Annotating the Insect Regulatory Genome.

arthropod cis-regulation enhancer genome annotation genomics

Journal

Insects
ISSN: 2075-4450
Titre abrégé: Insects
Pays: Switzerland
ID NLM: 101574235

Informations de publication

Date de publication:
29 Jun 2021
Historique:
received: 28 05 2021
revised: 23 06 2021
accepted: 25 06 2021
entrez: 2 7 2021
pubmed: 3 7 2021
medline: 3 7 2021
Statut: epublish

Résumé

An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical and computational discovery strategies, the past few decades have witnessed dramatic progress in our ability to identify

Identifiants

pubmed: 34209769
pii: insects12070591
doi: 10.3390/insects12070591
pmc: PMC8305585
pii:
doi:

Types de publication

Journal Article Review

Langues

eng

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM114067
Pays : United States
Organisme : U.S. Department of Agriculture
ID : 2018-08230
Organisme : National Science Foundation
ID : DBI-1758252
Organisme : NIH HHS
ID : R01 GM114067
Pays : United States

Références

Genome Res. 2012 Jul;22(7):1334-49
pubmed: 22456606
Curr Opin Genet Dev. 2018 Oct;52:70-76
pubmed: 29913329
Genes Dev. 2018 Feb 1;32(3-4):202-223
pubmed: 29491135
Nucleic Acids Res. 2011 Dec;39(22):9463-72
pubmed: 21821659
Insect Mol Biol. 2021 Aug;30(4):410-419
pubmed: 33866636
BMC Bioinformatics. 2017 Dec 1;18(Suppl 13):478
pubmed: 29219068
Genome Biol. 2020 Sep 10;21(1):243
pubmed: 32912294
BMC Bioinformatics. 2017 Aug 1;18(1):357
pubmed: 28764645
Proc Natl Acad Sci U S A. 2019 Jan 15;116(3):900-908
pubmed: 30598455
Genetics. 2016 May;203(1):203-18
pubmed: 26984057
BMC Bioinformatics. 2018 May 31;19(1):202
pubmed: 29855387
Cell Rep. 2015 Sep 22;12(11):1740-7
pubmed: 26344774
Genes Dev. 2017 Mar 15;31(6):590-602
pubmed: 28381411
J Biomed Semantics. 2013 Oct 18;4(1):32
pubmed: 24139062
Genome Res. 2021 May;31(5):877-889
pubmed: 33722938
Genome Biol. 2009;10(7):R80
pubmed: 19627575
Nat Commun. 2018 Sep 7;9(1):3647
pubmed: 30194434
Sci Rep. 2016 Jun 22;6:28517
pubmed: 27329130
Bioinformatics. 2010 Sep 1;26(17):2109-15
pubmed: 20624780
Methods Mol Biol. 2019;1858:89-97
pubmed: 30414113
Development. 2018 Apr 5;145(7):
pubmed: 29540499
Nature. 2019 Apr;568(7750):49-54
pubmed: 30886393
PLoS Comput Biol. 2010 Dec 02;6(12):e1001020
pubmed: 21152003
Curr Biol. 2016 Jan 11;26(1):38-51
pubmed: 26687625
PLoS Comput Biol. 2018 Oct 4;14(10):e1006484
pubmed: 30286077
Genome Biol. 2007;8(6):R101
pubmed: 17550599
BMC Bioinformatics. 2011 Dec 22;12:491
pubmed: 22192575
Elife. 2020 Apr 29;9:
pubmed: 32347792
Nat Methods. 2012 Mar 18;9(5):473-6
pubmed: 22426492
Nucleic Acids Res. 2009 Sep;37(17):5665-77
pubmed: 19651877
PLoS Genet. 2008 Jun 27;4(6):e1000106
pubmed: 18584029
Genes Dev. 2011 Aug 15;25(16):1686-701
pubmed: 21852534
Nat Rev Genet. 2009 Oct;10(10):669-80
pubmed: 19736561
Nat Commun. 2018 Dec 17;9(1):5345
pubmed: 30559361
Nat Rev Genet. 2013 Apr;14(4):288-95
pubmed: 23503198
Genome Biol. 2008 Jan 28;9(1):R22
pubmed: 18226245
Nat Commun. 2016 Feb 04;7:10528
pubmed: 26841971
Genome Biol Evol. 2014 Sep;6(9):2301-20
pubmed: 25173756
Nat Rev Genet. 2020 May;21(5):292-310
pubmed: 31988385
Genome Biol. 2009;10(9):R97
pubmed: 19758432
Genome Biol. 2007;8(5):R75
pubmed: 17490485
Genome Res. 2008 Oct;18(10):1592-601
pubmed: 18583644
Brief Funct Genomics. 2018 Jul 1;17(4):246-254
pubmed: 29342231
Nature. 2015 Jul 23;523(7561):486-90
pubmed: 26083756
BMC Genomics. 2019 Dec 24;20(Suppl 9):951
pubmed: 31874637
Nucleic Acids Res. 2019 Jan 8;47(D1):D828-D834
pubmed: 30329093
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Genome Res. 2011 Dec;21(12):2167-80
pubmed: 21875935
PLoS Genet. 2018 May 4;14(5):e1007367
pubmed: 29727464
Cell Res. 2011 Mar;21(3):381-95
pubmed: 21321607
Genome Biol. 2020 Dec 8;21(1):298
pubmed: 33292397
PLoS One. 2016 Sep 16;11(9):e0162968
pubmed: 27637070
Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56
pubmed: 25428369
Genome Res. 2020 Dec;30(12):1815-1834
pubmed: 32732264
Nat Commun. 2020 Jul 29;11(1):3696
pubmed: 32728046
Methods Mol Biol. 2012;786:229-45
pubmed: 21938630
Nature. 2020 Jul;583(7818):699-710
pubmed: 32728249
Anal Biochem. 2019 Apr 15;571:53-61
pubmed: 30822398
Genome Biol. 2006;7(7):R67
pubmed: 16872532
Front Genet. 2017 May 23;8:63
pubmed: 28588608
PLoS One. 2016 Jun 14;11(6):e0157147
pubmed: 27300486
Curr Protoc Mol Biol. 2015 Jan 05;109:21.29.1-21.29.9
pubmed: 25559105
Nat Genet. 2010 Sep;42(9):806-10
pubmed: 20729851
PLoS One. 2015 Jun 19;10(6):e0130622
pubmed: 26091399
Mol Biol Evol. 2017 Jun 1;34(6):1352-1362
pubmed: 28333240
Trends Genet. 2019 Feb;35(2):93-103
pubmed: 30553552
Wiley Interdiscip Rev Dev Biol. 2015 Mar-Apr;4(2):59-84
pubmed: 25704908
PLoS Biol. 2010 Aug 17;8(8):
pubmed: 20808951
PLoS Genet. 2011 Apr;7(4):e1002053
pubmed: 21572512
PLoS Comput Biol. 2013;9(3):e1002968
pubmed: 23526891
Dev Biol. 2015 Sep 1;405(1):173-81
pubmed: 26129990
Curr Biol. 2018 Nov 19;28(22):3547-3561.e9
pubmed: 30393032
Nature. 2014 Aug 7;512(7512):96-100
pubmed: 25043061
Nature. 2007 Nov 8;450(7167):203-18
pubmed: 17994087
Genome Biol Evol. 2021 Aug 3;13(8):
pubmed: 34152413
Comput Struct Biotechnol J. 2020 Jun 12;18:1429-1439
pubmed: 32637041
Science. 2015 May 22;348(6237):910-4
pubmed: 25953818
BMC Syst Biol. 2016 Aug 17;10(1):76
pubmed: 27531214
PLoS Genet. 2010 Jan 15;6(1):e1000814
pubmed: 20084099
Bioinformatics. 2010 Jul 1;26(13):1579-86
pubmed: 20453004
Nucleic Acids Res. 2012 May;40(10):e77
pubmed: 22328731
Elife. 2017 Aug 09;6:
pubmed: 28792889
Bioinformatics. 2018 Nov 15;34(22):3835-3842
pubmed: 29878118
NAR Genom Bioinform. 2021 Jan 06;3(1):lqaa108
pubmed: 33575650
Methods Mol Biol. 2019;1858:117-139
pubmed: 30414115
Dev Cell. 2009 Oct;17(4):568-79
pubmed: 19853570
Trends Genet. 2007 Jan;23(1):16-20
pubmed: 17097187
Sci Rep. 2020 Jun 23;10(1):10150
pubmed: 32576878
Nature. 2009 Nov 5;462(7269):65-70
pubmed: 19890324
Nucleic Acids Res. 2018 Jan 25;46(2):e9
pubmed: 29126307
Nucleic Acids Res. 2021 Jan 8;49(D1):D892-D898
pubmed: 33211864
Nat Methods. 2012 Feb 28;9(3):215-6
pubmed: 22373907
Mol Syst Biol. 2020 May;16(5):e9438
pubmed: 32431014
Nature. 2018 Mar 22;555(7697):538-542
pubmed: 29539636
Cell Rep. 2017 Oct 3;21(1):236-245
pubmed: 28978476
PLoS Biol. 2007 May;5(5):e117
pubmed: 17456005
Nat Rev Genet. 2011 Jul 12;12(8):554-64
pubmed: 21747402
J Theor Biol. 2020 Feb 7;486:110091
pubmed: 31790679
Genome Res. 2019 May;29(5):771-783
pubmed: 30962180
Nucleic Acids Res. 2015 Jan;43(1):e6
pubmed: 25378307
Cell Syst. 2020 Mar 25;10(3):298-306.e4
pubmed: 32213349
Nat Genet. 2011 Dec 04;44(1):89-93
pubmed: 22138689
Plant Cell. 2020 Jul;32(7):2057-2058
pubmed: 32434853
Genome Res. 2007 Jun;17(6):877-85
pubmed: 17179217
Bioinformatics. 2017 Jul 01;33(13):1930-1936
pubmed: 28334114
PLoS Biol. 2008 Feb;6(2):e27
pubmed: 18271625
Dev Cell. 2006 Dec;11(6):895-902
pubmed: 17141163
PLoS One. 2007 Nov 07;2(11):e1115
pubmed: 17973026
Proc Natl Acad Sci U S A. 2004 Mar 16;101(11):3851-6
pubmed: 15026577
Nature. 2009 Feb 12;457(7231):854-8
pubmed: 19212405
PLoS Genet. 2018 Sep 7;14(9):e1007644
pubmed: 30192762
PLoS Comput Biol. 2014 Jul 17;10(7):e1003711
pubmed: 25033408
Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19498-503
pubmed: 23129659
Science. 2006 Feb 10;311(5762):796-800
pubmed: 16469913
Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14414-9
pubmed: 19666595
Genome Biol. 2011;12(4):R34
pubmed: 21473766
Science. 2013 Mar 1;339(6123):1074-7
pubmed: 23328393
Mol Cell. 2020 Jan 16;77(2):324-337.e8
pubmed: 31704182
Nat Methods. 2014 May;11(5):559-65
pubmed: 24658142
Nat Rev Genet. 2012 Apr 18;13(5):329-42
pubmed: 22510764
J Hered. 2013 Sep-Oct;104(5):595-600
pubmed: 23940263
BMC Bioinformatics. 2019 Apr 5;20(1):174
pubmed: 30953451
Development. 2007 Jul;134(13):2415-24
pubmed: 17522157
Dev Cell. 2013 Nov 11;27(3):306-18
pubmed: 24229644
Genes Dev. 2018 Jan 1;32(1):42-57
pubmed: 29378788
Cell. 2008 Jan 25;132(2):311-22
pubmed: 18243105

Auteurs

Hasiba Asma (H)

Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA.

Marc S Halfon (MS)

Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA.
Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA.
Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA.
Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA.
NY State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY 14203, USA.

Classifications MeSH