Faculty, Staff and Student Publications
Parallel Degradome-Seq and Dms-MaPseq Substantially Revise the miRNA Biogenesis Atlas in Arabidopsis
Language
English
Publication Date
7-1-2024
Journal
Nature Plants
DOI
10.1038/s41477-024-01725-9
PMID
38918606
PMCID
PMC11578046
PubMedCentral® Posted Date
11-20-2024
PubMedCentral® Full Text Version
Author MSS
Abstract
MicroRNAs (miRNAs) are produced from highly structured primary transcripts (pri-miRNAs) and regulate numerous biological processes in eukaryotes. Due to the extreme heterogeneity of these structures, the initial processing sites of plant pri-miRNAs and the structural rules that determine their processing have been predicted for many miRNAs but remain elusive for others. Here we used semi-active DCL1 mutants and advanced degradome-sequencing strategies to accurately identify the initial processing sites for 147 of 326 previously annotated Arabidopsis miRNAs and to illustrate their associated pri-miRNA cleavage patterns. Elucidating the in vivo RNA secondary structures of 73 pri-miRNAs revealed that about 95% of them differ from in silico predictions, and that the revised structures offer clearer interpretation of the processing sites and patterns. Finally, DCL1 partners Serrate and HYL1 could synergistically and independently impact processing patterns and in vivo RNA secondary structures of pri-miRNAs. Together, our work sheds light on the precise processing mechanisms of plant pri-miRNAs.
Keywords
Arabidopsis, MicroRNAs, Arabidopsis Proteins, RNA, Plant, Ribonuclease III, Cell Cycle Proteins, RNA-Binding Proteins, Sequence Analysis, RNA, RNA Processing, Post-Transcriptional, Gene Expression Regulation, Plant
Published Open-Access
yes
Recommended Citation
Yan, Xingxing; Li, Changhao; Liu, Kaiye; et al., "Parallel Degradome-Seq and Dms-MaPseq Substantially Revise the miRNA Biogenesis Atlas in Arabidopsis" (2024). Faculty, Staff and Student Publications. 3928.
https://digitalcommons.library.tmc.edu/uthmed_docs/3928