Biology subjects

Srikant, T.

Publications and source records attributed to Srikant, T..

5 recordsLinked to original sources

bioRxiv2026

Chromosomal breakage in Arabidopsis thaliana neo-polyploids occurs preferentially at candidate fragile sites colocalized with ancient genome rearrangements

Newly formed polyploids often suffer extensive aneuploidy and chromosome rearrangement. We explored whether these are predictable and conserved across genotypes. We quantified whole-chromosome and segmental aneuploidy in progeny arrays of neo-polyploid Arabidopsis thaliana from two accessions (Col-0 and Ler). 29% of progeny had whole-chromosome and/or segmental aneuploidies. Strikingly, segmental aneuploidy arose exclusively from Ler, preferentially maternally, showing that genotype and sex of origin matter. Breakpoints of segmental aneuploidies were non-random, with over 2/3 mapping to five potentially fragile regions (PFRs). Two PFRs overlap with junctions of ancient chromosomal fusions that differentiate the A. thaliana genome from that of its relatives and also overlap more broadly with hotspots of recurrent chromosomal rearrangements differentiating species in the Brassicaceae family. Several PFRs overlap with large tandemly repeated disease resistance gene clusters. Our results support the hypothesis of a link between ancestral genome rearrangements and present-day chromosome fragility. Polyploidy serving as a context that makes aneuploidies more likely to arise and survive, with fragile sites lending a degree of predictability.

genomics↗

bioRxiv2022

Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation

BACKGROUNDEukaryotes employ epigenetic marks such as DNA methylation at cytosines both for gene regulation and genome defense. In Arabidopsis thaliana, a central role is played by methylation in the CG context, with profound effects on gene expression and transposable element (TE) silencing. Nevertheless, despite its conserved role, genome-wide CG methylation differs substantially between wild A. thaliana accessions. RESULTSWe hypothesized that global reduction of CG methylation would reduce epigenomic, transcriptomic and phenotypic diversity in A. thaliana accessions. To test our hypothesis, we knocked out MET1, which is required for CG methylation, in 18 early-flowering A. thaliana accessions. Homozygous met1 mutants in all accessions suffered from a range of common developmental defects such as dwarfism and delayed flowering, in addition to accession-specific abnormalities in rosette leaf architecture, silique morphology and fertility. Integrated analysis of genome-wide methylation, chromatin accessibility and transcriptomes confirmed that inactivation of MET1 greatly reduces CG methylation and alters chromatin accessibility at thousands of loci. While the effects on TE activation were similarly drastic in all accessions, the quantitative effects on non-TE genes varied greatly. The expression profiles of accessions became considerably more divergent from each other after genome-wide removal of CG methylation, although the expression of genes with diverse expression profiles across wild-type accessions tended to become more similar in mutants. CONCLUSIONSOur systematic analysis of MET1 requirement for genome function in different A. thaliana accessions revealed a dual role for CG methylation: for many genes, CG methylation appears to canalize expression levels, with methylation masking regulatory divergence. However, for a smaller subset of genes, CG methylation increases expression diversity beyond genetically encoded differences.

plant biology↗

bioRxiv2022

Pervasive Under-Dominance in Gene Expression as Unifying Principle of Biomass Heterosis in Arabidopsis

Complex traits, such as growth and fitness, are typically controlled by a very large number of variants, which can interact in both additive and non-additive fashion. In an attempt to gauge the relative importance of both types of genetic interactions, we have turned to hybrids, which provide a facile means for creating many novel allele combinations. We focused on the interaction between alleles of the same locus and performed a transcriptomic study involving 141 random crosses between different accessions of the plant model species Arabidopsis thaliana. Additivity is rare, consistently observed for only about 300 genes enriched for roles in stress response and cell death. Regulatory rare-allele burden affects the expression level of these genes but does not correlate with F1 rosette size. Non-additive gene expression in F1 hybrids is much more common, with the vast majority of genes (over 90%) being expressed below parental average. Unlike in the additive genes, regulatory rare-allele burden in the non-additive gene set is strongly correlated with F1 rosette size, even though it only mildly covary with the expression level of these genes. Our study underscores under-dominance as the predominant gene action associated with emergence of rosette growth trajectories in the A. thaliana hybrid model. Our work lays the foundation for understanding molecular mechanisms and evolutionary forces that lead to dominance complementation of rare regulatory alleles.

genomics↗

bioRxiv2020

Mutation bias shapes gene evolution in Arabidopsis thaliana

Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness 1-4 and evolutionary optimization of genic mutation rates remains controversial 3,5. However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities 6, which is predicted by more recent theory to be a prerequisite for beneficial mutation rates between different classes of genes to readily evolve 7. To test this possibility, we used de novo mutations in Arabidopsis thaliana to create a high resolution predictive model of mutation rates as a function of cytogenetic features across the genome. As expected, mutation rates are significantly predicted by features such as GC content, histone modifications, and chromatin accessibility. Deeper analyses of predicted mutation rates reveal effects of introns and untranslated exon regions in distancing coding sequences from mutational hotspots at the start and end of transcribed regions in A. thaliana. Finally, predicted coding region mutation rates are significantly lower in genes where mutations are more likely to be deleterious, supported by numerous estimates of evolutionary and functional constraint. These findings contradict neutral expectations that mutation probabilities are independent of fitness consequences. Instead they are consistent with the evolution of lower mutation rates in functionally constrained loci due to cytogenetic features, with important implications for evolutionary biology8.

evolutionary biology↗

bioRxiv2019

Position-dependent effects of cytosine methylation on FWA expression in Arabidopsis thaliana

Gene expression can be modulated by epigenetic modifications to chromatin, and variants of the same locus distinguished by fixed, heritable epigenetic differences are known as epialleles. DNA methylation at cytosines is a prominent epigenetic modification, particularly in plant genomes, that can modulate gene expression. There are several examples where epialleles are associated with differentially methylated regions that affect the expression of overlapping or close-by genes. However, there are also many differentially methylated regions that have not been assigned a biological function despite their proximity to genes. We investigated the positional importance of DNA methylation at the FWA (FLOWERING WAGENINGEN) locus in Arabidopsis thaliana, a paradigm for stable epialleles. We show that cytosine methylation can be established not only over the well-characterized SINE-derived repeat elements that overlap with the transcription start site, but also in more distal promoter regions. FWA silencing, however, is most effective when methylation covers the transcription start site.

genetics↗