Antagonistic Actions of FPA and IBM2 Regulate Transcript Processing from Genes Containing Heterochromatin

Deremetz, Aurélie; Roux, Clémentine Le; Idir, Yassir; Brousse, Cécile; Agorio, Astrid; Gy, Isabelle; Parker, Jane E.; Bouché, Nicolas

doi:10.1104/pp.18.01106

Cited by 25 publications

(25 citation statements)

References 49 publications

(87 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…If this observation is related to the use of alternative transcription start-sites identified downstream from exon 1 [ 36 ] remains to be examined. Furthermore, EDM2 was previously found to promote the alternative splicing-associated generation of RPP4-COPIA4 fusion transcripts consisting of RPP4 exon 1 and a part of COPIA4, but lacking the remaining RPP4 exons [ 46 , 47 ]. Consistent with its multi-facetted role in controlling RPP4 expression, EDM2 is required for maximal function of RPP4 in mediating resistance against the H .…”

Section: Discussionmentioning

confidence: 99%

The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression

Liu

Daron

et al. 2020

PLoS Genet

View full text Add to dashboard Cite

Plant NLR-type receptors serve as sensitive triggers of host immunity. Their expression has to be well-balanced, due to their interference with various cellular processes and dosedependency of their defense-inducing activity. A genetic "arms race" with fast-evolving pathogenic microbes requires plants to constantly innovate their NLR repertoires. We previously showed that insertion of the COPIA-R7 retrotransposon into RPP7 co-opted the epigenetic transposon silencing signal H3K9me2 to a new function promoting expression of this Arabidopsis thaliana NLR gene. Recruitment of the histone binding protein EDM2 to COPIA-R7associated H3K9me2 is required for optimal expression of RPP7. By profiling of genomewide effects of EDM2, we now uncovered additional examples illustrating effects of transposons on NLR gene expression, strongly suggesting that these mobile elements can play critical roles in the rapid evolution of plant NLR genes by providing the "raw material" for gene expression mechanisms. We further found EDM2 to have a global role in NLR expression control. Besides serving as a positive regulator of RPP7 and a small number of other NLR genes, EDM2 acts as a suppressor of a multitude of additional NLR genes. We speculate that the dual functionality of EDM2 in NLR expression control arose from the need to compensate for fitness penalties caused by high expression of some NLR genes by suppression of others. Moreover, we are providing new insights into functional relationships of EDM2 with its interaction partner, the RNA binding protein EDM3/AIPP1, and its target gene IBM1, encoding an H3K9-demethylase.

show abstract

Section: Discussionmentioning

confidence: 99%

The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression

Liu

Daron

et al. 2020

PLoS Genet

View full text Add to dashboard Cite

show abstract

“…In some well documented cases, specific RNA‐binding proteins play active roles in poly(A) site choice. For example, in Arabidopsis, the RNA‐binding proteins FPA, GRP7, and HLP1 have been reported to play important roles in poly(A) site choice in numerous genes (Simpson et al , ; Duc et al , ; Lyons et al , ; Zhang et al , ; Deremetz et al , ; Fang et al , ; Riester et al , ). Interestingly, FPA can be isolated from cell‐free extracts in complexes with many poly(A) complex subunits, including FIP1 (Fang et al , ).…”

Section: Discussionmentioning

confidence: 99%

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

et al. 2020

View full text Add to dashboard Cite

Alternative polyadenylation (APA) regulates diverse developmental and physiological processes through its effects on gene expression, mRNA stability, translatability, and transport. Sorghum is a major cereal crop in the world and, despite its importance, not much is known about the role of post-transcriptional regulation in mediating responses to abiotic stresses in Sorghum. A genome-wide APA analysis unveiled widespread occurrence of APA in Sorghum in response to drought, heat, and salt stress. Abiotic stress treatments incited changes in poly(A) site choice in a large number of genes. Interestingly, abiotic stresses led to the re-directing of transcriptional output into non-productive pathways defined by the class of poly(A) site utilized. This result revealed APA to be part of a larger global response of Sorghum to abiotic stresses that involves the re-direction of transcriptional output into non-productive transcriptional and translational pathways. Large numbers of stress-inducible poly(A) sites could not be linked with known, annotated genes, suggestive of the existence of numerous unidentified genes whose expression is strongly regulated by abiotic stresses. Furthermore, we uncovered a novel stress-specific cis-element in intronic poly(A) sites used in drought-and heat-stressed plants that might play an important role in non-canonical poly(A) site choice in response to abiotic stresses.

show abstract

“…Control of H3K9me2 homeostasis by antagonistic action of IBM1 and KYP may therefore prevent gain of CHG and CHH methylation, thus establishing an epigenetic signature distinguishable from those of other tDNA clusters. Recent reports revealed existence of a trade-off between heterochromatic TEs and gene functionality ( 85 , 86 ). Also, heterochromatic introns containing clustered tDNAs behave similarly to well characterized heterochromatic introns containing TE allowing the correct production of full transcripts ( 85 ).…”

Section: Discussionmentioning

confidence: 99%

Epigenetic silencing of clustered tRNA genes in Arabidopsis

Hummel

Berr

Graindorge

et al. 2020

Nucleic Acids Research

View full text Add to dashboard Cite

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.

show abstract

Antagonistic Actions of FPA and IBM2 Regulate Transcript Processing from Genes Containing Heterochromatin

Abstract: Intronic heterochromatic marks, associated with alternative polyadenylation sites, are decoded by RNA-binding proteins like FPA and IBM2, to tune the expression of key regulator genes such as IBM1 or RPP7.

Cited by 25 publications

References 49 publications

The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression

The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression

Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

Epigenetic silencing of clustered tRNA genes in Arabidopsis

Contact Info

Product

Resources

About