Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis.
Date hub
Feed-forward loop
MIR858A
MicroRNA
Transcription factor
Journal
Genomics, proteomics & bioinformatics
ISSN: 2210-3244
Titre abrégé: Genomics Proteomics Bioinformatics
Pays: China
ID NLM: 101197608
Informations de publication
Date de publication:
Aug 2022
Aug 2022
Historique:
received:
07
03
2019
revised:
04
12
2019
accepted:
14
06
2020
pubmed:
5
3
2021
medline:
25
1
2023
entrez:
4
3
2021
Statut:
ppublish
Résumé
MicroRNAs (miRNAs) are trans-acting small regulatory RNAs that work coordinately with transcription factors (TFs) to shape the repertoire of cellular mRNAs available for translation. Despite our growing knowledge of individual plant miRNAs, their global roles in gene regulatory networks remain mostly unassessed. Based on interactions obtained from public databases and curated from the literature, we reconstructed an integrated miRNA network in Arabidopsis that includes 66 core TFs, 318 miRNAs, and 1712 downstream genes. We found that miRNAs occupy distinct niches and enrich miRNA-containing feed-forward loops (FFLs), particularly those with miRNAs as intermediate nodes. Further analyses revealed that miRNA-containing FFLs coordinate TFs located in different hierarchical layers and that intertwined miRNA-containing FFLs are associated with party and date miRNA hubs. Using the date hub MIR858A as an example, we performed detailed molecular and genetic analyses of three interconnected miRNA-containing FFLs. These analyses revealed individual functions of the selected miRNA-containing FFLs and elucidated how the date hub miRNA fulfills multiple regulatory roles. Collectively, our findings highlight the prevalence and importance of miRNA-containing FFLs, and provide new insights into the design principles and control logics of miRNA regulatory networks governing gene expression programs in plants.
Identifiants
pubmed: 33662619
pii: S1672-0229(21)00042-5
doi: 10.1016/j.gpb.2020.02.004
pmc: PMC9880815
pii:
doi:
Substances chimiques
MicroRNAs
0
Transcription Factors
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
747-764Informations de copyright
Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.
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