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Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

Julie A. Law, Jiamu Du, Christopher J. Hale, Suhua Feng, Krzysztof Krajewski, Ana Marie S. Palanca, Brian D. Strahl, Dinshaw J. Patel, Steven E. Jacobsen
2013 Nature  
Fuchs for technical assistance, and to the UCLA BSCRC BioSequencing Core Facility for DNA sequencing.  ...  Acknowledgements We are grateful to the staff of beamlines 24ID-C/E at the Argonne National Laboratory and X29A at the Brookhaven National Laboratory for support in diffraction data collection, to M.  ...  Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating  ... 
doi:10.1038/nature12178 pmid:23636332 pmcid:PMC4119789 fatcat:4cjlnyfrpneilj3dlirsxuuuba

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

Suhua Feng, Christopher J. Hale, Dinshaw J. Patel, Krzysztof Krajewski, Steven E. Jacobsen, Jiamu Du, Ana Marie S. Palanca, Julie A. Law, Brian D. Strahl
2013
Finally, we show that key residues within both lysine binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating  ...  In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24 nt small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation  ...  Akhavan and Stephen Fuchs for technical assistance, and to the UCLA BSCRC BioSequencing Core Facility for DNA sequencing.  ... 
doi:10.17615/vpy9-ef92 fatcat:bwe5svnxjzbxxi27rs6utqrzla

RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules

Ming Zhou, Julie A Law
2015 Current opinion in plant biology  
noncoding RNAs that are required for transcriptional gene silencing via the RNA-directed DNA methylation (RdDM) pathway.  ...  In addition to the three canonical DNA dependent RNA polymerases (Pol) Pol I, II and III, two non-redundant plant-specific RNA polymerases, Pol IV and Pol V, have been identified and shown to generate  ...  Mechanistically, the observed defects in shh1 stem from loss of Pol IV occupancy specifically at SHH1-regulated genomic loci [96] .  ... 
doi:10.1016/j.pbi.2015.07.005 pmid:26344361 pmcid:PMC4618083 fatcat:rroyvrh2nvgqjmbgq7kpyx3cvu

Non-coding RNAs in Transcriptional Regulation

Yung-Chia Ariel Chen, Alexei A. Aravin
2015 Current Molecular Biology Reports  
Small RNAs loaded into Argonaute family proteins direct repressive histone modifications or DNA cytosine methylation to homologous regions of the genome.  ...  Small RNAmediated transcriptional silencing is required for many biological processes, including repression of transposable elements, maintaining the genome stability/integrity, and epigenetic inheritance  ...  RNA-Directed DNA Methylation in Arabidopsis In plants, the process of RNA-directed DNA methylation (RdDM) requires two atypical DNA-dependent RNA polymerases-Pol IV and Pol V (review in [3, 4•] ).  ... 
doi:10.1007/s40610-015-0002-6 pmid:26120554 pmcid:PMC4479201 fatcat:rc5awaqvnbf3tnblwxafpoj2mu

A Transcription Fork Model for Pol IV and Pol V-Dependent RNA-Directed DNA Methylation

C. S. Pikaard, J. R. Haag, O. M. F. Pontes, T. Blevins, R. Cocklin
2012 Cold Spring Harbor Symposia on Quantitative Biology  
direct DNA methylation and transcriptional silencing at target loci transcribed by nuclear multisubunit RNA polymerase V (Pol V).  ...  In Arabidopsis thaliana, nuclear multisubunit RNA polymerase IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) are required for the biogenesis of 24-nucleotide small interfering RNAs (siRNAs) that  ...  ACKNOWLEDGMENTS Pikaard laboratory studies of RNA-directed DNA methylation are supported by National Institutes of Health (NIH) grant GM077590 and C.S.P.'  ... 
doi:10.1101/sqb.2013.77.014803 pmid:23567894 fatcat:u7sn4n3lzbextofhq6libr6w64

Interplay between Active Chromatin Marks and RNA-Directed DNA Methylation in Arabidopsis thaliana

Maxim V. C. Greenberg, Angelique Deleris, Christopher J. Hale, Ao Liu, Suhua Feng, Steven E. Jacobsen, Xuemei Chen
2013 PLoS Genetics  
We previously showed that Arabidopsis thaliana plants with mutations in the H3K4m2/ m3 demethylase JUMONJI 14 (JMJ14) exhibit a mild reduction in RNA-directed DNA methylation (RdDM) that is associated  ...  Interestingly, the impact on DNA methylation was stronger at DNA-methylated regions adjacent to H3K4m2/m3-marked protein-coding genes, suggesting that the activity of H3K4 demethylases may be particularly  ...  DRM2-dependent methylation depends on two plant specific RNA polymerases: RNA Polymerase IV and V (Pol IV and V).  ... 
doi:10.1371/journal.pgen.1003946 pmid:24244201 pmcid:PMC3820799 fatcat:mh7oijzye5hn5a2e64o3tz6rgm

Non-coding RNAs and DNA methylation in plants

Yuanyuan Zhao, Xuemei Chen
2014 National Science Review  
The roles of many proteins as well as non-coding RNAs in DNA methylation have been uncovered.  ...  The DNA methylation patterns in plants are more complex than those in animals, and plants and animals have common as well as distinct pathways in regulating DNA methylation.  ...  ATXRCC1 AT1G80420 DNA repair protein Functions in DNA demethylation [65] Figure 1 . 1 The RNA-directed DNA methylation pathway (RdDM) in Arabidopsis At the early stage of RdDM, RNA Polymerase IV (Pol  ... 
doi:10.1093/nsr/nwu003 pmid:25635229 pmcid:PMC4307843 fatcat:fj3s7zuejrgezaurudflbkwadi

Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis

Javier Gallego-Bartolomé, Wanlu Liu, Peggy Hsuanyu Kuo, Suhua Feng, Basudev Ghoshal, Jason Gardiner, Jenny Miao-Chi Zhao, Soo Young Park, Joanne Chory, Steven E. Jacobsen
2019 Cell  
The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation.  ...  We also evaluated ectopic siRNA biogenesis, RNA polymerase V (Pol V) recruitment, targeted DNA methylation, and gene-expression changes at thousands of ZF-RdDM targets.  ...  IV and Pol V enhances DNA methylation and RDM1), DEFECTIVE IN MERISTEM SILENCING 3 (DMS3), and DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1), are required globally for Pol V occupancy on chromatin  ... 
doi:10.1016/j.cell.2019.01.029 pmid:30739798 pmcid:PMC6386582 fatcat:4o6ptm2aircydbwnlltmmu3y4y

DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance inArabidopsis

Xuehua Zhong, Christopher J. Hale, Minh Nguyen, Israel Ausin, Martin Groth, Jonathan Hetzel, Ajay A. Vashisht, Ian R. Henderson, James A. Wohlschlegel, Steven E. Jacobsen
2015 Proceedings of the National Academy of Sciences of the United States of America  
In Arabidopsis drm3 mutants, we observe a lower level of Pol V-dependent noncoding RNA transcripts even though Pol V chromatin occupancy is increased at many sites in the genome.  ...  Production of Pol V transcripts, as well as genome-wide Pol V chromatin occupancy, requires a complex termed DDR consisting of the putative chromatin-remodeling factor DEFECTIVE IN RNA-DIRECTED DNA METHYLATION  ...  In the current RdDM model, the DNA-DEPENDENT RNA POLYMERASE IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2, and DICER-LIKE 3 function together to produce small interfering RNAs (siRNAs) that are bound by  ... 
doi:10.1073/pnas.1423603112 pmid:25561521 pmcid:PMC4311829 fatcat:oexnpo32wvd2vcgckb77uxceda

Four putative SWI2/SNF2 chromatin remodelers have dual roles in regulating DNA methylation in Arabidopsis

Dong-Lei Yang, Guiping Zhang, Lili Wang, Jingwen Li, Dachao Xu, Cuiru Di, Kai Tang, Lan Yang, Liang Zeng, Daisuke Miki, Cheng-Guo Duan, Huiming Zhang (+1 others)
2018 Cell Discovery  
In Arabidopsis, the antagonistic activities of RNA-directed DNA methylation (RdDM) and ROS1-dependent active DNA demethylation are key for the dynamic regulation of locus-specific DNA methylation.  ...  The four CLSY proteins collectively are necessary for the canonical RdDM pathway; at the same time, each CLSY likely mediates DNA demethylation at specific loci where DNA methylation depends on RdDM.  ...  Supplementary Information accompanies the paper at (https://doi.org/ 10.1038/s41421-018-0056-8).  ... 
doi:10.1038/s41421-018-0056-8 pmid:30345072 pmcid:PMC6189096 fatcat:sjy2aoyy4zacffhximkao6idia

Arabidopsis RNA Polymerases IV and V Are Required To Establish H3K9 Methylation, but Not Cytosine Methylation, on Geminivirus Chromatin

Jamie N. Jackel, Jessica M. Storer, Tami Coursey, David M. Bisaro, A. Simon
2016 Journal of Virology  
ABSTRACTIn plants, RNA-directed DNA methylation (RdDM) employs small RNAs to target enzymes that methylate cytosine residues.  ...  chromatin.IMPORTANCEIn plants, RNA-directed DNA methylation (RdDM) uses small RNAs to target cytosine methylation, which is often linked to H3K9me2.  ...  IV/V occupancy at this locus (Fig. 6B ).  ... 
doi:10.1128/jvi.00656-16 pmid:27279611 pmcid:PMC4984644 fatcat:b3kdlv2bunhylfutjhagsqzykm

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

Lianna M. Johnson, Jiamu Du, Christopher J. Hale, Sylvain Bischof, Suhua Feng, Ramakrishna K. Chodavarapu, Xuehua Zhong, Giuseppe Marson, Matteo Pellegrini, David J. Segal, Dinshaw J. Patel, Steven E. Jacobsen
2014 Nature  
Abstract: RNA-directed DNA methylation in Arabidopsis thaliana depends on the upstream synthesis of 24nucleotide small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) and downstream synthesis of  ...  Abstract RNA-directed DNA methylation (RdDM) in Arabidopsis thaliana depends on the upstream synthesis of 24-nucleotide small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) 1,2 and downstream  ...  Wuxian Shi at National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL) for support in diffraction data collection.  ... 
doi:10.1038/nature12931 pmid:24463519 pmcid:PMC3963826 fatcat:sarjx32jobhzxdmovgeo6zkulu

The SET Domain Proteins SUVH2 and SUVH9 Are Required for Pol V Occupancy at RNA-Directed DNA Methylation Loci

Zhang-Wei Liu, Chang-Rong Shao, Cui-Jun Zhang, Jin-Xing Zhou, Su-Wei Zhang, Lin Li, She Chen, Huan-Wei Huang, Tao Cai, Xin-Jian He, Craig S. Pikaard
2014 PLoS Genetics  
RNA-directed DNA methylation (RdDM) is required for transcriptional silencing of transposons and other DNA repeats in Arabidopsis thaliana.  ...  Our CHIP assay demonstrated that SUVH2 and SUVH9 are required for the occupancy of Pol V at RdDM loci and facilitate the production of Pol V-dependent noncoding RNAs.  ...  A chromatin-remodeling complex was previously demonstrated to be required for the occupancy of DNAdependent RNA polymerase V at RNA-directed DNA methylation loci.  ... 
doi:10.1371/journal.pgen.1003948 pmid:24465213 pmcid:PMC3898904 fatcat:43epncz5x5e2hpw2wepkht2p5y

Dicer-independent RNA-directed DNA methylation in Arabidopsis

Dong-Lei Yang, Guiping Zhang, Kai Tang, Jingwen Li, Lan Yang, Huan Huang, Heng Zhang, Jian-Kang Zhu
2015 Cell Research  
RNA-directed DNA methylation (RdDM) is an important de novo DNA methylation pathway in plants.  ...  Small interfering RNAs (siRNAs) generated by Dicers from RNA polymerase IV (Pol IV) transcripts are thought to guide sequence-specific DNA methylation.  ...  to methylated DNA, are required for Pol V occupancy at RdDM loci [23, 24] .  ... 
doi:10.1038/cr.2015.145 pmid:26642813 pmcid:PMC4816133 fatcat:pelzcoupl5hkhdepgxwr376eru

How Can Plant DNA Viruses Evade siRNA-Directed DNA Methylation and Silencing?

Mikhail Pooggin
2013 International Journal of Molecular Sciences  
Hence, DNA viruses most likely evade or suppress RNA-directed DNA methylation.  ...  Plants infected with DNA viruses produce massive quantities of virus-derived, 24-nucleotide short interfering RNAs (siRNAs), which can potentially direct viral DNA methylation and transcriptional silencing  ...  Acknowledgments I thank Thomas Boller for supporting research of MMP group at the University of Basel and Rajendran Rajeswaran for fruitful collaboration and critical reading of the manuscript.  ... 
doi:10.3390/ijms140815233 pmid:23887650 pmcid:PMC3759858 fatcat:d4nblqtdjzhwzmhn6scpammuza
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