Coupling of microRNA-directed phased small interfering RNA generation from long noncoding genes with alternative splicing and alternative polyadenylation in small RNA-mediated gene silencing
© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.
| Veröffentlicht in: | The New phytologist. - 1979. - 217(2018), 4 vom: 01. März, Seite 1535-1550 |
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| 1. Verfasser: | |
| Weitere Verfasser: | , , , , , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2018
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| Zugriff auf das übergeordnete Werk: | The New phytologist |
| Schlagworte: | Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. alternative splicing/polyadenylation long terminal repeat (LTR) retrotransposon miR482/2118 microRNA (miRNA) noncoding PHAS locus phasiRNA sRNA-mediated gene silencing mehr... |
| Zusammenfassung: | © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust. MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play vital regulatory roles in plant growth and development. Little is known about these small RNAs in litchi (Litchi chinensis), an economically important fruit crop widely cultivated in Southeast Asia. We profiled the litchi small RNA population with various deep-sequencing techniques and in-depth bioinformatic analyses. The genome-wide identification of miRNAs, their target genes, and phasiRNA-generating (PHAS) genes/loci showed that the function of miR482/2118 has expanded, relative to its canonical function. We also discovered that, for 29 PHAS loci, miRNA-mediated phasiRNA production was coupled with alternative splicing (AS) and alternative polyadenylation (APA). Most of these loci encoded long noncoding RNAs. An miR482/2118 targeted locus gave rise to four main transcript isoforms through AS/APA, and diverse phasiRNAs generated from these isoforms appeared to target long terminal repeat (LTR) retrotransposons and other unrelated genes. This coupling enables phasiRNA production from different exons of noncoding PHAS genes and yields diverse phasiRNA populations, both broadening and altering the range of downstream phasiRNA-regulated genes. Our results reveal the diversity of miRNA and phasiRNA in litchi, and demonstrate AS/APA as a new layer of regulation in small RNA-mediated gene silencing |
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| Beschreibung: | Date Completed 13.09.2019 Date Revised 30.09.2020 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1469-8137 |
| DOI: | 10.1111/nph.14934 |