Biology subjects

Raxwal, V. K.

Publications and source records attributed to Raxwal, V. K..

8 recordsLinked to original sources

bioRxiv2026

A Cajal body assembly factor regulates cell fate transitions in Arabidopsis

Ribonucleoprotein (RNP) condensates are emerging as key regulators of cell fate transitions, yet their functions have been largely linked to mRNA storage and translational control. Here, we uncover a role for Cajal body (CB)-mediated pre-mRNA splicing in coordinating the transition from stem cell divisions to differentiation in plants. We identify THREE-DIVISION MUTANT 3 (TDM3) as a cell cycle-regulated factor required for post-mitotic CB assembly. Loss of TDM3 or the CB scaffold protein COILIN delays differentiation and prolongs formative cell divisions. Transcriptome analysis revealed that TDM3 and COILIN jointly regulate pre-mRNA splicing, including transcripts controlling cell cycle and fate transitions. These findings establish CB-mediated splicing as a mechanism linking cell cycle progression to cellular differentiation.

cell biology↗

bioRxiv2026

PAT: An Image Analysis Tool for Automated Scoring of Pollen in Alexander-Stained Anthers

Quantitative pollen viability analysis is a critical but labor-intensive step in plant reproductive biology. Existing deep-learning Segment Anything Models (SAM) fail to reliably segment viable pollen in Alexander-stained anthers. To address this, we fine-tuned an existing Cellpose-SAM model for pollen segmentation. We integrated it into PAT (Pollen Analysis Tool), a cross-platform desktop application. PAT features instance segmentation with interactive quality control, an in-app model retraining module, and publication-ready statistical outputs. We deployed PAT in an EMS suppressor screen of semi-sterile Arabidopsis smg7-6 mutants, enabling efficient candidate prioritization for whole genome sequencing and mapping candidate mutation. This screen led to the identification of a point mutation in CAP-D2 (capd2-2), a Condensin I subunit, that rescues the smg7-6 meiotic phenotype. Notably, mutation in a Condensin II subunits (CAP-D3 and CAP-H2) does not confer rescue. Further characterization suggests the capd2-2 allele is hypomorphic, showing no defects in vegetative growth, chromocenter compaction, or transposable element silencing. Collectively, we demonstrate that accessible AI tools have the potential to bridge gaps in plant phenotyping and accelerate the pace of biological discovery. HighlightWe combined AI-powered image analysis with an easy-to-use desktop app to automate plant pollen counting, then used it to identify a new genetic suppressor of meiotic defects.

plant biology↗

bioRxiv2026

Genome-wide mapping of DCP2-dependent 5' cap footprints in Arabidopsis thaliana

mRNA decapping mediated by DCP2 is a key mechanism controlling RNA stability and gene expression in eukaryotes, including plants. Despite its central role in regulating plant development and stress responses, the repertoire of mRNA 5 caps targeted by DCP2 remains undefined. Here, we combined in vitro decapping treatment with 5-end enriched and full-length transcriptome sequencing of DCP2-deficient mutants to comprehensively characterize the mRNA capping landscape in Arabidopsis thaliana. We mapped over 13,000 high-confidence capped transcripts at nucleotide resolution, revealing distinct 5 cap signatures in both wild type and dcp2 seedlings. Most caps were localized near annotated transcription start sites, validating the accuracy of our approach. Loss of DCP2 led to a substantial accumulation of capped mRNAs, including 275 capped transcripts originating from previously unannotated loci. It also increased prevalence of multi-capped genes highlighting the role of DCP2-mediated decapping in removing unwanted transcripts. Integration of these data with degradome resources revealed that targets of co-translational and cytosolic XRN4-dependent decay, as well as of nonsense-mediated decay, were enriched among capped mRNAs specifically accumulated in dcp2. These findings suggest that mRNA degradation in these decay pathways is mediated through decapping. In addition, this study provides a valuable resource for transcript annotation and isoform-aware analysis of RNA turnover. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/709597v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@3569a2org.highwire.dtl.DTLVardef@aa2ca3org.highwire.dtl.DTLVardef@58a27forg.highwire.dtl.DTLVardef@1147350_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2022

A complex role of Arabidopsis CDKD;3 in meiotic progression and cytokinesis

Meiosis is a specialized cell division that halves the number of chromosomes in two consecutive rounds of chromosome segregation. In angiosperm plants is meiosis followed by mitotic divisions to form rudimentary haploid gametophytes. In Arabidopsis, termination of meiosis and transition to gametophytic development is governed by TDM1 and SMG7 that mediate inhibition of translation. Mutants deficient in this mechanism do not form tetrads, but instead undergo multiple cycles of aberrant nuclear divisions, that are likely caused by the failure to downregulate cyclin dependent kinases during meiotic exit. A suppressor screen to identify genes that contribute to meiotic exit uncovered a mutation in CDKD;3 that alleviates meiotic defects in smg7 deficient plants. The CDKD;3 deficiency prevents aberrant meiotic divisions observed in smg7 mutants, or delays their onset after initiation of cytokinesis, which permits formation of functional microspores. Although CDKD;3 acts as an activator of CDKA;1, the main cyclin dependent kinase that regulates meiosis, cdkd;3 mutation appears to promote meiotic exit independently of CDKA;1. Furthermore, analysis of CDKD;3 interactome revealed enrichment for proteins implicated in cytokinesis suggesting a more complex function of CDKD;3 in cell cycle regulation.

plant biology↗

bioRxiv2021

Transcriptional and post-transcriptional regulation of young genes in plants

New genes continuously emerge from non-coding DNA or by diverging from existing genes, but most of them are rapidly lost and only a few become fixed within the population. We hypothesized that young genes are subject to transcriptional and post-transcriptional regulation to limit their expression and minimize their exposure to purifying selection. We found that young genes in rice have relatively low expression levels, which can be attributed to distal enhancers, and closed chromatin conformation at their transcription start sites (TSS). The chromatin in TSS regions can be re-modeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis tend to be targeted by nonsense-mediated RNA decay, presenting another layer of regulation limiting their expression. Together, these data suggest that transcriptional and post-transcriptional mechanisms contribute to the conditional expression of young genes, which may alleviate purging selection while providing an opportunity for phenotypic exposure and functionalization.

evolutionary biology↗

bioRxiv2021

A CENH3 mutation promotes meiotic exit and restores fertility in SMG7-deficient Arabidopsis

Meiosis in angiosperm plants is followed by mitotic divisions to form multicellular haploid gametophytes. Termination of meiosis and transition to gametophytic development is, in Arabidopsis, governed by a dedicated mechanism that involves SMG7 and TDM1 proteins. Mutants carrying the smg7-6 allele are semi-fertile due to reduced pollen production. We found that instead of forming tetrads, smg7-6 pollen mother cells undergo multiple rounds of chromosome condensation and spindle assembly at the end of meiosis, resembling aberrant attempts to undergo additional meiotic divisions. A suppressor screen uncovered a mutation in centromeric histone H3 (CENH3) that increased fertility and promoted meiotic exit in smg7-6 plants. The mutation led to inefficient splicing of the CENH3 mRNA and a substantial decrease of CENH3, resulting in smaller centromeres. The reduced level of CENH3 delayed formation of the mitotic spindle but did not have an apparent effect on plant growth and development. We suggest that impaired spindle re-assembly at the end of meiosis limits aberrant divisions in smg7-6 plants and promotes formation of tetrads and viable pollen. Furthermore, the reduced level of CENH3 did not induce haploid plants in crosses with wild plants, indicating that differences in centromere size is not the key determinant of centromere-mediate genome elimination.

genetics↗

bioRxiv2020

Nonsense mediated RNA decay factor UPF1 is critical for post-transcriptional and translational gene regulation in Arabidopsis

Nonsense mediated RNA decay (NMD) is an evolutionary conserved RNA control mechanism that has also been implicated in the broader regulation of gene expression. Nevertheless, a role for NMD in genome regulation has not been fully assessed, partially because NMD inactivation is lethal in many organisms. Here, we performed in depth comparative analysis of Arabidopsis mutants lacking key proteins involved in different steps of NMD. We observed that UPF3, UPF1, and SMG7 have different impacts on NMD and the Arabidopsis transcriptome, with UPF1 having the biggest effect. Transcriptome assembly using stringent pipeline in UPF1-null plants revealed genome wide changes in alternative splicing, including switches in mRNA variants, suggesting a role for UPF1 in splicing. We further found that UPF1 inactivation leads to translational repression, manifested by a global shift in mRNAs from polysomes to monosomes and a downregulation of genes involved in translation and ribosome biogenesis. Despite this global change, NMD targets and low-expressed mRNAs with short half-lives were enriched in polysomes, indicating that UPF1 specifically suppresses the translation of aberrant RNAs. Particularly striking was an increase in the translation of TIR domain-containing, nucleotide-binding, leucine-rich repeat (TNL) immune receptors. The regulation of TNLs via UPF1/NMD-mediated mRNA stability and translational de-repression offers a dynamic mechanism for the rapid activation of TNLs in response to pathogen attack.

molecular biology↗

bioRxiv2018

artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis

Mapping-by-sequencing is a rapid method for identifying both natural as well as induced variations in the genome. However, it requires extensive bioinformatics expertise along with the computational infrastructure to analyze the sequencing data and these requirements have limited its widespread adoption. In the current study, we develop an easy to use tool, artMAP, to discover ethyl methanesulfonate (EMS) induced mutations in the Arabidopsis genome. The artMAP pipeline consists of well-established tools including TrimGalore, BWA, BEDTools, SAMtools, and SnpEff which were integrated in a Docker container. artMAP provides a graphical user interface and can be run on a regular laptop and desktop, thereby limiting the bioinformatics expertise required. artMAP can process input sequencing files generated from single or paired-end sequencing. The results of the analysis are presented in interactive graphs which display the annotation details of each mutation. Due to its ease of use, artMAP made the identification of EMS-induced mutations in Arabidopsis possible with only a few mouse click. The source code of artMAP is available on Github (https://github.com/RihaLab/artMAP).

plant biology↗