scholarly journals Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing

Development ◽  
2012 ◽  
Vol 139 (15) ◽  
pp. 2792-2803 ◽  
Author(s):  
F. Mohammad ◽  
G. K. Pandey ◽  
T. Mondal ◽  
S. Enroth ◽  
L. Redrup ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Silencing ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Transcriptional Gene Silencing

Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing

2012 ◽  
Vol 125 (15) ◽  
pp. e1-e1
Author(s):  
F. Mohammad ◽  
G. K. Pandey ◽  
T. Mondal ◽  
S. Enroth ◽  
L. Redrup ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Silencing ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Transcriptional Gene Silencing

scholarly journals Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

2014 ◽  
Vol 204 (1) ◽  
pp. 61-75 ◽  
Author(s):  
He Zhang ◽  
Michael J. Zeitz ◽  
Hong Wang ◽  
Beibei Niu ◽  
Shengfang Ge ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Long Range ◽  
Ribonucleic Acid ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Transcriptional Gene Silencing ◽  
Chromatin Conformation ◽  
Polycomb Repressive Complex 2 ◽  
Allele Specific ◽  
Capture Method

Kcnq1ot1 is a long noncoding ribonucleic acid (RNA; lncRNA) that participates in the regulation of genes within the Kcnq1 imprinting domain. Using a novel RNA-guided chromatin conformation capture method, we demonstrate that the 5′ region of Kcnq1ot1 RNA orchestrates a long-range intrachromosomal loop between KvDMR1 and the Kcnq1 promoter that is required for maintenance of imprinting. PRC2 (polycomb repressive complex 2), which participates in the allelic repression of Kcnq1, is also recruited by Kcnq1ot1 RNA via EZH2. Targeted suppression of Kcnq1ot1 lncRNA prevents the creation of this long-range intrachromosomal loop and causes loss of Kcnq1 imprinting. These observations delineate a novel mechanism by which an lncRNA directly builds an intrachromosomal interaction complex to establish allele-specific transcriptional gene silencing over a large chromosomal domain.

scholarly journals Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1187
Author(s):  
Michael Wassenegger ◽  
Athanasios Dalakouras
Keyword(s):  
Dna Methylation ◽  
Rna Interference ◽  
Gene Silencing ◽  
Plant Cells ◽  
Transcriptional Gene Silencing ◽  
Rnai Machinery ◽  
Double Stranded Rna ◽  
Post Transcriptional Gene Silencing ◽  
Cumulative Amount

Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems.

scholarly journals Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis

2019 ◽  
Vol 47 (17) ◽  
pp. 9104-9114 ◽  
Author(s):  
Christelle Taochy ◽  
Agnès Yu ◽  
Nicolas Bouché ◽  
Nathalie Bouteiller ◽  
Taline Elmayan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Silencing ◽  
De Novo ◽  
Transcriptional Silencing ◽  
Transcriptional Gene Silencing ◽  
Gene Body ◽  
Coding Sequence ◽  
Post Transcriptional Gene Silencing ◽  
Methylation Signal ◽  
Rule Out

Abstract Spontaneous post-transcriptional silencing of sense transgenes (S-PTGS) is established in each generation and is accompanied by DNA methylation, but the pathway of PTGS-dependent DNA methylation is unknown and so is its role. Here we show that CHH and CHG methylation coincides spatially and temporally with RDR6-dependent products derived from the central and 3′ regions of the coding sequence, and requires the components of the RNA-directed DNA methylation (RdDM) pathway NRPE1, DRD1 and DRM2, but not CLSY1, NRPD1, RDR2 or DCL3, suggesting that RDR6-dependent products, namely long dsRNAs and/or siRNAs, trigger PTGS-dependent DNA methylation. Nevertheless, none of these RdDM components are required to establish S-PTGS or produce a systemic silencing signal. Moreover, preventing de novo DNA methylation in non-silenced transgenic tissues grafted onto homologous silenced tissues does not inhibit the triggering of PTGS. Overall, these data indicate that gene body DNA methylation is a consequence, not a cause, of PTGS, and rule out the hypothesis that a PTGS-associated DNA methylation signal is transmitted independent of a PTGS signal.

scholarly journals Geminivirus Rep protein interferes with the plant DNA methylation machinery and suppresses transcriptional gene silencing

2013 ◽  
Vol 199 (2) ◽  
pp. 464-475 ◽  
Author(s):  
Edgar Rodríguez-Negrete ◽  
Rosa Lozano-Durán ◽  
Alvaro Piedra-Aguilera ◽  
Lucia Cruzado ◽  
Eduardo R. Bejarano ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Silencing ◽  
Transcriptional Gene Silencing ◽  
Rep Protein ◽  
Plant Dna

scholarly journals Two Populations of Viral Minichromosomes Are Present in a Geminivirus-Infected Plant Showing Symptom Remission (Recovery)

2016 ◽  
Vol 90 (8) ◽  
pp. 3828-3838 ◽  
Author(s):  
Esther Adriana Ceniceros-Ojeda ◽  
Edgar Antonio Rodríguez-Negrete ◽  
Rafael Francisco Rivera-Bustamante
Keyword(s):  
Dna Methylation ◽  
Gene Silencing ◽  
Infected Plant ◽  
Micrococcal Nuclease ◽  
Transcriptional Gene Silencing ◽  
Viral Dna ◽  
Low Concentration ◽  
Infected Cells ◽  
Two Populations

ABSTRACTGeminiviruses are important plant pathogens characterized by circular, single-stranded DNA (ssDNA) genomes. However, in the nuclei of infected cells, viral double-stranded DNA (dsDNA) associates with host histones to form a minichromosome. In phloem-limited geminiviruses, the characterization of viral minichromosomes is hindered by the low concentration of recovered complexes due to the small number of infected cells. Nevertheless, geminiviruses are both inducers and targets of the host posttranscriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) machinery. We have previously characterized a “recovery” phenomenon observed in pepper plants infected with pepper golden mosaic virus (PepGMV) that is associated with a reduction of viral DNA and RNA levels, the presence of virus-related siRNAs, and an increase in the levels of viral DNA methylation. Initial micrococcal nuclease-based assays pinpointed the presence of different viral chromatin complexes in symptomatic and recovered tissues. Using the pepper-PepGMV system, we developed a methodology to obtain a viral minichromosome-enriched fraction that does not disturb the basic chromatin structural integrity, as evaluated by the detection of core histones. Using this procedure, we have further characterized two populations of viral minichromosomes in PepGMV-infected plants. After further purification using sucrose gradient sedimentation, we also observed that minichromosomes isolated from symptomatic tissue showed a relaxed conformation (based on their sedimentation rate), are associated with a chromatin activation marker (H3K4me3), and present a low level of DNA methylation. The minichromosome population obtained from recovered tissue, on the other hand, sedimented as a compact structure, is associated with a chromatin-repressive marker (H3K9me2), and presents a high level of DNA methylation.IMPORTANCEViral minichromosomes have been reported in several animal and plant models. However, in the case of geminiviruses, there has been some recent discussion about the importance of this structure and the significance of the epigenetic modifications that it can undergo during the infective cycle. Major problems in this type of studies are the low concentration of these complexes in an infected plant and the asynchronicity of infected cells along the process; therefore, the complexes isolated in a given moment usually represent a mixture of cells at different infection stages. The recovery process observed in PepGMV-infected plants and the isolation procedure described here provide two distinct populations of minichromosomes that will allow a more precise characterization of the modifications of viral DNA and its host proteins associated along the infective cycle. This structure could be also an interesting model to study several processes involving plant chromatin.

Sign in / Sign up

Export Citation Format

Share Document