A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation.

Nature Communications
Qingfeng NiuZhaobo Lang

Abstract

In plants, RNA-directed DNA methylation (RdDM) is a well-known de novo DNA methylation pathway that involves two plant-specific RNA polymerases, Pol IV and Pol V. In this study, we discovered and characterized an RdDM factor, RDM15. Through DNA methylome and genome-wide siRNA analyses, we show that RDM15 is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. We show that RDM15 contributes to Pol V-dependent downstream siRNA accumulation and interacts with NRPE3B, a subunit specific to Pol V. We also show that the C-terminal tudor domain of RDM15 specifically recognizes the histone 3 lysine 4 monomethylation (H3K4me1) mark. Structure analysis of RDM15 in complex with the H3K4me1 peptide showed that the RDM15 tudor domain specifically recognizes the monomethyllysine through an aromatic cage and a specific hydrogen bonding network; this chemical feature-based recognition mechanism differs from all previously reported monomethyllysine recognition mechanisms. RDM15 and H3K4me1 have similar genome-wide distribution patterns at RDM15-dependent RdDM target loci, establishing a link between H3K4me1 and RDM15-mediated RdDM in vivo. In summary, we have identified and characterized a histone ...Continue Reading

References

Aug 6, 1996·Proceedings of the National Academy of Sciences of the United States of America·E J FinneganE S Dennis
May 12, 2001·Science·A M LindrothS E Jacobsen
Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Aug 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Xiaofeng Cao, Steven E Jacobsen
Dec 19, 2003·Current Biology : CB·Xiaofeng CaoSteven E Jacobsen
Jul 21, 2006·Acta Crystallographica. Section D, Biological Crystallography·Wladek MinorMaksymilian Chruszcz
Nov 21, 2007·Nature Structural & Molecular Biology·Jinrong MinCheryl H Arrowsmith
Dec 2, 2008·PLoS Genetics·Lianna M JohnsonSteven E Jacobsen
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jul 29, 2009·BMC Bioinformatics·Yuanxin Xi, Wei Li
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsPeter H Zwart
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
Jan 15, 2011·Current Opinion in Plant Biology·Qian Liu, Zhizhong Gong
Feb 16, 2011·Cell Research·Xin-Jian HeJian-Kang Zhu
Mar 23, 2011·Current Opinion in Plant Biology·Huiming Zhang, Jian-Kang Zhu
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 1, 2012·Epigenetics : Official Journal of the DNA Methylation Society·Tzuu-fen LeeBlake C Meyers
Oct 30, 2012·Nature Structural & Molecular Biology·Cecilia BallaréLuciano Di Croce
Nov 13, 2012·Nature Structural & Molecular Biology·Catherine A MusselmanTatiana G Kutateladze
Dec 6, 2012·Nature Structural & Molecular Biology·Catherine A MusselmanTatiana G Kutateladze
May 3, 2013·Proceedings of the National Academy of Sciences of the United States of America·Heng ZhangJian-Kang Zhu
May 7, 2013·Annual Review of Biochemistry·Dinshaw J Patel, Zhanxin Wang
Sep 17, 2013·Trends in Biochemical Sciences·Rui Lu, Gang Greg Wang
Nov 19, 2013·PLoS Genetics·Maxim V C GreenbergSteven E Jacobsen
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
May 9, 2014·Nature Reviews. Genetics·Marjori A Matzke, Rebecca A Mosher
Mar 4, 2015·Proceedings of the National Academy of Sciences of the United States of America·Mingguang LeiJian-Kang Zhu

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Software Mentioned

Phenix
SAMtools
HKL2000
R package methylKit
Trimmomatic
methratio
BSMAP
featureCounts
- toolkit
FASTX

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.