Biology subjects

Capella, M.

Publications and source records attributed to Capella, M..

11 recordsLinked to original sources

bioRxiv2026

Protein-independent regulation by transgene-derived small interfering RNAs rewires endogenous regulatory networks to enhance plant growth, architecture, and drought performance

Plants produce diverse small interfering RNA (siRNA) molecules that modulate development, environmental responses, and immunity. Although transgene-derived siRNAs are traditionally viewed as mediators of gene silencing, whether they can actively regulate endogenous host pathways remains largely unexplored. Previously obtained Arabidopsis, wheat, and soybean plants expressing the sunflower gene encoding the transcription factor HaHB4 exhibited water deficit tolerance. Here, we show that expressing inverted-repeat constructs that generate HaHB4-derived siRNAs without producing the HaHB4 protein bypasses transgenic growth penalties and instead enhances vegetative vigor and reproductive performance. In Arabidopsis, these DCL-dependent siRNA-producing lines exhibited enhanced root growth, increased stem and pith areas, increased cauline branching, and higher seed yield under both optimal and water-limiting conditions. Transcriptomic analysis revealed convergent repression of biotic stress-related genes, accompanied by increased bacterial susceptibility and reduced sensitivity to salicylic acid-mediated growth inhibition, suggesting an altered balance between immunity and growth. Functional characterization of candidate endogenous HD-Zip I targets further showed that athb20 and athb53 mutants recapitulated the increased stem expansion and cauline branching of the RNAi lines, respectively, pointing to endogenous HD-Zip I genes as candidate mediators of these traits. Remarkably, these effects were observed in newly obtained transgenic soybean plants, where expression of HaHB4-derived siRNAs enhanced vegetative vigor under controlled growth conditions. Overall, these findings show that transgene-derived siRNAs act independently of protein function to rewire endogenous regulatory networks, providing a potential strategy to optimize crop architecture and yield.

plant biology↗

bioRxiv2026

The segregase CDC48 integrates blue light and hormonal cues to regulate photomorphogenesis in Arabidopsis

Photomorphogenesis allows plants to adjust growth to ambient light conditions and relies on protein quality control to ensure the timely turnover of signaling components. The conserved AAA+ ATPase CDC48, along with its cofactors NPL4 and UFD1, is a crucial regulator of proteasomal degradation. While well characterized in other organisms, its role in plant development remains largely unexplored. Here, we show that CDC48 is required for blue light-mediated photomorphogenesis in Arabidopsis. Under blue light, CDC48A accumulates at the plasma membrane and in the nucleus, and cdc48a mutants fail to repress hypocotyl elongation properly. Similar phenotypes are observed upon inhibition of CDC48 or in npl4 and ufd1 mutants. Genetic and biochemical analyses further reveal that CDC48A negatively regulates gibberellin (GA) signaling. Consistently, UFD1 directly interacts with the GA receptor GID1 to promote its degradation. Together, these findings demonstrate that CDC48A integrates light and hormonal cues through protein homeostasis to regulate photomorphogenic development.

plant biology↗

bioRxiv2026

Mechanical stress modulates source-to-sink partitioning and drought response in Arabidopsis

Mechanical stimuli provoked by wind, soil compaction, rainfall, and biotic interactions strongly influence plant phenotype, growth, and development. Previous studies indicated that weight-treated Arabidopsis thaliana plants increase stem diameter, vascular bundle number, and seed yield, involving auxin, brassinosteroid, and strigolactone-related genes. In this work, we investigated how the mechanically induced increase in phloem area improves source-to-sink partitioning, while the increase in xylem area negatively affects long-term drought tolerance. Transcriptomic profiling confirmed a large-scale reprogramming of drought-responsive genes in treated plants. Moreover, quantification of sucrose and starch content highlighted an enhanced synthesis and carbohydrate transport, which ultimately and positively impacted lipid and protein contents in seeds. Using loss-of-function mutants, we demonstrate that the phloem loader SUC2 and exporters SWEET11, 12, and 16 are essential for the yield gains triggered by mechanical stress. Furthermore, mechanical treatment alters sugar metabolism. Overall, our findings indicate that weight treatment elicits a complex physiological response, in which sucrose transporters and starch metabolism play a crucial role in mediating its positive effects on seed quality and yield. Significance statementMechanical cues are ubiquitous in natural environments, but their impact on plant carbon allocation and yield remains poorly understood. This study reveals that mechanical stress reshapes vascular architecture and carbohydrate transport, enhancing source-to-sink partitioning and seed quality in Arabidopsis. By identifying sucrose transporters and sugar metabolism as key mediators of mechanically induced yield gains, our findings provide mechanistic insight into how physical forces integrate with metabolic regulation influence plant productivity.

plant biology↗

bioRxiv2024

Non-CG DNA methylation modulates hypocotyl elongation during thermormorphogenesis

Plants adapt to warm environments through physiological and morphological changes termed thermomorphogenesis, which involve transcriptional reprogramming exerted mainly by PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Fluctuating temperatures can also influence the patterns of cytosine DNA methylation, thereby influencing gene expression. However, whether these epigenetic changes provide an adaptative advantage remains unclear. Here, we provide evidence that DNA methylation is required to regulate thermomorphogenesis. Hypomethylated drm1 drm2 cmt3 mutants or seedlings treated with 5-azacytidine to block DNA methylation exhibit reduced hypocotyl growth at warm temperatures, primarily due to impaired cell elongation. Moreover, DNA hypomethylation compromises auxin biosynthesis and transport in response to warmth, partially by reducing PIF4 protein levels. Notably, the loss of DNA methylation leads to increased expression of SUPPRESSOR OF drm1 drm2 cmt3 (SDC), which in turn restricts hypocotyl elongation during thermomorphogenesis. Finally, we demonstrate that DNAme regulates the inhibition of SDC expression to promote gibberellin biosynthesis. Our findings underscore the critical role of DNA methylation in modulating gene expression in response to temperature fluctuations and provide new insights into the epigenetic regulation of thermomorphogenesis. HighlightsDNA methylation regulates the expression of key genes involved in auxin and gibberellin metabolism, to ensure hypocotyl growth in response to warm temperatures.

plant biology↗

bioRxiv2024

A systematic quantitative approach comprehensively defines domain-specific functional pathways linked to Schizosaccharomyces pombe heterochromatin regulation

Heterochromatin plays a critical role in regulating gene expression and maintaining genome integrity. While structural and enzymatic components have been linked to heterochromatin establishment, a comprehensive view of the underlying pathways at diverse heterochromatin domains remains elusive. Here, we developed a systematic approach to identify factors involved in heterochromatin silencing at pericentromeres, subtelomeres, and the silent mating type locus in Schizosaccharomyces pombe. Using quantitative measures, iterative genetic screening, and domain-specific heterochromatin reporters, we identified 369 mutants with different degrees of reduced or enhanced silencing. As expected, mutations in the core heterochromatin machinery globally decreased silencing. However, most other mutants exhibited distinct qualitative and quantitative profiles that indicate domain-specific functions. For example, decreased mating type silencing was linked to mutations in heterochromatin maintenance genes, while compromised subtelomere silencing was associated with metabolic pathways. Furthermore, similar phenotypic profiles revealed shared functions for subunits within complexes. We also discovered that the uncharacterized protein Dhm2 plays a crucial role in maintaining constitutive and facultative heterochromatin, while its absence caused phenotypes akin to DNA replication-deficient mutants. Collectively, our systematic approach unveiled a landscape of domain-specific heterochromatin regulators controlling distinct states and identified Dhm2 as a previously unknown factor linked to heterochromatin inheritance and replication fidelity.

genomics↗

bioRxiv2021

The inner nuclear membrane protein Lem2 coordinates RNA degradation at the nuclear periphery

Transcriptionally silent chromatin often localizes to the nuclear periphery. However, whether the nuclear envelope (NE) is a site for post-transcriptional gene repression is unknown. Here we demonstrate that S. pombe Lem2, an NE protein, regulates nuclear exosome-mediated RNA degradation. Lem2 deletion causes accumulation of non-coding RNAs and meiotic transcripts. Indeed, an engineered exosome substrate RNA shows Lem2-dependent localization to the nuclear periphery. Lem2 does not directly bind RNA, but instead physically interacts with the exosome-targeting MTREC complex and promotes RNA recruitment. The Lem2-assisted pathway acts independently of nuclear bodies where exosome factors assemble, revealing that multiple spatially distinct degradation pathways exist. The Lem2 pathway is environmentally responsive: nutrient availability modulates Lem2 regulation of meiotic transcripts. Our data indicate that Lem2 recruits exosome co-factors to the nuclear periphery to coordinate RNA surveillance and regulates transcripts during the mitosis-to-meiosis switch.

molecular biology↗

bioRxiv2021

Crosstalk between H2A variant-specific modifications impacts vital cell functions

Histone variants are distinguished by specific substitutions and motifs that might be subject to post-translational modifications (PTMs). Compared with the high conservation of H3 variants, the N- and C-terminal tails of H2A variants are more divergent and are potential substrates for a more complex array of PTMs, which have remained largely unexplored. We used mass spectrometry to inventory the PTMs of the two heterochromatin-enriched variants H2A.W.6 and H2A.W.7 of Arabidopsis, which harbor the C-terminal motif KSPK. This motif is also found in macroH2A variants in animals and confers specific properties to the nucleosome. We showed that H2A.W.6 is phosphorylated by the cell cycle-dependent kinase CDKA specifically at KSPK. In contrast, this modification is absent on H2A.W.7, which also harbors the SQ motif associated with the variant H2A.X. Phosphorylation of the SQ motif is critical for the DNA damage response but is suppressed in H2A.W.7 by phosphorylation of KSPK. To identify factors involved in this suppression mechanism, we performed a synthetic screen in fission yeast expressing a mimic of the Arabidopsis H2A.W.7. Among those factors was the BRCT-domain protein Mdb1. We showed that phosphorylation of KSPK prevents binding of the BRCT-domain protein Mdb1 to phosphorylated SQ and as a result hampers response to DNA damage. Hence, cross-talks between motif-specific PTMs interfere with the vital functions of H2A variants. Such interference could be responsible for the mutual exclusion of specific motifs between distinct H2A variants. We conclude that sequence innovations in H2A variants have potentiated the acquisition of many specific PTMs with still unknown functions. These add a layer of complexity to the nucleosome properties and their impact in chromatin regulation.

synthetic biology↗

bioRxiv2021

Relocation of rDNA repeats for repair is dependent on SUMO-mediated nucleolar release by the Cdc48/p97 segregase

Ribosomal RNA genes (rDNA) are highly unstable and susceptible to rearrangement due to active transcription and their repetitive nature. Compartmentalization of rDNA in the nucleolus suppresses uncontrolled recombination. However, broken repeats must be released to the nucleoplasm to allow repair by homologous recombination. The process of rDNA relocation is conserved from yeast to humans, but the underlying molecular mechanisms are currently unknown. Here we show that DNA damage induces phosphorylation of the CLIP-cohibin complex, releasing membrane-tethered rDNA from the nucleolus in Saccharomyces cerevisiae. Downstream of phosphorylation, SUMOylation targets CLIP-cohibin for disassembly mediated by the Cdc48/p97 chaperone, which recognizes SUMOylated CLIP-cohibin through its cofactor, Ufd1. Consistent with a conserved mechanism, UFD1L depletion impairs rDNA release in human cells. The dynamic and regulated assembly and disassembly of the rDNA-tethering complex is therefore a key determinant of nucleolar rDNA release and genome integrity.

molecular biology↗

bioRxiv2020

ESCRT recruitment by the inner nuclear membrane protein Heh1 is regulated by Hub1-mediated alternative splicing

Misassembled nuclear pore complexes (NPCs) are removed by sealing off the surrounding nuclear envelope (NE), which is mediated by members of the ESCRT (endosomal sorting complexes required for transport) machinery. Recruitment of ESCRT proteins to the NE is mediated by the interaction between the ESCRT member Chm7 and the inner nuclear membrane protein Heh1, which belongs to the conserved LEM family. Increased ESCRT recruitment results in excessive membrane scission at damage sites but its regulation remains poorly understood. Here, we show that Hub1-mediated alternative splicing of HEH1 pre-mRNA, resulting into its shorter form Heh1-S, is critical for the integrity of the NE. ESCRT-III mutants lacking Hub1 or Heh1-S display severe growth defects and accumulate improperly assembled NPCs. This depends on the interaction of Chm7 with the conserved MSC domain only present in the longer spliced variant Heh1-L. Heh1 variants assemble into heterodimers and we demonstrate that a unique splice segment in Heh1-S suppresses growth defects associated with uncontrolled interaction between Heh1-L and Chm7. Together, our findings reveal that Hub1-mediated splicing generates Heh1-S to regulate ESCRT recruitment to the nuclear envelope. Summary statementHeh1-S, the Hub1-mediated spliced version of HEH1 pre-mRNA, contributes to nuclear envelope maintenance by preventing excessive recruitment of Chm7.

cell biology↗

bioRxiv2019

The euchromatic histone mark H3K36me3 preserves heterochromatin through sequestration of an acetyltransferase complex in fission yeast

Maintaining the identity of chromatin states requires mechanisms that ensure their structural integrity through the concerted actions of histone modifiers, readers, and erasers. Histone H3K9me and H3K27me are hallmarks of repressed heterochromatin, whereas H3K4me and H3K36me are associated with actively transcribed euchromatin. Paradoxically, several studies have reported that loss of Set2, the methyltransferase responsible for H3K36me, causes de-repression of heterochromatin. Here we show that unconstrained activity of the acetyltransferase complex Mst2C, which antagonizes heterochromatin, is the main cause of the silencing defects observed in Set2-deficient cells. As previously shown, Mst2C is sequestered to actively transcribed chromatin via binding to H3K36me3 that is recognized by the PWWP domain protein Pdp3. We demonstrate that combining deletions of set2+ and pdp3+ results in an epistatic silencing phenotype. In contrast, deleting mst2+, or other members of Mst2C, fully restores silencing in Set2-deficient cells. Suppression of the silencing defect in set2{Delta} cells is specific for pericentromeres and subtelomeres, which are marked by H3K9me, but not seen for loci that lack genuine heterochromatin. Although Mst2 catalyzes acetylation of H3K14, this modification is likely not involved in the Set2-dependent pathway due to redundancy with the HAT Gcn5. Moreover, while Mst2 is required for acetylation of the H2B ubiquitin ligase Brl1 in euchromatin, we find that its role in heterochromatin silencing is not affected by Brl1 acetylation. We propose that it targets another, unknown substrate critical for heterochromatin silencing. Our findings demonstrate that maintenance of chromatin states requires spatial constraint of opposing chromatin activities.

genetics↗

bioRxiv2018

Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability

Telomeres and the shelterin complex cap and protect the ends of chromosomes. Telomeres are flanked by the subtelomeric sequences that have also been implicated in telomere regulation, although their role is not well defined. Here we show that, in Schizosaccharomyces pombe, the telo-mere-associated sequences (TAS) present on most subtelomeres are hyper-recombinogenic, have metastable nucleosomes, and unusual low levels of H3K9 methylation. Ccq1, a subunit of shelter-in, protects TAS from nucleosome loss by recruiting the heterochromatic repressor complexes CLRC and SHREC, thereby linking nucleosome stability to gene silencing. Nucleosome instability at TAS is independent of telomeric repeats and can be transmitted to an intrachromosomal locus containing an ectopic TAS fragment, indicating that this is an intrinsic property of the underlying DNA sequence. When telomerase recruitment is compromised in cells lacking Ccq1, DNA se-quences present in the TAS promote recombination between chromosomal ends, independent of nucleosome abundance, implying an active function of these sequences in telomere maintenance. We propose that Ccq1 and fragile subtelomeres co-evolved to regulate telomere plasticity by con-trolling nucleosome occupancy and genome stability.

genomics↗