Biology subjects

Boopathi, R.

Publications and source records attributed to Boopathi, R..

4 recordsLinked to original sources

bioRxiv2026

ULTRAPETALA1 remodels PRC2 recruitment to nucleosomes

Polycomb Repressive Complex 2 (PRC2) establishes transcriptional repression through trimethylation of histone H3 lysine 27 (H3K27me3), a modification essential for developmental patterning. Here, we describe a novel plant-specific PRC2 variant (PRC2.3) that employs a distinct nucleosome-targeting mechanism mediated by accessory factor ULTRAPETALA1 (ULT1), which promotes H3K27me3 deposition at over 1,300 developmental genes. The cryo-EM structure of the PRC2SWN-ULT1-nucleosome complex reveals that ULT1 antagonizes the canonical PRC2 binding mode and instead bridges PRC2 to the nucleosome using its own interaction surfaces. ULT1 binds consecutive purines in the nucleosomal DNA and the histone H2A/H2B acidic patch, while enabling PRC2 to accommodate H3K36 modifications. We further show that in planta ULT1 enhances H3K27me3 at purine-rich loci and at genes associated with H3K36 marks, and identify the ULT1-H2A/H2B interface as required for reproductive transition and flower organogenesis. Our findings demonstrate that PRC2 can deploy mechanistically distinct recruitment strategies to control key developmental switches.

Molecular Biology↗

bioRxiv2021

Differential Histone-DNA Interactions Dictate Nucleosome Recognition of the Pioneer Transcription Factor Sox

Pioneer transcription factors (PTFs) have the remarkable ability to directly bind to chromatin for stimulating vital cellular processes. In this work, we dissect the universal binding mode of Sox PTF by combining extensive molecular simulations and DNA footprinting techniques. As a result, we show that when Sox consensus DNA is located at the solvent-facing DNA strand, Sox binds to the compact nucleosome without imposing any significant conformational changes. We also reveal that the basespecific Sox:DNA interactions (base reading) and the Sox-induced DNA changes (shape reading) are concurrently required for the sequence-specific DNA recognition. Among different nucleosomal positions, such a specific reading mechanism is satisfied solely at superhelical location 2 (SHL2). While SHL2 acts transparently to Sox binding, SHL4 permits only shape reading, and SHL0 (dyad) allows no reading mechanism. These findings demonstrate for the first time that Sox-based nucleosome recognition is essentially guided by the distinct histone-DNA interactions, permitting varying degrees of DNA flexibility.

biophysics↗

bioRxiv2019

Aurora kinase A mediated phosphorylation of mPOU is critical for skeletal muscle differentiation

Aurora kinases are Ser/Thr-directed protein kinases which play pivotal roles in mitosis. Recent evidences highlight the importance of these kinases in non-mitotic biological events like skeletal myogenesis. Our earlier study identified POU6F1 (or mPOU) as a novel Aurora kinase A (AurkA) substrate. Here, we report that AurkA phosphorylates POU6F1 at Ser197 and inhibits its DNA binding ability. Delving into POU6F1 physiology, we find that the phospho-mimic (S197D) POU6F1 mutant exhibits enhancement, while wild type (WT) or phospho-deficient (S197A) mutant shows retardation in C2C12 myoblast differentiation. Interestingly, POU6F1 depletion phenocopies S197D-POU6F1 overexpression in the differentiation context. Collectively, our results signify mPOU as a negative regulator of skeletal muscle differentiation and strengthens the importance of AurkA in skeletal myogenesis.

cell biology↗

bioRxiv2019

The Largest Subunit of Human TFIIIC Complex, TFIIIC220, a Lysine Acetyltransferase Targets Histone H3K18

TFIIIC is a multisubunit complex that recognizes promoter elements and recruits TFIIIB and RNA polymerase III. Human TFIIIC complex possess lysine acetyltransferase activity which is critical in relieving chromatin mediated repression for RNA polymerase III-mediated transcription; two subunits of the TFIIIC complex, TFIIIC110 and TFIIIC90, were shown to acetylate H3 in vitro. Here we show that the largest and DNA binding subunit of TFIIIC complex, TFIIIC220, possesses intrinsic lysine acetyltransferase activity and acetylates histone H3K18 residue. By employing homology search we have identified the potential catalytic domain of TFIIIC220 which efficiently acetylate core histones in vitro. Point mutations at the critical residues of the identified acetyltransferase domain drastically reduces the acetyltransferase activity. Significantly, knockdown of TFIIIC220 in HepG2 cell line dramatically reduces global H3K18 acetylation level suggesting that TFIIIC220 is a crucial KAT to maintain acetylation homeostasis in the cell.

molecular biology↗