Transcriptome-wide analysis of Arabidopsis DICER-LIKE1 RNA substrates.

ABSTRACT: In plants, DICER-LIKE1 (DCL1) orchestrates microRNA (miRNA) biogenesis by cleaving imperfect stem-loop precursors within primary transcripts (pri-miRNAs). However, the full spectrum of DCL1 RNA substrates remains unexplored. Here, we report transcriptome-wide RNA immunoprecipitation and deep-sequencing (RIP-Seq) analyses of the Arabidopsis catalytically inactive DCL1 (DCL1ci), designed to bind but not cleave its targets. In inflorescences, DCL1ci-RIP retrieved nearly all evolutionarily conserved MIRNA loci and uncovered many hitherto unknown young MIRNA loci. Extensive interactions with both pre-miRNA stem-loops and flanking single-stranded regions were detected, suggesting that DCL1 scans pri-miRNAs prior to stem-loop cleavage. Quantitative binding profiles resolved the specific contribut

SUBMITTER: Bologna NG 

PROVIDER: S-EPMC12825306 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature