Mapping responsive genomic elements to heat stress in a maize diversity panel.
Chromatin footprints
Heat stress
Maize
Response eGene
Response eQTL
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
07 11 2022
07 11 2022
Historique:
received:
20
07
2022
accepted:
29
10
2022
entrez:
7
11
2022
pubmed:
8
11
2022
medline:
10
11
2022
Statut:
epublish
Résumé
Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress. By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.
Sections du résumé
BACKGROUND
Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress.
RESULTS
By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies.
CONCLUSIONS
Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.
Identifiants
pubmed: 36345007
doi: 10.1186/s13059-022-02807-7
pii: 10.1186/s13059-022-02807-7
pmc: PMC9639295
doi:
Substances chimiques
Transcription Factors
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
234Informations de copyright
© 2022. The Author(s).
Références
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
Plant J. 2017 Feb;89(4):706-717
pubmed: 28188666
Genome Biol. 2014;15(12):550
pubmed: 25516281
Mol Plant. 2011 Jan;4(1):97-115
pubmed: 20924027
Sci Rep. 2020 May 15;10(1):8073
pubmed: 32415117
Dev Cell. 2022 May 9;57(9):1177-1192.e6
pubmed: 35504287
Nucleic Acids Res. 2017 Apr 7;45(6):e41
pubmed: 27903897
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
Genomics Proteomics Bioinformatics. 2021 Aug;19(4):619-628
pubmed: 33662620
Front Plant Sci. 2017 Jun 29;8:1147
pubmed: 28706531
Genome Biol. 2017 Jul 21;18(1):137
pubmed: 28732548
BMC Genomics. 2011 Jun 30;12:336
pubmed: 21718468
Cell. 2016 Oct 6;167(2):313-324
pubmed: 27716505
Front Genet. 2021 Oct 08;12:728166
pubmed: 34691151
Nature. 2017 Jun 22;546(7659):524-527
pubmed: 28605751
Photosynth Res. 2004 Feb;79(2):209
pubmed: 16228395
Genome Biol. 2020 Jul 6;21(1):163
pubmed: 32631406
Proc Natl Acad Sci U S A. 2019 Dec 5;:
pubmed: 31806758
BMC Bioinformatics. 2016 May 10;17:208
pubmed: 27161244
Am J Hum Genet. 2018 Sep 6;103(3):338-348
pubmed: 30100085
BMC Genomics. 2015 Jan 23;16:18
pubmed: 25928563
Bioinformatics. 2012 May 15;28(10):1353-8
pubmed: 22492648
Mol Plant. 2017 Jul 5;10(7):990-999
pubmed: 28602693
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Annu Rev Plant Biol. 2009;60:93-114
pubmed: 19012536
Plant Mol Biol. 2014 Jan;84(1-2):125-43
pubmed: 23975147
Nat Plants. 2019 Dec;5(12):1237-1249
pubmed: 31740773
BMC Biol. 2021 Mar 19;19(1):53
pubmed: 33740972
Hum Genet. 2012 May;131(5):747-56
pubmed: 22143225
Cell. 2014 Sep 11;158(6):1431-1443
pubmed: 25215497
Bioinformatics. 2011 Nov 1;27(21):2957-63
pubmed: 21903629
Nat Commun. 2020 Jul 28;11(1):3761
pubmed: 32724101
G3 (Bethesda). 2021 Sep 27;11(10):
pubmed: 34568911
Nucleic Acids Res. 2018 Dec 14;46(22):e133
pubmed: 30189032
Plant J. 2019 Apr;98(1):19-32
pubmed: 30548709
Sci Rep. 2018 Jul 18;8(1):10872
pubmed: 30022098
Commun Biol. 2021 Nov 4;4(1):1266
pubmed: 34737387
Nat Protoc. 2012 Feb 16;7(3):500-7
pubmed: 22343431
Bioinformatics. 2021 Mar 24;:
pubmed: 33760053
Nat Rev Genet. 2015 Apr;16(4):237-51
pubmed: 25752530
Front Plant Sci. 2013 Jul 02;4:170
pubmed: 23874343
Science. 2014 Mar 7;343(6175):1246949
pubmed: 24604202
F1000Res. 2016 Jun 23;5:1479
pubmed: 27429743
Nat Genet. 2018 Mar;50(3):424-431
pubmed: 29379200
Plant Cell. 2022 Jan 20;34(1):514-534
pubmed: 34735005
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Plant Direct. 2018 Apr 11;2(4):e00052
pubmed: 31245718
BMC Genomics. 2011 Jan 27;12:76
pubmed: 21272351
Nature. 2018 Mar 22;555(7697):520-523
pubmed: 29539638
PLoS Genet. 2016 Feb 01;12(2):e1005767
pubmed: 26828793
Plant Physiol. 2021 May 27;186(1):420-433
pubmed: 33591319
Nat Rev Genet. 2021 Apr;22(4):203-215
pubmed: 33268840
Plant Cell Physiol. 2016 Jan;57(1):57-68
pubmed: 26561535
PLoS Genet. 2013;9(1):e1003202
pubmed: 23341782
Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6644-6649
pubmed: 29891651
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Plant Cell. 2020 Jan;32(1):139-151
pubmed: 31641024
BMC Genomics. 2022 Jan 4;23(1):18
pubmed: 34983397
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Front Plant Sci. 2017 Nov 28;8:2027
pubmed: 29250089
Curr Opin Plant Biol. 2022 Feb;65:102139
pubmed: 34837823
Cell. 2021 May 27;184(11):3041-3055.e21
pubmed: 33964211
PLoS Genet. 2021 Aug 12;17(8):e1009689
pubmed: 34383745
Mol Plant. 2021 Mar 1;14(3):411-425
pubmed: 33276159
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158