Biology subjects

Manavella, P. A.

Publications and source records attributed to Manavella, P. A..

4 recordsLinked to original sources

bioRxiv2023

Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response

Infectious diseases drive the evolution of wild plants and impact yield in crop plants. Like animals, plants can sense biotic threats via conserved pathogen-associated patterns (PAMPs). Since an overly robust immune response can harm plants, understanding the mechanisms for tuning defense responses to the appropriate level is vital as we endeavor to develop pathogen-resistant crops. In this paper, we studied the Arabidopsis pattern recognition receptor (PRR) EFR, which senses bacterial EF-Tu. An inverted-repeat transposon (Ea-IR) between EFR and the neighboring XI-k locus controls local chromatin organization, promoting the formation of a repressive chromatin loop. Upon pathogen infection, the chromatin landscape around EFR and Xl-k dynamically changes to allow for increased EFR transcription. Chromatin opening facilitates the passage of RNA polymerase II across the neighboring XI-k gene termination site, leading to a longer XI-k transcript that includes Ea-IR sequences. Dicer-like (DCL) enzymes process the longer Xl-k transcript into small RNAs (sRNAs), which reset chromatin topology to a repressive state, attenuating, in turn, the immune response, reminiscent of attenuation of receptor signaling in other systems. From an evolutionary point of view, we found that natural Arabidopsis accessions missing Ea-IR have a constitutive "EFR-open" chromatin configuration that correlates with higher basal EFR levels and higher background resistance to pathogens. Collectively, our study offers evidence for a scenario in which a transposon, chromatin organization, and gene expression interact to fine-tune immune responses, both during the course of infection and in the course of evolution. Similar gene-associated IRs in crops could provide valuable non-coding targets for genome editing or assisted plant breeding programs.

plant biology↗

bioRxiv2023

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controlling shade avoidance syndrome in Arabidopsis thaliana

The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loop) and modulating local three-dimensional chromatin conformation. Here we show that APOLO is involved in regulating the shade avoidance syndrome (SAS) by dynamically modulating the expression of key factors. In response to far-red (FR) light, the expression of APOLO anticorrelates with its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. APOLO transcriptional accumulation fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves as well as in a late response to FR treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of YUCCA2 (auxin synthesis), PID and WAG2 (auxin efflux). We found that direct application of APOLO RNA to leaves results in a rapid increase in auxin accumulation that is associated with changes in the response of the plants to FR light. Collectively, our data support the view that lncRNAs coordinate the shade avoidance syndrome in Arabidopsis thaliana and shed light on the potential of lncRNAs as bioactive exogenous molecules. Deploying exogenous RNAs that modulate plant-environment interactions are important new tools for sustainable agriculture.

plant biology↗

bioRxiv2022

Polymorphic Inverted Repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana

Transposons are mobile elements that are commonly silenced to protect eukaryotic genome integrity. In plants, transposable elements (TEs) can be activated during stress conditions and subsequently insert into gene-rich regions. TE-derived inverted repeats (IRs) are commonly found near plant genes, where they affect host gene expression with potentially positive effects on adaptation. However, the molecular mechanisms by which these IRs control gene expression is unclear in most cases. Here, we identify in the Arabidopsis thaliana genome hundreds of IRs located near genes that are transcribed by RNA Polymerase II, resulting in the production of 24-nt small RNAs that trigger methylation of the IRs. The expression of these IRs is associated with drastic changes in the local 3D chromatin organization, which alter the expression pattern of the hosting genes. Notably, the presence and structure of many IRs differ between A. thaliana accessions. Capture-C sequencing experiments revealed that such variation changes short-range chromatin interactions, which translates into changes in gene expression patterns. CRISPR/Cas9-mediated disruption of two of such IRs leads to a switch in genome topology and gene expression, with phenotypic consequences. Our data demonstrate that the insertion of an IR near a gene provides an anchor point for chromatin interactions that can profoundly impact the activity of neighboring loci. This turns IRs into powerful evolutionary agents that can contribute to rapid adaptation.

plant biology↗

bioRxiv2021

R-loops between nascent pri-miRNAs and the encoding loci promote co-transcriptional processing of miRNAs in plants

In most organisms, the maturation of nascent RNAs is coupled to transcription, undergoing many processing steps co-transcriptionally. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNAs (miRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we show that plant miRNA biogenesis is coupled to transcription in a process that relies on the formation of DNA:RNA hybrids (R-loops) between the nascent transcript and the encoding loci. We used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs co-transcriptionally. We found that the entire biogenesis occurs coupled to transcription for pri-miRNAs processed from the loop but requires a second nucleoplasmic step for those processed from the base of the hairpin. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops between the 5-end single-stranded arm of the pri-miRNAs and the encoding loci anchor the transcript, promoting co-transcriptional processing. Our data demonstrate the coupling of transcription and miRNA processing in plants and discovered an unexpected function for R-loops promoting RNA processing. Furthermore, our results suggest the neo-functionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.

plant biology↗