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Resource: Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants
- Alice Lunardon,
- Nathan R. Johnson,
- Emily Hagerott,
- Tamia Phifer,
- Seth Polydore,
- Ceyda Coruh,
- and Michael J. Axtell
Genome Res. March 2020 30: 497-513; Published in Advance March 16, 2020, doi:10.1101/gr.256750.119
...-directed DNA methylation (RdDM) pathway, involving 24 or 21–22 nt siRNAs. Twenty-four-nucleotide siRNAs are derived from Polymerase IV (Pol IV) transcripts that are converted to dsRNAs by RNA-dependent RNA polymerase 2 (RDR2), which are then processed by DCL3. They act in canonical RdDM, primarily targeting...
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LETTER: Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
- Simon Moxon,
- Runchun Jing,
- Gyorgy Szittya,
- Frank Schwach,
- Rachel L. Rusholme Pilcher,
- Vincent Moulton,
- and Tamas Dalmay
Genome Res. October 2008 18: 1602-1609; Published in Advance July 24, 2008, doi:10.1101/gr.080127.108
.... ( 2006 ) MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant . Genome Res. 16 : 1276 – 1288 . ↵ Manning, K. , Tör, M. , Poole, M. , Hong, Y. , Thompson, A.J. , King, G.J. , Giovannoni, J.J. , Seymour, G.B. ( 2006 ) A naturally occurring epigenetic mutation...
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Research: Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis
- Shaofang Li,
- Lee E. Vandivier,
- Bin Tu,
- Lei Gao,
- So Youn Won,
- Shengben Li,
- Binglian Zheng,
- Brian D. Gregory,
- and Xuemei Chen
Genome Res. February 2015 25: 235-245; Published in Advance November 20, 2014, doi:10.1101/gr.182238.114
..., the methyltransferases DRM2 and CMT2 establish DNA methylation in all sequence contexts and maintain asymmetric CHH methylation (Cao and Jacobsen 2002; Zemach et al. 2013). Themaintenance of symmetric CG and CHG methylation is mediated by MET1 and CMT3, respectively (Stroud et al. 2013). In Arabidopsis, RNA-dependent...
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12 Drosophila Genomes/Letter: Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
- J. Graham Ruby,
- Alexander Stark,
- Wendy K. Johnston,
- Manolis Kellis,
- David P. Bartel,
- and Eric C. Lai
Genome Res. December 2007 17: 1850-1864; Published in Advance November 7, 2007, doi:10.1101/gr.6597907
...Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs J. Graham Ruby 1 , 2 , Alexander Stark 3 , 4 , Wendy K. Johnston 1 , 2 , Manolis Kellis 3 , 4 , David P. Bartel 1 , 2...
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LETTER: Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa
- Xuefeng Zhou,
- Ramanjulu Sunkar,
- Hailing Jin,
- Jian-Kang Zhu,
- and Weixiong Zhang
Genome Res. January 2009 19: 70-78; Published in Advance October 29, 2008, doi:10.1101/gr.084806.108
...transcripts in the human . Trends Genet. 18 : 63 – 65 . ↵ Lu, C. , Kulkarni, K. , Souret, F.F. , MuthuValliappan, R. , Tej, S.S. , Poethig, R.S. , Henderson, I.R. , Jacobsen, S.E. , Wang, W. , Green, P.J. , et al. ( 2006 ) MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase...
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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
...IV) and, in peculiar cases, by Pol II itself (Nuthikattu et al. 2013; Cuerda-Gil and Slotkin 2016). The Pol IV transcripts, majorly originating from the repeats and transposons, are acted upon by RNA-dependent RNA polymerase 2 (RDR2), whereas the Pol II aberrant transcripts are acted upon by RDR6...
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Research: CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize
- Jonathan I. Gent,
- Nathanael A. Ellis,
- Lin Guo,
- Alex E. Harkess,
- Yingyin Yao,
- Xiaoyu Zhang,
- and R. Kelly Dawe
Genome Res. April 2013 23: 628-637; Published in Advance December 26, 2012, doi:10.1101/gr.146985.112
...al. 2009; Stonaker et al. 2009). One of these is an RNAdependent RNA polymerase mutant homologous to rdr2 in Arabidopsis, called mop1 in maize (Alleman et al. 2006). Prior studies of the mop1 mutant found that Mutator transposons, which are enriched in genic areas (for review, see Lisch 2002) tend...

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