Mobile small RNAs regulate genome-wide DNA methylation

Proceedings of the National Academy of Sciences of the United States of America
Mathew G LewseyJoseph R Ecker

Abstract

RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses. Key components of the mechanism are small RNAs (sRNAs) of 21-24 nt that guide the silencing machinery to their nucleic acid targets in a nucleotide sequence-specific manner. Transcriptional gene silencing is associated with 24-nt sRNAs and RNA-directed DNA methylation (RdDM) at cytosine residues in three DNA sequence contexts (CG, CHG, and CHH). We previously demonstrated that 24-nt sRNAs are mobile from shoot to root in Arabidopsis thaliana and confirmed that they mediate DNA methylation at three sites in recipient cells. In this study, we extend this finding by demonstrating that RdDM of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot and that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. Mobile sRNA-dependent non-CG methylation is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) RdDM pathway but is independent of the CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. Specific superfamilies of TEs, including those typically found in gene-rich euc...Continue Reading

Associated Datasets

Jan 4, 2016·Thomas J HardcastleJoseph R Ecker

References

Nov 24, 2001·Molecular Biology and Evolution·A LenoirJ M Deragon
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Aug 29, 2002·The EMBO Journal·Andrew HamiltonDavid Baulcombe
Oct 18, 2002·The Plant Journal : for Cell and Molecular Biology·Colin G N TurnbullH M Ottoline Leyser
Jul 15, 2003·Plant Physiology·István PappAntonius J M Matzke
Feb 28, 2004·Science·Simon W-L ChanSteven E Jacobsen
Apr 6, 2004·Proceedings of the National Academy of Sciences of the United States of America·Xiaoyu Zhang, Susan R Wessler
Jul 10, 2004·Current Biology : CB·Daniel ZilbermanSteven E Jacobsen
Apr 30, 2005·Nature Reviews. Genetics·Simon W-L ChanSteven E Jacobsen
Aug 6, 2005·Proceedings of the National Academy of Sciences of the United States of America·N Baumberger, D C Baulcombe
Mar 15, 2006·Nature Reviews. Genetics·Eric J Richards
Feb 27, 2007·Cell·Bradley E BernsteinEric S Lander
May 25, 2007·Nature·Ian R Henderson, Steven E Jacobsen
Dec 13, 2007·Biotechnology Journal·Joshua S YuanC Neal Stewart
Feb 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Rebecca A MosherDavid C Baulcombe
Apr 21, 2009·Nature Genetics·Andrzej T WierzbickiCraig S Pikaard
Jun 13, 2009·Science·Tzung-Fu HsiehDaniel Zilberman
Feb 10, 2010·Nature Reviews. Genetics·Julie A Law, Steven E Jacobsen
Sep 28, 2010·Proceedings of the National Academy of Sciences of the United States of America·Sascha LaubingerDetlef Weigel
Jan 27, 2011·Proceedings of the National Academy of Sciences of the United States of America·Michael GroszmannElizabeth S Dennis
Jul 23, 2011·Nature Reviews. Molecular Cell Biology·Jeremy R Haag, Craig S Pikaard
Sep 1, 2011·The EMBO Journal·Charles W MelnykDavid C Baulcombe
Dec 6, 2011·Nucleic Acids Research·Philippe LameschEva Huala
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 27, 2012·Proceedings of the National Academy of Sciences of the United States of America·Robert H DowenJoseph R Ecker
Jul 4, 2012·The Plant Cell·UNKNOWN International Arabidopsis Informatics Consortium
Sep 4, 2012·Current Opinion in Plant Biology·Claude Becker, Detlef Weigel
Dec 28, 2012·Genome Research·Jonathan I GentR Kelly Dawe

❮ Previous
Next ❯

Citations

Jun 2, 2016·Nature Plants·Germán MartínezR Keith Slotkin
Apr 8, 2016·Epigenomics·Xinyi LinJoanna D Holbrook
Aug 6, 2016·Annual Review of Phytopathology·A DelerisL Navarro
Oct 30, 2016·RNA Biology·Thomas J Hardcastle, Mathew G Lewsey
Oct 4, 2016·Frontiers in Microbiology·Ida Bagus AndikaLiying Sun
Oct 16, 2016·Journal of Experimental Botany·Simon C Groen
Dec 20, 2016·The New Phytologist·Jing WangRongling Wu
Jan 27, 2017·Annual Review of Plant Biology·Byung-Kook Ham, William J Lucas
Jul 4, 2017·Nature Reviews. Genetics·Nathan M Springer, Robert J Schmitz
Nov 7, 2017·The New Phytologist·Muluneh TamiruMathew G Lewsey
Aug 8, 2018·The Plant Journal : for Cell and Molecular Biology·Ningning YuLiping Chen
Sep 1, 2018·Plant & Cell Physiology·Chin Hong Lee, Bernard J Carroll
Nov 6, 2018·Nature Plants·Lin Liu, Xuemei Chen
Nov 18, 2018·The Plant Journal : for Cell and Molecular Biology·Maricris L ZaidemMichael D Purugganan
Sep 2, 2018·Journal of Integrative Plant Biology·Zhaoliang ZhangWilliam J Lucas
Jun 2, 2016·Nature Plants·Zhaoliang ZhangWilliam J Lucas
Jan 12, 2020·Plant Biotechnology Journal·Pallavi SinhaRajeev K Varshney
Jan 4, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Yue LuYu Zhao
Jul 28, 2020·Nucleic Acids Research·Kun HuangJeffrey L Caplan
Aug 5, 2017·Frontiers in Plant Science·Silvia FarinatiClaudio Bonghi
Aug 3, 2019·Nucleic Acids Research·Christelle TaochyHervé Vaucheret
Jun 28, 2019·Plant Direct·Sunil Kumar Kenchanmane RajuSally Mackenzie
Aug 14, 2019·Annual Review of Cell and Developmental Biology·Yu YuYueqin Chen
Mar 10, 2017·RNA Biology·James H Westwood, Gunjune Kim
Sep 6, 2019·International Journal of Molecular Sciences·Chiara Pagliarani, Giorgio Gambino
Dec 8, 2016·Nucleic Acids Research·Daogang GuanShoudong Zhang
Sep 26, 2017·Genome Biology·Daniel BouyerVincent Colot

❮ Previous
Next ❯

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.