Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information.
Journal
The Plant cell
ISSN: 1532-298X
Titre abrégé: Plant Cell
Pays: England
ID NLM: 9208688
Informations de publication
Date de publication:
20 01 2022
20 01 2022
Historique:
received:
02
08
2021
accepted:
27
10
2021
pubmed:
5
11
2021
medline:
23
2
2022
entrez:
4
11
2021
Statut:
ppublish
Résumé
Changes in gene expression are important for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes identifies many changes in transcript abundance. We used comparisons of expression responses in multiple genotypes to identify alleles with variable responses to heat or cold stress and to distinguish examples of cis- or trans-regulatory variation for stress-responsive expression changes. We used motifs enriched near the transcription start sites (TSSs) for thermal stress-responsive genes to develop predictive models of gene expression responses. Prediction accuracies can be improved by focusing only on motifs within unmethylated regions near the TSS and vary for genes with different dynamic responses to stress. Models trained on expression responses in a single genotype and promoter sequences provided lower performance when applied to other genotypes but this could be improved by using models trained on data from all three genotypes tested. The analysis of genes with cis-regulatory variation provides evidence for structural variants that result in presence/absence of transcription factor binding sites in creating variable responses. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and defines a framework for developing models to predict expression responses across multiple genotypes.
Identifiants
pubmed: 34735005
pii: 6420714
doi: 10.1093/plcell/koab267
pmc: PMC8773969
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
514-534Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.
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