
08
2021
accepted:
12
11
2021
revised:
16
12
2021
pubmed:
7
12
2021
medline:
15
2
2022
entrez:
6
12
2021
Statut:
epublish
Résumé
This work studies the effects of the two rounds of Whole Genome Duplication (WGD) at the origin of the vertebrate lineage on the architecture of the human gene regulatory networks. We integrate information on transcriptional regulation, miRNA regulation, and protein-protein interactions to comparatively analyse the role of WGD and Small Scale Duplications (SSD) in the structural properties of the resulting multilayer network. We show that complex network motifs, such as combinations of feed-forward loops and bifan arrays, deriving from WGD events are specifically enriched in the network. Pairs of WGD-derived proteins display a strong tendency to interact both with each other and with common partners and WGD-derived transcription factors play a prominent role in the retention of a strong regulatory redundancy. Combinatorial regulation and synergy between different regulatory layers are in general enhanced by duplication events, but the two types of duplications contribute in different ways. Overall, our findings suggest that the two WGD events played a substantial role in increasing the multi-layer complexity of the vertebrate regulatory network by enhancing its combinatorial organization, with potential consequences on its overall robustness and ability to perform high-level functions like signal integration and noise control. Lastly, we discuss in detail the RAR/RXR pathway as an illustrative example of the evolutionary impact of WGD duplications in human.
Identifiants
pubmed: 34871317
doi: 10.1371/journal.pcbi.1009638
pii: PCOMPBIOL-D-21-01527
pmc: PMC8675932
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1009638Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Nature. 2000 Dec 14;408(6814):796-815
pubmed: 11130711
PLoS Comput Biol. 2015 Jul 16;11(7):e1004394
pubmed: 26181593
Nucleic Acids Res. 2021 Jan 8;49(D1):D884-D891
pubmed: 33137190
Plant Cell. 2011 May;23(5):1719-28
pubmed: 21540436
Nucleic Acids Res. 2021 Jan 8;49(D1):D939-D946
pubmed: 33152070
Nucleic Acids Res. 2013 Jan;41(Database issue):D828-33
pubmed: 23193263
New Phytol. 2009 Aug;183(3):557-564
pubmed: 19555435
Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5454-9
pubmed: 15800040
Nature. 2003 Jan 2;421(6918):63-6
pubmed: 12511954
Nucleic Acids Res. 2018 Jan 4;46(D1):D239-D245
pubmed: 29156006
Proc Natl Acad Sci U S A. 2010 May 18;107(20):9270-4
pubmed: 20439718
Genome Res. 2007 Sep;17(9):1254-65
pubmed: 17652425
Science. 2000 Nov 10;290(5494):1151-5
pubmed: 11073452
Genetics. 2007 Feb;175(2):933-43
pubmed: 17151249
Genes Dev. 2001 Jan 15;15(2):213-25
pubmed: 11157777
J Struct Funct Genomics. 2003;3(1-4):35-44
pubmed: 12836683
Endocrinology. 2014 Nov;155(11):4275-86
pubmed: 25116705
BMC Genomics. 2012 Aug 17;13:405
pubmed: 22900683
Science. 2002 May 3;296(5569):910-3
pubmed: 11988575
PLoS Comput Biol. 2011 Mar;7(3):e1001101
pubmed: 21423718
BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7
pubmed: 16723010
PLoS Genet. 2006 Jul;2(7):e102
pubmed: 16839186
Bioessays. 2009 Jan;31(1):29-39
pubmed: 19153999
J Mol Evol. 1999 Aug;49(2):169-81
pubmed: 10441669
Nat Genet. 2002 May;31(1):64-8
pubmed: 11967538
Trends Genet. 2008 Oct;24(10):485-8
pubmed: 18786741
PLoS Biol. 2005 Oct;3(10):e314
pubmed: 16128622
Bioinformatics. 2006 May 1;22(9):1152-3
pubmed: 16455747
BMC Biol. 2010 Dec 13;8:146
pubmed: 21144020
Nature. 2004 Apr 8;428(6983):617-24
pubmed: 15004568
PLoS Biol. 2019 Nov 22;17(11):e3000519
pubmed: 31756186
Science. 2020 Jun 26;368(6498):
pubmed: 32586993
Genome Res. 2006 Jul;16(7):805-14
pubmed: 16818725
Nat Rev Genet. 2008 Dec;9(12):938-50
pubmed: 19015656
Nat Rev Genet. 2005 Nov;6(11):836-46
pubmed: 16304599
Nat Rev Genet. 2017 Jul;18(7):411-424
pubmed: 28502977
Nature. 2012 Sep 6;489(7414):91-100
pubmed: 22955619
Genome Res. 2019 Aug;29(8):1363-1375
pubmed: 31340985
Plant Physiol. 2013 Jun;162(2):769-78
pubmed: 23580595
Nature. 1997 Jun 12;387(6634):708-13
pubmed: 9192896
Cell Rep. 2012 Nov 29;2(5):1387-98
pubmed: 23168259
Nat Genet. 2004 May;36(5):492-6
pubmed: 15107850
Sci Adv. 2018 Feb 21;4(2):eaao1261
pubmed: 29492455
Nat Plants. 2018 May;4(5):258-268
pubmed: 29725103
Nature. 2018 Dec;564(7734):64-70
pubmed: 30464347
Nat Rev Genet. 2008 Jul;9(7):541-53
pubmed: 18542081
Curr Opin Struct Biol. 2004 Jun;14(3):283-91
pubmed: 15193307
Genome Biol. 2006;7(5):R43
pubmed: 16723033
BMC Syst Biol. 2010 Jun 03;4:77
pubmed: 20525287
Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613
pubmed: 30476243
PLoS Biol. 2019 Nov 22;17(11):e3000289
pubmed: 31756183
PLoS Comput Biol. 2011 Apr;7(4):e1002029
pubmed: 21490719
Front Plant Sci. 2011 Oct 11;2:64
pubmed: 22645545
Nucleic Acids Res. 2018 Jan 4;46(D1):D380-D386
pubmed: 29087512
Nucleic Acids Res. 2018 Jan 4;46(D1):D360-D370
pubmed: 29194489
Curr Opin Plant Biol. 2014 Jun;19:91-8
pubmed: 24907529
PLoS Comput Biol. 2007 Oct;3(10):1993-2002
pubmed: 17967049
Plant Cell. 2020 May;32(5):1434-1448
pubmed: 32184347
PLoS Comput Biol. 2014 Feb 27;10(2):e1003490
pubmed: 24586138
Genome Biol. 2007;8(10):R209
pubmed: 17916239
Mol Biol Evol. 2006 May;23(5):887-92
pubmed: 16368775
BMC Syst Biol. 2012 Oct 10;6:131
pubmed: 23050836
Science. 2016 May 20;352(6288):1009-13
pubmed: 27199432
BMC Genomics. 2016 Jan 22;17:71
pubmed: 26801093
Genetics. 2008 Aug;179(4):2319-24
pubmed: 18689880
Trends Genet. 2010 Oct;26(10):425-30
pubmed: 20708291
Sci Rep. 2017 Aug 8;7(1):7596
pubmed: 28790414
Nat Rev Genet. 2009 Oct;10(10):725-32
pubmed: 19652647
Nucleic Acids Res. 2017 Jan 9;45(1):81-91
pubmed: 27634932
Science. 2013 Oct 4;342(6154):104-8
pubmed: 24092741
Nucleic Acids Res. 2020 Jan 8;48(D1):D724-D730
pubmed: 31612943
Science. 2002 Oct 25;298(5594):824-7
pubmed: 12399590