Browsing by Author "Junaid, Alim"

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Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo
(Life Science Alliance LLC, 2024) Junaid, Alim; Singh, Baljinder; Bhatia, Sabhyata
Eukaryotic genomes show an intricate three-dimensional (3D) organization within the nucleus that regulates multiple biological processes including gene expression. Contrary to animals, understanding of 3D genome organization in plants remains at a nascent stage. Here, we investigate the evolution of 3D chromatin architecture in legumes. By using cutting-edge PacBio, Illumina, and Hi-C contact reads, we report a gap-free, chromosome-scale reference genome assembly of Vigna mungo, an important minor legume cultivated in Southeast Asia. We spatially resolved V. mungo chromosomes into euchromatic, transcriptionally active A compartment and heterochromatic, transcriptionally-dormant B compartment. We report the presence of TAD-like-regions throughout the diagonal of the HiC matrix that resembled transcriptional quiescent centers based on their genomic and epigenomic features. We observed high syntenic breakpoints but also high coverage of syntenic sequences and conserved blocks in boundary regions than in the TAD-like region domains. Our findings present unprecedented evolutionary insights into spatial 3D genome organization and epigenetic patterns and their interaction within the V. mungo genome. This will aid future genomics and epigenomics research and breeding programs of V. mungo.
Integrated genomic approaches delineate the novel role of ROP1 ENHANCER1 in regulating seed protein content of chickpea
(Oxford University Press, 2023) Chakraborty, Anirban; Junaid, Alim; Parida, Swarup K.; Bhatia, Sabhyata
Utilizing a combinatorial approach of QTL-Seq and candidate gene-based association mapping, the QTLs and genes responsible for seed protein content (SPC), a major quality trait in chickpea were identified. Whole Genome Re-sequencing based QTL-Seq analysis of bulked RILs from a mapping population contrasting for SPC led to identification of two QTLs (0.94 Mb on Linkage Group (LG)5 and 1.16 Mb on LG6) encompassing three SNPs displaying the highest ΔSNP-index. These highly significant SNPs and their associated genes were validated in 211 chickpea mini-core accessions varying in SPC that revealed a tightly associated marker affecting CaREN1 (ROP1 ENHANCER1) with phenotypic variation explained of 23%. This SNP was subsequently converted into a cost effective allele specific PCR based marker that could be utilized for rapid screening of SPC during marker assisted breeding. Further, in planta functional validation via knockdown of CaREN1 led to significant reduction in SPC of chickpea. This decrease in seed protein is likely due to disruption in the formation of CaREN1 protein complexes comprising of chaperones, phosphopeptide-binding proteins and GTPases that mediate folding, transport and accumulation of seed storage proteins as indicated through AP-MS. Taken together, the information generated would expedite tailoring of chickpea cultivars with augmented SPC.
MEDIATOR SUBUNIT17 integrates jasmonate and auxin signaling pathways to regulate thermomorphogenesis
(Oxford University Press, 2022) Agrawal, Rekha; Sharma, Mohan; Dwivedi, Nidhi; Maji, Sourobh; Thakur, Pallabi; Junaid, Alim; Fajkus, Jiří; Laxmi, Ashverya; Thakur, Jitendra K.
Plant adjustment to environmental changes involves complex crosstalk between extrinsic and intrinsic cues. In the past two decades, extensive research has elucidated the key roles of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and the phytohormone auxin in thermomorphogenesis. In this study, we identified a previously unexplored role of jasmonate (JA) signaling components, the Mediator complex, and their integration with auxin signaling during thermomorphogenesis in Arabidopsis (Arabidopsis thaliana). Warm temperature induces expression of JA signaling genes including MYC2, but, surprisingly, this transcriptional activation is not JA dependent. Warm temperature also promotes accumulation of the JA-signaling receptor CORONATINE INSENSITIVE1 (COI1) and degradation of the JA-signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9 (JAZ9), which probably leads to de-repression of MYC2, enabling it to contribute to the expression of MEDIATOR SUBUNIT17 (MED17). In response to warm temperature, MED17 occupies the promoters of thermosensory genes including PIF4, YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE19 (IAA19), and IAA29. Moreover, MED17 facilitates enrichment of H3K4me3 on the promoters of PIF4, YUC8, IAA19, and IAA29 genes. Interestingly, both occupancy of MED17 and enrichment of H3K4me3 on these thermomorphogenesis-related promoters are dependent on PIF4 (or PIFs). Altered accumulation of COI1 under warm temperature in the med17 mutant suggests the possibility of a feedback mechanism. Overall, this study reveals the role of the Mediator complex as an integrator of JA and auxin signaling pathways during thermomorphogenesis.