Transcriptome-wide analysis of Arabidopsis DICER-LIKE1 RNA substrates
Bologna, Nicolás (Centre de Recerca en Agrigenòmica)
Sarazin, Alexis (Swiss Federal Institute of Technology)
Schott, Gregory (Swiss Federal Institute of Technology)
Bouet, Antoine (Centre de Recerca en Agrigenòmica)
Achkar, , Natalia P. (Centre de Recerca en Agrigenòmica)
Moro, Belen (Centre de Recerca en Agrigenòmica)
Jay, Florence (Swiss Federal Institute of Technology)
Chorostecki, Uciel Pablo (Universitat Internacional de Catalunya)
Devers, Emanuel (Swiss Federal Institute of Technology)
Voinnet, Olivier (Swiss Federal Institute of Technology)

Date:	2026
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 contribution of paralogous MIRNA family members in inflorescences, enabling tissue-level discrimination of pri-miRNA engagement. The analysis also identified hundreds of DCL1ci-interacting non-MIRNA loci, including protein-coding genes, transposons, and intergenic regions, with many lacking canonical stem-loop structures. We show that DCL1 promotes 24-nt small RNA biogenesis mostly from helitron-derived transcripts via a pathway genetically distinct from RNA-directed DNA methylation. Moreover, we identify a conserved stem-loop in the DCL1 5'-UTR suggesting autoregulatory feedback control. Collectively, our study establishes DCLci-RIP as a robust noninvasive approach for profiling DCL substrates, broadens DCL1's functional landscape, and provides a foundation for dissecting dynamic DCL-RNA interactions across developmental and stress contexts.
Grants:	Agencia Estatal de Investigación PID2022-143130NB-I00 Ministerio de Ciencia e Innovación CNS2022-136187 Ministerio de Ciencia e Innovación PRE2019-089555 Generalitat de Catalunya 2019/BP-00159 European Commission 101111007
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	Nucleic acids research, Vol. 54, Num. 3 (February 2026) , art. gkaf1434, ISSN 0305-1048

DOI: 10.1093/nar/gkaf1434

18 p, 3.9 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles