Biology subjects

Shivaprasad, P. V.

Publications and source records attributed to Shivaprasad, P. V..

12 recordsLinked to original sources

bioRxiv2026

Distinct development-associated roles of rice histonevariant H2A.X in suppressing deposition of activeH3K4me3 marks and in restricting H2A.W incorporation

Histone variant H2A.X is a well-conserved histone that plays crucial roles in mediating DNA damage response across eukaryotes. Although H2A.X expresses even without any stress, and decorates gene bodies of actively expressed genes, it is not known if H2A.X has functions beyond DNA damage repair. Using genetic, high throughput genomics and molecular approaches, we identified a previously unappreciated role of H2A.X in regulating development-associated genes. Using custom-made antibodies specific to H2A.X variant, we show that it suppressed the deposition of active H3K4me3 marks over gene bodies and Transposable elements (TE)s, specifically regulating several root development, photosynthesis, and pigmentation-related genes as seen by the impairment of these processes in h2a.x ko (knockout) plants. H2A.X also suppressed global deposition of repressive mark H3K9me2 by restricting activity of H2A variant H2A.W. In agreement with this, there was a genome-wide re-localization of H2A.W to TEs and a few genes in h2a.x ko plants. H2A.X overexpressing plants exhibited stress phenotypes including increased anthocyanin levels, mimicking the transcriptome of DNA damaged wildtype plants. The transcriptome of kd lines of FACT complex, a known chaperone of H2A.X, was largely similar to that of h2a.x ko, suggesting that the development-associated functions of FACT are at least partially due to H2A.X. These results suggest a key role of H2A.X in regulating the competing histone marks and this function might be conserved across plants. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/707635v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1b2fe74org.highwire.dtl.DTLVardef@5fa3c8org.highwire.dtl.DTLVardef@f9b741org.highwire.dtl.DTLVardef@6e1101_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2025

Loss of function of chromatin remodeler OsCLSY4 leads to RdDM-mediated mis-expression of endosperm-specific genes affecting grain qualities

RNA-directed DNA methylation (RdDM) sequence-specifically targets transposable elements (TEs) and repeats in plants, often in a tissue-specific manner. In triploid endosperm tissue, RdDM also acts as a parental dosage regulator, mediating spatio-temporal expression of genes required for its development. It is unclear how RdDM is initiated and established in endosperm. Rice endosperm-specific imprinted chromatin remodeler OsCLSY3 recruits RNA polymerase IV to specific genomic sites for silencing and optimal gene expression. Here we show that, in addition to OsCLSY3, ubiquitously expressed OsCLSY4 is also crucial for proper reproductive growth and endosperm development. Loss of function of OsCLSY4 led to reproductive and nutrient-filling defects in endosperm. Using genetic and molecular analysis, we show that OsCLSY3 and OsCLSY4 play both overlapping and unique silencing roles in rice endosperm by targeting specific and common TEs, repeats and genic regions. These results indicate the importance of optimal expression of two OsCLSYs in regulating endosperm-specific gene expression, genomic imprinting and suppression of specific TEs. Results presented here provide new insights into the functions of rice CLSYs as upstream RdDM regulators in rice endosperm development, and we propose that functions of their homologs might be conserved across monocots.

plant biology↗

bioRxiv2025

Copper-sensitive OsSPL9 TF regulates expression of indica rice domestication-associated miRNAs and phenotypes

Domestication of indica rice facilitated better harvest and yield, however the molecular mechanisms that drove multitude of the associated phenotypes is poorly understood. A few genetic and epigenetic mechanisms have been attributed to indica rice domestication; however, upstream regulators of these variations are unknown. Here, we identified a copper (Cu)-dependent regulatory module, involved in the regulation of OsSPL9 TF and two classes of RNAs under its control. Differential accumulation of Cu-associated micro(mi)RNAs and Cu-associated protein-coding RNAs were a major portion of the differences between wild (Oryza nivara) and cultivated rice lines. We identified OsSPL9 as an upstream regulator of these changes through genetic and molecular analysis as well as by using Cu stressed conditions. OsSPL9 bound to the promoters of these genes through a conserved GTAC enriched motif. OsSPL9, Cu-associated miRNAs and their targets acted as a regulatory loop, since mis-expression of SPL9 alone, or any individual Cu-associated miRNA, also altered levels of other Cu-miRNAs and their cognate targets. OsSPL9-mediated regulation was closely linked to Cu accumulation and metabolism, indicating previously unappreciated roles of metal ions in mediating domestication-associated phenotypes. Our study facilitates a better understanding of the crosstalk between genetic and epigenetic regulation that contributed to indica rice domestication.

plant biology↗

bioRxiv2025

OsWRKY53 dictates wound responses in rice through fine-tuning cross-talk between PEP and PSK mediated signalling

Wounding and tissue damage are major events among the multitude of stresses that plants face in their natural environment. Wound response is a very dynamic event that involves the integration of various regulatory networks culminating in successful wound-induced downstream signalling. Plants depend on endogenously derived molecular signals to initiate wound responses. Transcriptional response is paramount in dictating successful transition of early defense to late growth responses. Here we show the involvement of a WRKY transcription factor (TF) named OsWRKY53, that is responsive to both wounding as well as wound-derived plant elicitor peptide (PEP), OsPep2 treatments. OsWRKY53 is involved in positive regulation of gene expression of OsPep2 responsive genes. OsWRKY53 displays altered DNA occupancy in response to OsPep2 treatment over time correlating with the altered gene expression. Further, OsWRKY53 is involved in simultaneous activation and suppression of OsPep2-responsive and phytosulfokine (PSK) responsive genes, respectively. In agreement with these, mis-expression of OsWRKY53 led to compromised wound responses. Collectively, we establish that OsWRKY53 acts at the intersection of PEP and PSK mediated transition of wound responses and positively regulates the early defense-related gene expression.

plant biology↗

bioRxiv2024

Transcriptional and epigenetic response of rapeseed (Brassica napus L.) to PEG-triggered osmotic stress

Drought hinders growth, development, and productivity of higher plants. While physiological and molecular background of plant responses to drought has extensively studied, the role of epigenetic modifications in response to dehydration remains largely elusive. In this study, we deciphered genome-wide transcriptomic and epigenetic responses of rapeseed (Brassica napus L.) to dehydration. High-throughput transcript profiling (RNA-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) of PEG-treated rapeseed plants revealed genome-scale changes in transcription and histone methylation patterns, focusing on histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 tri-methylated lysine 27 (H3K27me3). We have identified large gene sets with altered transcript profiles and changed histone methylation marks in response to osmotic stress, revealed a close correlation between gain or loss of histone methylation and activation or repression of gene expression. Significant epigenetic regulation of Delta 1-Pyrroline-5-Carboxylate Synthetase (P5CS) genes, which control the key step in proline synthesis, was discovered as several PEG-induced BnP5CSA genes displayed enhanced H3K4me3 and/or H3K36me3 marks. Targeted bisulphite sequencing revealed that one BnP5CSA gene has stress-dependent gene body DNA methylation also. By integrating physiological, transcriptional and epigenetic data, our study facilitates better understanding drought response control in higher plants.

plant biology↗

bioRxiv2023

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable elements (TEs) and repeat-derived small(s)RNAs mediate epigenetic changes in plants. In imprinting, uniparental gene expression arises due to parent-specific epigenetic marks on one allele but not on the other. The importance of sRNAs and their regulation in endosperm development or in imprinting is poorly understood in crops. Here we show that a previously uncharacterized CLASSY (CLSY)-family chromatin remodeler named OsCLSY3 is essential for rice endosperm development and imprinting, acting as an upstream player in sRNA pathway. Comparative transcriptome and genetic analysis indicated its endosperm-preferred expression and its paternally imprinted nature. These important features were modulated by RNA-directed DNA methylation (RdDM) of tandemly arranged TEs in its promoter. Upon perturbation of OsCLSY3 in transgenic lines we observed defects in endosperm development and loss of around 70% of all sRNAs. Interestingly, well-conserved endosperm-specific sRNAs (siren) that are vital for reproductive fitness in angiosperms were dependent on OsCLSY3. We also observed many imprinted genes and seed development-associated genes under the control of CLSY3-dependent RdDM. These results support an essential role of OsCLSY3 in rice endosperm development and imprinting, and propose similar regulatory strategies involving CLSY3 homologs among other cereals. HighlightsO_LIUnlike among dicots, in rice and maize, CLSY3 is a maternally expressed imprinted gene majorly expressed in endosperm. C_LIO_LIEndosperm-preferred expression of OsCLSY3 is regulated by RNA-directed DNA methylation at two tandem transposon elements present in its promoter. C_LIO_LIOsCLSY3 is crucial for endosperm development and grain filling. It regulates expression of key seed development and endosperm-specific imprinted genes through RNA directed DNA methylation. C_LI

plant biology↗

bioRxiv2023

Oryza genera-specific novel Histone H4 variant predisposes H4 Lysine5 Acetylation marks to modulate salt stress responses

Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the occurrence, mechanism of action and functional significance of several variants of core histones are well known except that of histone H4. Here we show that a novel variant of H4 (H4.V), expressing tissue-specifically among members of Oryza genera, mediates specific epigenetic changes contributing majorly to salt tolerance. H4.V was incorporated to specific chromosomal locations where it blocked deposition of active histone marks. Under salt stress, large scale re-distribution of H4.V enabled incorporation of stress dependent histone H4 Lysine5 Acetylation (H4K5Ac) marks. Mis-expression of H4.V led to defects at morphological level especially in reproductive tissues, and in mounting stress responses. H4.V mediated these alterations by condensing chromatin at specific genomic regions as seen with cryo-EM structure of reconstituted H4.V containing nucleosomes. These results not only uncovered the presence of a H4 variant in plants, but also a novel chromatin regulation of stress responses that might have contributed to success of semi-aquatic Oryza members under variable water-limiting conditions. One-line summaryHistone H4 variant predisposes chromatin for stress responses O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/551207v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@101fa0forg.highwire.dtl.DTLVardef@c7fda9org.highwire.dtl.DTLVardef@1de9a0aorg.highwire.dtl.DTLVardef@1532641_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2023

Wound induced small-peptide mediated signalling cascade regulated by OsPSKR, dictates balance between growth and defense in rice

Wounding is a general stress in plants that results from various pest and pathogenic infections in addition to environment induced mechanical damages. Plants have sophisticated molecular mechanisms to recognize and respond to pests and pathogens. Although several molecules such as phytohormones, peptides and receptors have been attributed to wound responses in dicots, such mechanisms for monocots probably having distinct wound responses are less understood. Here, we show the involvement of two distinct categories of temporally separated, endogenously derived peptides, namely, plant elicitor peptides (PEPs) and phytosulfokine (PSK), that mediate wound responses in rice. These peptides trigger a dynamic signal relay in which a novel receptor kinase named OsPSKR played a major role. OsPSKR perceived PSK ligand, acting in association with a co-receptor OsSERK1, to activate downstream responses in a kinase activity-dependent manner. Perturbation of OsPSKR expression in rice led to compromised development and constitutive autoimmune phenotypes. These results suggested that OsPSKR maintains the trade-off between growth and exaggerated defense responses, both during homeostasis and wounding. Collectively, these findings indicate the presence of a stepwise peptide-mediated signal relay that regulates the transition from defense to growth upon wounding in monocots. One line summaryEndogenous peptide signalling initiated wound responses through a receptor-like kinase OsPSKR to maintain the balance between growth and defense responses.

plant biology↗

bioRxiv2021

Geminiviral βC1 orchestrates organellar genomic instability to augment viral infection by hijacking host RecA

Chloroplast is the site for transforming light energy to chemical energy. It also acts as a production unit for a variety of defense-related molecules. These defense moieties are necessary to mount a successful counter defence against pathogens including viruses. Geminiviruses disrupt chloroplast homeostasis as a basic strategy for their successful infection inducing vein-clearing, mosaics and chlorosis in infected plants. Here we show that a geminiviral pathogenicity determinant protein {beta}C1 directly interferes with plastid homeostasis. {beta}C1 was capable of inducing organelle-specific nuclease to degrade plastid genome as well as diverted functions of RecA1 protein, a major player in plastid genome maintenance. {beta}C1 interacted with RecA1 in plants and its homolog in bacteria to reduce the ability of host cells to maintain genomic integrity under stresses. Further, reduction in the coding capacity of plastids severely affected retrograde signalling necessary for viral perception and activation of defense. Induction of chloroplast-specific nuclease by {beta}C1 is similar to phosphate starvation-response in which nucleotides are recycled to augment synthesis of new, potentially viral, DNA. These results indicate the presence of a novel strategy in which a viral protein alters host defence by targeting regulators of chloroplast DNA. We predict that the mechanism identified here might have similarities in other plant-pathogen interactions. One line summary{beta}C1 alters plastid genome metabolism.

plant biology↗

bioRxiv2021

Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains

Across eukaryotes, gene regulation is manifested via chromatin states roughly distinguished as heterochromatin and euchromatin. The establishment, maintenance and modulation of the chromatin states is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein coding genes are poorly understood. Here we show that a plant specific paralogue of RNA polymerase (pol) II, named pol IV, is involved in avoidance of facultative heterochromatic marks in protein coding genes, in addition to its well-established functions in silencing repeats and transposons. In its absence, H3K27 trimethylation (me3) mark intruded the protein coding genes, more profoundly in genes embedded with repeats. In a subset of genes, spurious transcriptional activity resulted in small(s) RNA production leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with larger genome with distributed heterochromatin when compared to Arabidopsis. Our results indicate the surprising division of labour among plant-specific polymerases, not just in establishing effective silencing via sRNAs and DNA methylation, but also in influencing chromatin boundaries.

molecular biology↗

bioRxiv2020

Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

tRNA-derived fragments (tRFs) have recently gained a lot of scientific interest due to their diverse regulatory roles in several cellular processes. However, their function in dynamic biological process such as development and regeneration remains unexplored. Here, we identify and characterise a role for tRFs in planarian regeneration. In order to characterise planarian tRFs, we first annotated 457 tRNA loci in S.mediterranea combining two tRNA prediction programs. Annotation of tRNAs facilitated the identification of three main species of tRFs in planarians - the shorter tRF-5s and itRFs, and the abundantly expressed 5-tsRNAs. Spatial profiling of tRFs in sequential transverse sections of planarians revealed diverse expression patterns of these small RNAs, including those that are enriched in the head and pharyngeal regions. Expression analysis of these tRF species revealed dynamic expression of these small RNAs over the course of regeneration suggesting an important role in planarian anterior and posterior regeneration. Finally, we show that 5-tsRNA in planaria interact with all three SMEDWI proteins while sequence analysis revealed a possible involvement of Dicers in the processing of itRFs. In summary, our findings implicate a novel role for tRFs in planarian regeneration, highlighting their importance in regulating complex systemic processes. Our study adds to the catalogue of post-transcriptional regulatory systems in planarian, providing valuable insights on the biogenesis and the function of tRFs in neoblasts and planarian regeneration.

molecular biology↗

bioRxiv2019

Phenotypic diversity of Methylobacterium associated with rice landraces in Northeast India

The ecology and distribution of many bacteria is strongly associated with specific eukaryotic hosts. However, the impact of such host association on bacterial ecology and evolution is not well understood. Bacteria from the genus Methylobacterium consume plant-derived methanol, and are some of the most abundant and widespread plant-associated bacteria. In addition, many of these species impact plant fitness. To determine the ecology and distribution of Methylobacterium in nature, we sampled bacteria from 36 distinct rice landraces, traditionally grown in geographically isolated locations in North-East (NE) India. These landraces have been selected for diverse phenotypic traits by local communities, and we expected that the divergent selection on hosts may have also generated divergence in associated Methylobacterium strains. We determined the ability of 91 distinct rice-associated Methylobacterium isolates to use a panel of carbon sources, finding substantial variability in carbon use profiles. Consistent with our expectation, across spatial scales this phenotypic variation was largely explained by host landrace identity rather than geographical factors or bacterial taxonomy. However, variation in carbon utilisation was not correlated with sugar exudates on leaf surfaces, suggesting that bacterial carbon use profiles do not directly determine bacterial colonization across landraces. Finally, experiments showed that at least some rice landraces gain an early growth advantage from their specific phyllosphere-colonizing Methylobacterium strains. Together, our results suggest that landrace-specific host-microbial relationships may contribute to spatial structure in rice-associated Methylobacterium in a natural ecosystem. In turn, association with specific bacteria may provide new ways to preserve and understand diversity in one of the most important food crops of the world.

ecology↗