MTHFD1 controls DNA methylation in Arabidopsis.

DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. Here, we identify the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Decreased levels of oxidized tetrahydrofolates in mthfd1-1 and lethality of loss-of-function demonstrate the essential enzymatic role of MTHFD1 in Arabidopsis. Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1. Comparative analysis of DNA methylation revealed that the CMT3 and CMT2 pathways involving positive feedback with H3K9me are mostly affected. Our work highlights the sensitivity of epigenetic networks to one-carbon metabolism due to their common S-adenosylmethionine-dependent transmethylation and has implications for human MTHFD1-associated diseases

MORC1 represses transposable elements in the mouse male germline

The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. ​MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that ​MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue ​DNMT3L. ​Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify ​MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation

Etude de l'induction, de la suppression et de l'amplification du RNA silencing en contexte phytoviral

L ARN silencing est un mécanisme de régulation négative de l expression des gènes par des interactions entre molécules d ARN. Un ARN double-brin est découpé par Dicer en short-interfering (si)RNA de 21 à 24-nt incorporant un RNA-Induced Silencing Complex , pour guider le clivage d ARNm cible de manière séquence spécifique. Le silencing joue un rôle important dans la lutte antivirale chez les plantes. De plus, la plupart des phytovirus produisent des protéines suppresseurs de silencing. Le silencing peut être amplifié par l activité d ARN-dépendante ARN polymérases (RDR) cellulaires. Nous avons étudié l ARN silencing au cours de l infection par le Cauliflower mosaic virus (CaMV) et montré que les quatre protéines Dicer-like (DCLs) d Arabidopsis étaient impliquées dans ce mécanisme. Nous avons analysé les interactions entre cinq suppresseurs et l activité de RDR6 et identifié les DCLs associés à RDR6. Nous avons découvert que dans certains cas, RDR6 utilise le siRNA comme une amorce.RNA silencing is a mechanism involved in the suppression of gene expression through nucleotide sequence-specific interactions mediated by RNA. A double-stranded RNA is processed by Dicer into 21- to 24-nt RNAs, called short-interfering (si)RNA that incorporate into a RNA-Induced Silencing Complex, to guide cleavage target mRNA in a sequence-specific manner. RNA silencing plays important antiviral role in plants. In parallel, most of phytoviruses produce suppressor proteins to counteract RNA silencing. RNA silencing can be amplified through the activity of the cellular RNA-dependent RNA polymerase (RDR). We studied RNA silencing during Cauliflower mosaic virus (CaMV) infection. We found that the four Arabidopsis Dicer-like (DCLs) proteins are involved to produce two classes of viral siRNAs. Then, we analysed the interactions between five silencing suppressors and RDR6 and identified the DCLs associated to RDR6. We also showed that, at least in some cases, RDR6 uses small RNAs as primers.STRASBOURG-Sc. et Techniques (674822102) / SudocSudocFranceF

The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events

Editorial: Plant epigenetics and chromatin dynamics - EPIPLANT 2021-2022

International audienc

Transitivity-dependent and -independent cell-to-cell movement of RNA silencing

One manifestation of RNA silencing, known as post-transcriptional gene silencing (PTGS) in plants and RNA interference (RNAi) in animals, is a nucleotide sequence-specific RNA turnover mechanism with the outstanding property of propagating throughout the organism, most likely via movement of nucleic acids. Here, the cell-to-cell movement of RNA silencing in plants is investigated. We show that a short-distance movement process, once initiated from a small group of cells, can spread over a limited and nearly constant number of cells, independent of the presence of homologous transcripts. There is also a long-range cell-to-cell movement process that occurs as a relay amplification, which requires the combined activity of SDE1, a putative RNA-dependent RNA polymerase, and SDE3, a putative RNA helicase. Extensive and limited cell-to-cell movements of silencing are triggered by the same molecules, occur within the same tissues and likely recruit the same plasmodesmata channels. We propose that they are in fact manifestations of the same process, and that extensive cell-to-cell movement of RNA silencing results from re-iterated short-distance signalling events. The likely nature of the nucleic acids involved is presented

Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins

In plants, worms, and fungi, RNA-dependent RNA polymerases (RDRs) amplify the production of short-interfering RNAs (siRNAs) that mediate RNA silencing. In Arabidopsis, RDR6 is thought to copy endogenous and exogenous RNA templates into double-stranded RNAs (dsRNAs), which are subsequently processed into siRNAs by one or several of the four Dicer-like enzymes (DCL1→4). This reaction produces secondary siRNAs corresponding to sequences outside the primary targeted regions of a transcript, a phenomenon called transitivity. One recognized role of RDR6 is to strengthen the RNA silencing response mounted by plants against viruses. Accordingly, suppressor proteins deployed by viruses inhibit this defense. However, interactions between silencing suppressors and RDR6 have not yet been documented. Additionally, the mechanism underlying transitivity remains poorly understood. Here, we report how several viral silencing suppressors inhibit the RDR6-dependent amplification of virus-induced and transgene-induced gene silencing. Viral suppression of primary siRNA accumulation shows that transitivity can be initiated with minute amounts of DCL4-dependent 21-nucleotide (nt)-long siRNAs, whereas DCL3-dependent 24-nt siRNAs appear dispensable for this process. We further show that unidirectional (3→5′) transitivity requires the hierarchical and redundant functions of DCL4 and DCL2 acting downstream from RDR6 to produce 21- and 22-nt-long siRNAs, respectively. The 3→5′ transitive reaction is likely to be processive over >750 nt, with secondary siRNA production progressively decreasing as the reaction proceeds toward the 5′-proximal region of target transcripts. Finally, we show that target cleavage by a primary small RNA and 3→5′ transitivity can be genetically uncoupled, and we provide in vivo evidence supporting a key role for priming in this specific reaction