Biology subjects

de Leone, M. J.

Publications and source records attributed to de Leone, M. J..

6 recordsLinked to original sources

bioRxiv2026

DECAPPING PROTEIN 5 regulates the circadian clock in Arabidopsis

The Arabidopsis transcriptome must be continuously reshaped to integrate endogenous and environmental cues, including the circadian clock and ambient light. This reprogramming relies on the coordinated synthesis and degradation of mRNAs, yet the contribution of RNA decay factors to circadian regulation remains poorly characterized. Here, we show that nearly all core clock genes are high-amplitude clock-controlled genes (HA-CCGs). A meta-analysis of transcriptome-wide mRNA decay datasets revealed that HA-CCGs have consistently shorter half-lives across multiple studies. We further identify the mRNA decapping activator DECAPPING PROTEIN 5 (DCP5) as a key regulator of circadian RNA stability. Using iCLIP, we show that DCP5 binds preferentially to HA-CCG transcripts at AU-rich motifs in their 3' UTRs, thereby modulating their stability. Accordingly, the dcp5 mutant displays an extended circadian period at both physiological and molecular levels. Our findings establish mRNA decay as a post-transcriptional regulatory layer that fine-tunes the decay of multiple key transcripts within the circadian system.

plant biology↗

bioRxiv2025

In vivo binding by Arabidopsis SPLICING FACTOR 1 shifts 3' splice site choice, regulating circadian rhythms and immunity in plants

Alternative splicing expands proteome diversity and enables phenotypic plasticity across eukaryotes. In plants, mutations in spliceosomal components impair development and stress responses, but the molecular mechanisms remain unclear. Here, we define the molecular function of SPLICING FACTOR1 (AtSF1) in Arabidopsis thaliana using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) combined with RNA sequencing of sf1 mutants. We identify the in vivo branch point sequences bound by AtSF1 and delineate its RNA-binding landscape, revealing pervasive splicing defects dominated by aberrant 3' splice site selection. Structural comparison with human SF1 indicates that AtSF1 retains branch point recognition capacity but features a distinct domain organization, including a restructured C-terminal region absent in metazoans, suggesting a divergent RNA-binding mode that evolved to meet plant-specific splicing demands. AtSF1 targets are enriched for core circadian clock and defense genes, consistent with the long-period phenotype and immune-compromised phenotypes of sf1 mutants. Together, these findings establish that AtSF1 orchestrates alternative 3' splice site choice through intron binding and branch point recognition, coupling RNA processing with circadian and immune regulation in plants. SignificancePre-mRNA splicing is a fundamental process that shapes gene expression and proteome diversity, yet how it integrates with physiological pathways in plants remains poorly understood. Our study identifies the spliceosomal component SPLICING FACTOR1 (AtSF1) as a central modulator of alternative 3' splice site choice in Arabidopsis thaliana. By defining branch point sequences and direct RNA targets of AtSF1 in vivo, we reveal its dual regulatory role in circadian timing and immune responses. Comparative analysis with human SF1 uncovers a distinct domain architecture in the plant homolog, suggesting an alternative RNA-binding mode that evolved to meet plant-specific demands. These findings illuminate how conserved splicing machinery was molecularly adapted in the plant lineage to coordinate RNA processing with environmental and developmental cues.

plant biology↗

bioRxiv2024

Arabidopsis PRMT5 Buffers Pre-mRNA Splicing and Development Against Genetic Variation in Donor Splice Sites

Genetic variation at splice site signals significantly influences alternative splicing, leading to transcriptomic and proteomic diversity that enhances phenotypic plasticity and adaptation. However, novel splice variants can negatively impact gene expression and developmental stability. Canalization--the ability of an organism to maintain a consistent phenotype despite genetic or environmental variations--helps balance the effects of genetic variation on development and evolution. Protein arginine methyltransferase 5 (PRMT5) is a key splicing regulator in plants and animals. Most splicing changes in prmt5 mutants are linked to weak donor splice sites, suggesting that PRMT5 may buffer splicing against genetic variation. We examined PRMT5s effects on splicing and development in two genetically divergent Arabidopsis thaliana accessions with different single nucleotide polymorphisms (SNPs) affecting donor splice sites. While PRMT5 inactivation similarly affected splicing in both backgrounds, it significantly increased splicing and phenotypic differences between the accessions. Our findings suggest that PRMT5 contributes to canalization, mitigating the impact of splice site polymorphisms and facilitating the evolution of adaptive splicing patterns.

molecular biology↗

bioRxiv2024

Assessing the role of AtGRP7 arginine 141, a target of dimethylation by PRMT5, in flowering time control

Arginine (R) methylation, catalyzed by PROTEIN ARGININE METHYLTRANSFERASES (PRMTs), is critical for regulation of gene expression at the transcriptional and post-transcriptional level. Among nine PRMT genes in Arabidopsis, PRMT5 catalyzing symmetric R dimethylation of its targets is best characterized. PRMT5 mutants are late flowering and show altered responses to environmental stress. Among PRMT5 targets are Arabidopsis thaliana GLYCINE RICH RNA BINDING PROTEIN 7 (AtGRP7) and AtGRP8 that promote the transition to flowering. AtGRP7 R141 has been shown to be modified by PRMT5. Here, we tested whether this symmetric dimethylation of R141 is important for AtGRP7s physiological role in flowering time control. We constructed AtGRP7 mutant variants with non-methylable R141 (R141A, R141K). Genomic clones containing these variants complemented the late flowering phenotype of the grp7-1 mutant to the same extend as wild-type AtGRP7. Furthermore, overexpression of AtGRP7 R141A or R141K promoted flowering similar to overexpression of the wild-type protein. Thus, flowering time does not depend on R141 and its modification. However, AtGRP7 R141 contributes to the activity of GRP7 in response to abscisic. Immunoprecipitation of AtGRP7-GFP in the prmt5 background revealed that antibodies against dimethylated arginine still recognized AtGRP7, suggesting that additional methyltransferases may be responsible for modification of AtGRP7.

plant biology↗

bioRxiv2023

Antagonistic effects of arginine methylation of LSM4 on alternative splicing during plant stress responses

Arabidopsis PROTEIN ARGININE METHYLTRANSFERASE 5 (PRMT5) post-translationally modifies RNA-binding proteins by arginine (R) methylation. The impact of this modification on the regulation of RNA processing is largely unknown. Here we use LSM4, a component of the spliceosome, as a paradigm to study the impact of R-methylation on its function in RNA processing. We identify in vivo targets of LSM4 and show that LSM4 regulates alternative splicing of a suite of them. Furthermore, LSM4 affects mRNA levels of some of the targets, showing for the first time its role in both AS and steady-state abundance. The lsm4 and prmt5 mutants show a considerable overlap of genes with altered splicing patterns, suggesting that these might be regulated by PRMT5-dependent LSM4 methylation. Wild-type LSM4 and an unmethylable version complement the lsm4-1 growth and circadian rhythms defects, suggesting that methylation is not critical for growth in normal environments. However, LSM4 methylation increases with ABA and is necessary for plants to respond properly to salt stress. In contrast, LSM4 methylation is reduced by bacterial infection, and plants expressing unmethylable LSM4 are more resistant than plants expressing wild-type LSM4. This tolerance correlates with decreased intron retention of immune-response genes upon infection, augmenting the functional isoform. Taken together, this provides the first direct evidence that R methylation adjusts LSM4 function on pre-mRNA splicing in an antagonistic manner in response to biotic and abiotic stress. HighlightPlease provide a statement that, in fewer than 30 words, highlights the novelty of the paper for the non-expert. Arginine methylation of the LSM4 spliceosome component by PROTEIN ARGININE METHYLTRANSFERASE 5 fine-tunes alternative splicing of a set of stress-related genes to antagonistically control biotic and abiotic responses in Arabidopsis.

plant biology↗

bioRxiv2020

Building a pathway for diversity in plant sciences in Argentina: highlighting the work of women scientists through virtual activities

Encouraging the participation of a diverse workforce in academia increases plurality as it broadens the range of skills, ways of thinking and experiences. Institutions and professional societies have been putting efforts on building plans that help make workplaces, conferences, education and extension programs more relatable to a highly diverse population. Argentina has an overall gender-balanced workforce in the sciences (~53% women/total), with an even higher representation in disciplines related to plant sciences. However, media outlets and national conferences related to genetics, botany, plant physiology, ecology and molecular biology, fail to reflect those numbers as the proportion of women invited for interviews, plenary lectures, and symposia falls below ~30%. As a way to increase the visibility of the wealth of plant science topics and experimental approaches in which Argentinian women work, and to facilitate connections among them across the country and abroad, we created the Argentinian Women in Plant Science network (https://argplantwomen.weebly.com/). This group has grown to over 200 members, representing a wide range of career stages and research topics. Since April, and taking advantage of the confinement situation, our weekly webinar series highlighting women plant scientists has reached an average audience of 60-70 participants, with a record of 100. Recently, we have begun a series of open professional development webinars to reach a wider public. Our first webinar, focused on Scientific poster design, had ~250 participants, most of them undergrad and graduate students from all over the country covering a diverse range of disciplines, including the social sciences. Even though we have immersed ourselves in the plant science community with our weekly seminars, we have expanded our goals with activities aimed to reach out to a much wider audience with webinars and teacher training workshops, hopefully making plant science more attainable to all.

scientific communication and education↗