Biology subjects

Sureshkumar, S.

Publications and source records attributed to Sureshkumar, S..

7 recordsLinked to original sources

bioRxiv2025

Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis

Short tandem repeats (STRs) mutations are one of the most important fuels of evolution, but are often largely ignored despite their huge effects on phenotypic variations. Here, we leveraged seven Arabidopsis mutation accumulation lines to assess the STR mutation rate, which ranged from 1.93x10-2 to 4.40x10-3 per STR locus per generation and was much higher than the common SNP mutation rate at the level of 10-9-10-8. Interspecific comparison revealed rapid STR turnover, with a large proportion (71.8%) only present in Arabidopsis. In addition, intraspecific comparison of the ten assembled Arabidopsis genomes revealed that 29.3% of STRs were presence/absence variation (PAV), 36.5% of STRs were length variation (LV), 13.0% of STRs were no variation (NV) and the 21.1% STR loci with both LV and PAV. Based on 413 RNA-seq datasets, we identified that length variation of 3,871 STR loci (eSTRs) was associated with gene expression and 651 STR loci (sSTRs) were associated with splicing variation, and over one thousand eSTRs or sSTRs were linked with published genome-wide association study signals. In addition, a direct association between STR length variation and phenotypic variation uncovered a series of STR-trait associations. More notably, using the expression levels of 24,175 genes, the splice strength values of 12,784 splice sites, and 16 phenotypes of natural Arabidopsis populations, we revealed that the STR heritability is 0.111, 0.143 and 0.101, respectively. Overall, our results not only revealed the evolutionary dynamics of STRs, but highlighted the importance of STR variations as an important contributor to missing heritability in the regulation of complex traits.

evolutionary biology↗

bioRxiv2024

REDD1 is a determinant of the sensitivity of renal cell carcinoma cells to autophagy inhibition that can be therapeutically exploited by targeting PIM kinase activity

PurposeRepurposing FDA approved drugs with off-target autophagy inhibition such as chloroquine/hydroxychloroquine (CQ, HCQ) has produced modest anticancer activity in clinical trials, due in part, to a failure to define predictive biomarkers that enable the selection of patients that best respond to this treatment strategy. We identified a new role for REDD1 as a determinant of sensitivity to autophagy inhibition in renal cell carcinoma (RCC). Experimental DesignRNA sequencing, qRT-PCR, immunoblotting, gene silencing, knockout and overexpression studies revealed that REDD1 expression is a key regulator of cell death stimulated by autophagy inhibitors. Comprehensive in vitro and in vivo studies were conducted to evaluate the selectivity, tolerability, and efficacy of the PIM kinase inhibitor TP-3654 and CQ in preclinical models of renal cell carcinoma (RCC). Markers of autophagy inhibition and cell death were evaluated in tumor specimens. ResultsTranscriptomic analyses identified REDD1 (DDIT4) as a highly induced gene in RCC cells treated with the PIM kinase inhibitor TP-3654. Focused studies confirmed that PIM1 inhibition was sufficient to induce REDD1 and stimulate autophagy through the AMPK cascade. DDIT4 knockout and overexpression studies established its mechanistic role as a regulator of sensitivity to autophagy inhibition. Inhibition of autophagy with CQ synergistically enhanced the in vitro and in vivo anticancer activity of TP-3654. ConclusionsOur findings identify REDD1 as a novel determinant of the sensitivity of RCC cells to autophagy inhibition and support further investigation of PIM kinase inhibition as a precision strategy to drive sensitivity to autophagy-targeted therapies through REDD1 upregulation. Translational RelevancePIM kinases are overexpressed in renal cell carcinoma (RCC) and other malignancies. Here we show that targeting PIM1 significantly upregulates REDD1/DDIT4 expression, resulting in inhibition of mTOR and autophagy activation. REDD1 induction was determined to be a major factor that regulates the sensitivity of RCC cells to autophagy inhibition. Comprehensive in vitro and in vivo studies in preclinical models of RCC demonstrated that the PIM kinase inhibitor TP-3654 induced REDD1-mediated autophagy and synergistically sensitized cells to autophagy inhibition. Our findings define a new role for REDD1 as a determinant of the sensitivity of RCC cells to autophagy inhibition and demonstrate that antagonizing PIM kinase activity is a precision approach to augment REDD1 levels and potentiate the therapeutic benefit of targeting the autophagy pathway.

pharmacology and toxicology↗

bioRxiv2024

A basic framework governing splice-site choice in eukaryotes

Changes in splicing are observed between cells, tissues, organs, individuals, and species. These changes can mediate phenotypic variation ranging from flowering time differences in plants to genetic diseases in humans. However, the genomic determinants of splicing variation are largely unknown. Here, we quantified the usage of individual splice-sites and uncover extensive variation between individuals (genotypes) in Arabidopsis, Drosophila and Humans. We used this robust quantitative measure as a phenotype and mapped variation in splice-site usage using Genome-Wide Association Studies (GWAS). By carrying out more than 130,000 GWAS with splice-site usage phenotypes, we reveal genetic variants associated with differential usage of specific splice-sites. Our analysis conclusively shows that most of the common, genetically controlled variation in splicing is cis and there are no major trans hotspots in any of the three analyzed species. High-resolution mapping allowed us to determine genome-wide patterns that govern splice-site choice. We reveal that the variability in the intronic hexamer sequence (GT[N]4 or [N]4AG) differentiates intrinsic splice-site strength and is among the primary determinants of splice-site choice. Experimental analysis validates the primary role for intronic hexamer sequences in conferring splice-site decisions. Transcriptome analyses in diverse species across the tree of life reveals that hexamer rankings explains splice-site choices from yeast to plants to humans, forming the basic framework of the splicing code in eukaryotes.

genetics↗

bioRxiv2023

SUMO protease FUG1, histone reader AL3 and the PRC1 Complex are integral to repeat-expansion induced epigenetic silencing in Arabidopsis thaliana

Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreichs ataxia in humans1. The molecular mechanisms underlying repeat expansion-induced epigenetic silencing remain largely unknown2,3. Using a plant model, we have previously shown that expanded repeats can induce smallRNAs which in turn can lead to epigenetic silencing through the RNA-dependent DNA methylation pathway4,5. Here, using a genetic suppressor screen, we confirm a key role for the RdDM pathway and identify novel components required for epigenetic silencing caused by expanded repeats. We show that FOURTH ULP LIKE GENE CLASS 1 (FUG1) - a SUMO protease, ALFIN-LIKE 3 - a histone reader and LIKE HETEROCHROMATIN 1 (LHP1) - a component of the PRC1 complex are required for repeat expansion-induced epigenetic silencing. Loss of any of these components suppress repeat expansion-associated phenotypes. SUMO protease FUG1 physically interacts with AL3 and perturbing its potential SUMOylation site disrupts its nuclear localisation. AL3 physically interacts with LHP1 of the PRC1 complex and the FUG1-AL3-LHP1 module is essential to confer repeat expansion-associated epigenetic silencing. Our findings highlight the importance post-translational modifiers and histone readers in epigenetic silencing caused by repeat expansions.

genetics↗

bioRxiv2020

Splice-site Strength Estimation: A simple yet powerful approach to analyse RNA splicing

RNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms1-3. Current approaches for analysing splicing rely on quantifying variant transcripts (i.e., isoforms) or splicing events (i.e., intron retention, exon skipping etc)4, 5. However, regulation of splicing occurs at the level of selection of individual splice sites, which results in variation in the abundance of isoforms and/or splicing events. Here, we present a simple approach to quantify the strength of individual splice sites, which determines their selection in a splicing reaction. Splice-site strength, as a quantitative phenotype, allows us to analyse splicing precisely in unprecedented ways. We demonstrate the power of this approach in defining the genomic determinants of the strength of individual splice-sites through GWAS. Our pilot-GWAS with more than thousand splice sites hints that cis-sequence divergence and competition between splice-sites and are among the primary determinants of variation in splicing among natural accessions of Arabidopsis thaliana. This approach allows deciphering the principles of splicing, which in turn has implications that range from agriculture to medicine.

genetics↗

bioRxiv2019

GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

Transition to flowering at the right time is critical for local adaptation and to maximize seed yield in canola, which is an important oilseed crop. There is extensive variation among canola varieties in flowering time. However, our understanding of underlying genes and their role in canola productivity is still limited. We reveal natural variation in flowering time and response to photoperiod in a diverse GWAS panel (up to 368 accessions) of canola and identify associated SNPs across multiple experiments. Complementary QTL and eQTL mapping studies were also conducted in an Australian doubled haploid (DH) population for flowering time and other grain yield related traits. We show that several associations that were repeatedly detected across experiments map in the vicinity of FLOWERING LOCUS T (FT) paralogues and its known transcriptional regulators. QTL mapping study in a DH population detected consistent genomic regions close to FT paralogs. FT sequences vary between accessions and FT expression in field and controlled environment grown plants was correlated with flowering time. FT paralogs displayed association not only with flowering time, but also with plant emergence, shoot biomass and grain yield. Our findings suggest that FT paralogs not only modulate flowering time but also modulate yield-related productivity traits in canola. HighlightThe genetic association, eQTL and expression analyses suggest that FT paralogs have multifaceted roles in canola flowering time, plant development and productivity traits.

plant biology↗

bioRxiv2017

POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana

Ambient temperature influences plant growth and development and minor changes can substantially impact crop yields. The underlying mechanisms for temperature perception and response are just beginning to emerge. Chromatin remodeling via the eviction of the histone variant H2A.Z in nucleosomes that alters gene expression is a critical component of thermal response in plants. However, whether chromatin-remodeling processes such as histone modifications play a global role in thermal response remains unknown. Using a combination of genetic analysis, chemical inhibition studies and RNA-seq analysis coupled with meta-analysis, here we identify POWERDRESS (PWR), a SANT-domain containing protein that is known to interact with HISTONE DEACETYLASE 9 (HDA9), as a novel key factor required for thermomorphogenesis in Arabidopsis thaliana. We identify that mutations in PWR impede thermomorphogenesis exemplified by severely attenuated temperature-induced hypocotyl/petiole elongation and early flowering. We show that inhibitors of histone deacetylases diminish temperature-induced hypocotyl elongation, which demonstrates for the first time a requirement for histone deacetylation in thermomorphogenesis. Genes that are misregulated in pwr mutants showed enrichment for GO terms associated with \"response\". Our expression studies coupled with meta-analysis revealed a significant overlap between genes misregulated in pwr mutants and genes that are enriched for H2A.Z in their gene bodies. Meta-analyses reveal that genes misregulated in pwr mutants in diverse conditions also overlap with genes that are differentially expressed in the mutants of the components of the SWR1 complex that mediates H2A.Z nucleosome dynamics. Our findings thus uncover a role for PWR in facilitating thermal response and suggest a potential link between histone deacetylation and H2A.Z nucleosome dynamics in regulation of gene expression in plants.\n\nAuthor summaryPlant growth and development is influenced by a variety of external environmental cues. Ambient temperature affects almost all stages of plant development but the underlying molecular mechanisms remain largely unknown. In this paper, the authors show that histone deacetylation, one of the major chromatin remodeling processes, is essential for eliciting growth temperature-induced responses in plants. The authors identify POWERDRESS, a protein known to interact with HISTONE DEACETYLASE 9, as a novel key player essential for eliciting high temperature induced responses in Arabidopsis. Another chromatin remodeling mechanism that is known to play a role in thermal response is the eviction of histone variant H2A.Z from nucleosomes. Through transcriptome studies the authors demonstrate an overlap between gene regulations conferred through PWR-mediated histone H3 deacetylation and that conferred via histone H2A.Z eviction/incorporation dynamics. This study identifies a key novel gene that is essential for plants to elicit high temperature responses and reveals close links between two seemingly distinct chromatin-remodeling processes in regulating gene expression in plants.

genetics↗