The plant mobile domain proteins MAIN and MAIL1 interact with the phosphatase PP7L to regulate gene expression and silence transposable elements in <i>Arabidopsis thaliana</i>

Nicolau, Mélody; Picault, Nathalie; Descombin, Julie; Jami‐Alahmadi, Yasaman; Feng, Suhua; Bucher, Etienne; Jacobsen, Steven E.; Deragon, Jean-Marc; Wohlschlegel, James A.; Moissiard, Guillaume

doi:10.1101/710905

Cited by 4 publications

(3 citation statements)

References 56 publications

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“…However, we cannot exclude the involvement of other mechanisms. For instance, in Arabidopsis, plant mobile domains MAIN and MAIL1 were shown to be required for silencing of TEs ( 92 ). Whether such proteins are involved in the regulation of tDNA expression remains to be established.…”

Section: Discussionmentioning

confidence: 99%

Epigenetic silencing of clustered tRNA genes in Arabidopsis

Hummel

Berr

Graindorge

et al. 2020

Nucleic Acids Research

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Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. This work demonstrates that both genomic and epigenomic contexts are key players in the regulation of tDNAs transcription. The conservation of most of these regulatory processes suggests that this pioneering work in Arabidopsis can provide new insights into the regulation of RNA Pol III transcription in other organisms, including vertebrates.

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Section: Discussionmentioning

confidence: 99%

Epigenetic silencing of clustered tRNA genes in Arabidopsis

Hummel

Berr

Graindorge

et al. 2020

Nucleic Acids Research

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“…PP7L seems to participate in several stress responses (Xu et al, 2019). PP7L interacts with plant mobile proteins MAINTENANCE OF MERISTEMS (MAIN) and MAIN-LIKE 1 (MAIL1) to silence a subset of transposable elements (de Luxan-Hernandez et al, 2020; Nicolau et al, 2020), but the exact molecular function of those proteins is still unclear. Here we want to emphasize, that it was not our intention to clarify PP7L’s function in this study, but used (post)-transcriptomics behavior of the pp7l mutant for comparison with that of the wild- type Col-0.…”

Section: Discussionmentioning

confidence: 99%

Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought stress

Xu¹,

Qian²,

Leister³

et al. 2022

Preprint

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Plants have evolved sophisticated mechanisms to cope with drought, which involve massive changes in nuclear gene expression. However, little is known about the roles of post-transcriptional processing of nuclear or organellar transcripts and how meaningful these changes are. To address these issues, we used long non-coding RNA-sequencing to monitor (post)transcriptional changes during different times of drought exposure in Arabidopsis Col-0 and a mutant (protein phosphatase 7-like, pp7l), from which we demonstrated that it can survive long periods of drought stress. The changes detected in the pp7l mutant were marginal, while in the wild type chloroplast transcript levels were globally reduced, editing efficiency dropped, but splicing was not affected. Mitochondrial transcripts were slightly elevated, while editing and splicing were unchanged. Also, transcriptional activation of transposable elements played only a minor role. Conversely, alternative splicing (AS) affected nearly 2,000 genes (11% of expressed nuclear genes). Of these, 25% underwent isoform switching, and 15% were regulated solely at the level of AS, representing transcripts that would have gone unnoticed in a microarray-based approach. Our data show that AS enhances proteome diversity to counteract drought stress and represent a valuable resource that will facilitate the development of new strategies to improve plant performance under drought. Moreover, altering the relative contributions of spliced isoforms might enhance drought resistance. For instance, our data imply that accumulation of a non-functional FLM (FLOWERING LOCUS M) isoform and not the ratio of functional isoforms as suggested for temperature responses - accounts for the early-flowering phenotype under drought conditions.

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“…The expanded gene family contained four duplicates of Maintenance of Meristems (MAIN) and MAIN-like 1 genes (Table S14). MAIN and MAIN-like 1 interact with protein phosphatase PP7like 83 to regulate transposable element silencing, as well as chloroplast development and abiotic stress tolerance 84 . PP7L is closely related to PP7, a component in cryptochrome-mediated blue-light signaling 85 and a regulator of the perception of red/far red light through the control of the phytochrome pathway 86 .…”

Section: Genome Evolution In V Darrowiimentioning

confidence: 99%

Dissecting the subtropical adaptation traits and cuticle synthesis pathways via the genome of the subtropical blueberryVaccinium darrowii

Cui

et al. 2021

Preprint

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Vaccinium darrowii is a subtropical wild blueberry species, which was used to breed economically important southern highbush cultivars. The adaptation traits of V. darrowii to subtropical climate would provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembled the V. darrowii genome into 12 pseudochoromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies, and predicted 41 815 genes using RNAseq evidence. Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure, with the highest collinearity between V. darrowii and V. corymbosum. This conserved genome structure may explain the high fertilization during crossbreeding between V. darrowii and other blueberry cultivars. Gene expansion and tandem duplication analysis indicated possible roles of defense and flowering associated genes in adaptation of V. darrowii to the subtropics. The possible SOC1 genes in V. darrowii were identified with phylogeny and expression analysis. Blueberries are covered in a thick cuticle layer and contain anthocyanins, which confer their powdery blue color. Using RNA-sequencing, the cuticle biosynthesis pathways of Vaccinium species were delineated here in V. darrowii. This result could serve as a reference for breeding berries with customer-desired colors. The V. darrowii reference genome, together with the unique traits of this species, including diploid genome, short vegetative phase, and high compatibility in hybridization with other blueberries, make V. darrowii a potential research model for blueberry species.

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The plant mobile domain proteins MAIN and MAIL1 interact with the phosphatase PP7L to regulate gene expression and silence transposable elements in Arabidopsis thaliana

Cited by 4 publications

References 56 publications

Epigenetic silencing of clustered tRNA genes in Arabidopsis

Epigenetic silencing of clustered tRNA genes in Arabidopsis

Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought stress

Dissecting the subtropical adaptation traits and cuticle synthesis pathways via the genome of the subtropical blueberryVaccinium darrowii

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