siRNAs from miRNA sites mediate DNA methylation of target genes.

Nucleic Acids Research
Padmanabhan ChellappanHailing Jin

Abstract

Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give rise to two small RNA species, a 20- to 22-nt species and a 23- to 27-nt species, at the same site. Genetic analysis using small RNA pathway mutants reveals that the 20- to 22-nt small RNAs are typical miRNAs generated by DCL1 and are associated with Argonaute 1 (AGO1). In contrast, the accumulation of the 23- to 27-nt small RNAs from the miRNA-generating sites is dependent on DCL3, RDR2 and Pol IV, components of the typical heterochromatic small interfering RNA (hc-siRNA) pathway. We further demonstrate that these MIR-derived siRNAs associate with AGO4 and direct DNA methylation at some of their target loci in trans. In addition, we find that at the miRNA-generating sites, some conserved canonical MIR genes also produce siRNAs, which also induce DNA methylation at some of their target sites. Our systematic examination of published small RNA deep sequencing datasets of rice and moss suggests that this type of dual...Continue Reading

References

Aug 29, 2002·The EMBO Journal·Andrew HamiltonDavid Baulcombe
Jun 26, 2003·Nucleic Acids Research·Ivo L Hofacker
Jul 19, 2003·Science·James C Carrington, Victor Ambros
Jun 18, 2004·Molecular Cell·Matthew W Jones-Rhoades, David P Bartel
Oct 8, 2004·Molecular Cell·Franck VazquezPatrice Crété
Nov 5, 2004·Developmental Cell·Yuval Eshed, John L Bowman
Feb 12, 2005·Science·Bin YuXuemei Chen
Jun 28, 2005·Nucleic Acids Research·Yuanji Zhang
Oct 31, 2006·Proceedings of the National Academy of Sciences of the United States of America·Surekha Katiyar-AgarwalHailing Jin
Dec 22, 2006·Genes & Development·Ramya RajagopalanDavid P Bartel
May 25, 2007·Nature·Ian R Henderson, Steven E Jacobsen
Oct 19, 2007·Nature Reviews. Genetics·Elisabeth J Chapman, James C Carrington
Nov 16, 2007·Genes & Development·Surekha Katiyar-AgarwalHailing Jin
Mar 4, 2008·BMC Plant Biology·Ramanjulu SunkarJian-Kang Zhu
May 30, 2008·Trends in Plant Science·Hervé Vaucheret
Jun 3, 2008·Trends in Plant Science·Craig S PikaardAndrzej T Wierzbicki
Jul 1, 2008·Bioinformatics·Yunpen XuWeixiong Zhang
Jul 18, 2008·Proceedings of the National Academy of Sciences of the United States of America·Zhicheng DongNina Fedoroff
Oct 10, 2008·Nucleic Acids Research·Franck VazquezFrederick Meins
Dec 17, 2008·The Plant Cell·Blake C MeyersJian-Kang Zhu
Dec 17, 2008·Methods in Molecular Biology·Padmanabhan Chellappan, Hailing Jin
Jan 17, 2009·Nature Reviews. Genetics·Megha Ghildiyal, Phillip D Zamore
Jan 24, 2009·Nature Reviews. Molecular Cell Biology·V Narry KimMikiko C Siomi
Feb 27, 2009·Current Opinion in Cell Biology·Marjori MatzkeAntonius J M Matzke
Oct 6, 2009·Methods in Molecular Biology·Noah Fahlgren, James C Carrington
Dec 18, 2009·Current Biology : CB·Liang SongNina V Fedoroff
Dec 18, 2009·Current Biology : CB·Schallum WernerDetlef Weigel
Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Josh T CuperusJames C Carrington
Jan 21, 2010·Cell·Basel KhraiweshWolfgang Frank
Feb 5, 2010·Current Biology : CB·Blake C MeyersJixian Zhai
Apr 13, 2010·Molecular Cell·Liang WuYijun Qi
Apr 30, 2010·Trends in Plant Science·Franck VazquezDavid Windels

❮ Previous
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Citations

Apr 27, 2013·Integrative and Comparative Biology·Kevin B FloresGro V Amdam
Mar 2, 2011·Journal of Experimental Botany·Filipe BorgesJörg D Becker
Mar 16, 2013·Molecular Plant-microbe Interactions : MPMI·Jang-Kyun SeoHailing Jin
Oct 18, 2011·Plant Physiology·Yijun MengMing Chen
Dec 25, 2010·The Plant Cell·Allison Mallory, Hervé Vaucheret
May 9, 2012·BMC Genomics·Marie TurnerSenthil Subramanian
May 11, 2011·Genome Biology·Michael J AxtellEric C Lai
Apr 15, 2011·PLoS Genetics·Marcel LafosDaniel Schubert
Sep 6, 2012·International Journal of Molecular Sciences·Marina C CostaFrancisco J Enguita
Feb 28, 2013·International Journal of Molecular Sciences·Heidi GielenAnn Cuypers
Oct 3, 2013·International Journal of Molecular Sciences·Virginie GébelinPascal Montoro
Sep 29, 2011·Yi chuan = Hereditas·Miao He, Zi-Wei Wang
Nov 28, 2013·Scientifica·Franck Vazquez, Thomas Hohn
Mar 4, 2014·Annual Review of Plant Biology·Nicolas G Bologna, Olivier Voinnet
Jan 22, 2013·Annual Review of Plant Biology·Michael J Axtell
Nov 8, 2014·Journal of Experimental Botany·Zhiqiang XianZhengguo Li
Feb 3, 2016·Molecular Biotechnology·Gunjan SirohiJitender Giri
Jun 21, 2011·Biochimica Et Biophysica Acta·Thomas Hohn, Franck Vazquez
May 10, 2011·Biochimica Et Biophysica Acta·Hanako Shimura, Vitantonio Pantaleo
Apr 7, 2011·Trends in Plant Science·Ignacio Rubio-Somoza, Detlef Weigel
Apr 8, 2011·Trends in Plant Science·J Rodriguez-EnriquezR T Grant-Downton
Mar 1, 2016·Wiley Interdisciplinary Reviews. RNA·Hsiao-Lin V Wang, Julia A Chekanova
Jan 15, 2015·Plant Biotechnology Journal·Jannatul FerdousBu-Jun Shi
Nov 5, 2015·Nature Reviews. Molecular Cell Biology·Filipe Borges, Robert A Martienssen
Nov 21, 2012·The New Phytologist·Dorothee StaigerLionel Navarro
Apr 5, 2011·The Plant Journal : for Cell and Molecular Biology·Huan WangXiu-Jie Wang

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Datasets Mentioned

BETA
GSE19694

Methods Mentioned

BETA
PCR
AGO
pull down
RNA-gel

Software Mentioned

fold
TargetFinder
RNA
miRBASE

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