Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development.
DNA replication timing
embryonic development
germline mutations
zebrafish
Journal
Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707
Informations de publication
Date de publication:
01 06 2019
01 06 2019
Historique:
accepted:
02
05
2019
pubmed:
12
5
2019
medline:
5
11
2019
entrez:
12
5
2019
Statut:
ppublish
Résumé
The DNA replication timing program is modulated throughout development and is also one of the main factors influencing the distribution of mutation rates across the genome. However, the relationship between the mutagenic influence of replication timing and its developmental plasticity remains unexplored. Here, we studied the distribution of copy number variations (CNVs) and single nucleotide polymorphisms across the zebrafish genome in relation to changes in DNA replication timing during embryonic development in this model vertebrate species. We show that CNV sites exhibit strong replication timing plasticity during development, replicating significantly early during early development but significantly late during more advanced developmental stages. Reciprocally, genomic regions that changed their replication timing during development contained a higher proportion of CNVs than developmentally constant regions. Developmentally plastic CNV sites, in particular those that become delayed in their replication timing, were enriched for the clustered protocadherins, a set of genes important for neuronal development that have undergone extensive genetic and epigenetic diversification during zebrafish evolution. In contrast, single nucleotide polymorphism sites replicated consistently early throughout embryonic development, highlighting a unique aspect of the zebrafish genome. Our results uncover a hitherto unrecognized interface between development and evolution.
Identifiants
pubmed: 31076752
pii: 5487996
doi: 10.1093/gbe/evz098
pmc: PMC6582765
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1663-1678Subventions
Organisme : NIGMS NIH HHS
ID : DP2 GM123495
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM121703
Pays : United States
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Mol Biol Evol. 2012 Feb;29(2):873-82
pubmed: 22046001
Nature. 2015 Oct 1;526(7571):75-81
pubmed: 26432246
Cell Rep. 2014 Nov 20;9(4):1228-34
pubmed: 25456125
Genome Res. 2004 Mar;14(3):354-66
pubmed: 14993203
Prog Mol Biol Transl Sci. 2013;116:145-67
pubmed: 23481194
Genome Biol Evol. 2011;3:799-811
pubmed: 21666225
Nucleic Acids Res. 2018 Sep 19;46(16):8299-8310
pubmed: 29986092
Nat Genet. 2015 Jul;47(7):822-826
pubmed: 25985141
Nucleic Acids Res. 2017 Jan 4;45(D1):D331-D338
pubmed: 27899567
Biotechnol Adv. 1996;14(1):57-72
pubmed: 14536924
Nat Commun. 2015 Feb 20;6:6315
pubmed: 25697895
Semin Cancer Biol. 2013 Apr;23(2):80-9
pubmed: 23327985
Genome Res. 2009 Dec;19(12):2288-99
pubmed: 19767418
Nature. 2013 Jul 11;499(7457):214-218
pubmed: 23770567
Genome Res. 2012 Oct;22(10):2043-53
pubmed: 22593555
BMC Evol Biol. 2007 Mar 30;7:49
pubmed: 17394664
Nat Biotechnol. 2011 Nov 20;29(12):1103-8
pubmed: 22101487
Mol Biol Evol. 2010 May;27(5):1077-86
pubmed: 20026481
Science. 2019 Jan 4;363(6422):81-84
pubmed: 30606845
Nat Genet. 2009 Apr;41(4):393-5
pubmed: 19287383
Genome Res. 2015 Aug;25(8):1091-103
pubmed: 26055160
Zebrafish. 2019 Feb;16(1):29-36
pubmed: 30418105
Cell. 2011 Dec 23;147(7):1537-50
pubmed: 22196729
Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):529-34
pubmed: 22203992
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Nucleic Acids Res. 1995 Apr 25;23(8):1350-3
pubmed: 7753625
Development. 2013 Aug;140(16):3297-302
pubmed: 23900538
Genome Res. 2010 Apr;20(4):447-57
pubmed: 20103589
Genetics. 2002 Aug;161(4):1395-410
pubmed: 12196388
Dev Biol. 2008 Sep 1;321(1):175-87
pubmed: 18602383
Nature. 2012 Aug 23;488(7412):517-21
pubmed: 22842903
Genetics. 2012 Mar;190(3):1017-24
pubmed: 22174069
Elife. 2013 Feb 26;2:e00348
pubmed: 23467541
Development. 2015 Apr 15;142(8):1542-52
pubmed: 25813542
Genome Biol Evol. 2010;2:859-69
pubmed: 20978102
Mol Biol Evol. 2012 Mar;29(3):905-13
pubmed: 22114361
Genetics. 2005 Apr;169(4):2179-88
pubmed: 15744052
Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44
pubmed: 19966280
Nat Genet. 2008 Sep;40(9):1124-9
pubmed: 19165926
Nucleic Acids Res. 2016 May 19;44(9):4222-32
pubmed: 27085808
Nat Commun. 2013;4:1502
pubmed: 23422670
Genetics. 2014 Sep;198(1):167-70
pubmed: 25009150
Trends Genet. 2010 Jun;26(6):243-7
pubmed: 20416969
Nature. 2011 Feb 3;470(7332):59-65
pubmed: 21293372
Am J Hum Genet. 2012 Dec 7;91(6):1033-40
pubmed: 23176822
Genome Res. 2017 Aug;27(8):1406-1416
pubmed: 28512193
Nature. 2015 Feb 19;518(7539):360-364
pubmed: 25693567
Nat Commun. 2012;3:1004
pubmed: 22893128
PLoS Genet. 2006 Feb;2(2):e20
pubmed: 16482228
Nature. 2015 May 7;521(7550):81-4
pubmed: 25707793