Biology subjects

Bandyopadhyay, T.

Publications and source records attributed to Bandyopadhyay, T..

4 recordsLinked to original sources

bioRxiv2024

Histone H2B Monoubiquitylation Regulates Elongation-to-Termination Transition in RNA Polymerase II Transcription

RNA Polymerase II (Pol II)-dependent transcription is meticulously regulated during initiation, elongation, termination, and two pivotal transitions: from initiation to elongation and from elongation to termination 1. The successful transition from elongation to termination is vital for accurate transcription termination 2,3. While elongation and termination have been extensively studied, the regulatory mechanisms governing the transition between these stages are not fully understood. Here we report that, in fission yeast Schizosaccharomyces pombe (S. pombe) and human cells, Cdk9 and its cyclin partner (Cyclin T in humans, and Pch1 in S. pombe) disengage from the elongation machinery near gene 3-ends, as Pol II crosses the cleavage and polyadenylation signal (CPS). Concurrently, chromatin immunoprecipitation (ChIP) data shows an increased association of Dis2 (the PP1 ortholog in S. pombe)4 beyond the CPS. Additionally, ChIP-seq indicates that histone H2B monoubiquitylation (H2Bub1) is pivotal for Cdk9 occupancy but serves differential roles along the gene. H2Bub1 facilitates Cdk9 chromatin recruitment during elongation but prompts Cdk9 dissociation from the elongation complex as Pol II traverses the CPS. Furthermore, in S. pombe, disruptions of H2Bub1 in htb1-K119R 5 and sustained levels in ubp8D 6 inversely affect the chromatin occupancy of Pol II, Pol II CTD phosphorylation within the heptad repeats, Spt5, phosphorylated Spt5 (pSpt5), Dis2, components of the mRNA 3-end processing complex (Pfs2 and Pla1), and termination factors Rhn1 (Rtt103) and Pcf1 around the CPS-- diminishing with H2Bub1 loss and increasing with H2Bub1 stabilization. In essence, our data indicates that the H2Bub1-mediated eviction of Cdk9 as Pol II navigates the CPS precipitates a rise in PP1 binding, which, in turn, dephosphorylates pSpt5, slowing Pol II to facilitate efficient termination. The unique modulation of Cdk9 occupancy by H2Bub1 during transcription progression presents a compelling, novel concept requiring further exploration.

molecular biology↗

bioRxiv2020

Grain number and genotype drive nitrogen-dependent yield response in the C4 model Setaria italica (L.) P. Beauv.

Fertiliser nitrogen (N) drives crop yields and requires the breeding and selection of cultivars that are inherently highly N responsive. For major cereal crops such as wheat (Triticum aestivum L.) breeding over time has led to enhanced N use in modern cultivars however there remains a gap in understanding the N responsiveness of minor cereals grains, many of which are highly relevant to global food security. Here we investigate response to increasing N availability in a diverse population of Setaria italica (L., foxtail millet) accessions demonstrating that N-driven yield increase is dependent on grain number rather than individual grain weight. Within the population, some accessions responded strongly to increased N availability while others show little yield improvement under high N. Genetic markers were generated to enable investigation of N responsiveness at a genome-wide level, highlighting likely underlying causal loci, especially for grains per plant. Despite the lack of response in terms of yield increase, a non-responsive accession shows a strong transcriptional response suggesting different metabolic functioning under high vs low N. Our results show major differences in N responsiveness in S. italica and provide novel insight into the genetic and molecular basis for this variation. One sentence summaryNitrogen dependent yield response in Setaria italica L. is driven by grain number and genotypes with low N yield responsive genotypes being more transcriptionally dynamic under varied N levels post-flowering compared to high N yield responsive genotypes.

plant biology↗

bioRxiv2019

Draft genome sequence of a popular Indian tea genotype TV-1

Camellia assamica L. (O). Kuntze. var. TV-1 from Assam, India is one of the most important tea cultivar of Indian Tea Industry which botanically belongs to Assam type and has distinct morphological as well as chemical constituent in leaf than China type of tea. We here present the first draft genome sequence of TV-1, assembled in 2.93 Gb size comprising of 14,824 scaffolds and covering 97.66% of the predicted genome size (3.0 Gb) as determined by flow cytometry. The N50 value, longest and average contig size for this draft genome was found to be as 538.96 Kb, 3.64 Mb and 197.99 Kb, respectively. There were 495,747 SSRs (Di- to Hexa-mers) in the genome and the repeat contents accounted for 71.87% of the genome. About 94.40% genome completeness was predicted with BUSCO, maximum among the published and reported tea genomes. The clustering of the assembled genome with Hi-C data resulted in 15 clusters ranging from the size of 631.46 Mb to 14.39 Mb and accounting 99.32% of assembled genome. This data will act as the starting point for unravelling the important genes and differentiating Indian tea from other commercially available tea varieties.

plant biology↗

bioRxiv2018

Theaflavins, polyphenols of black tea, inhibit entry of hepatitis C virus

The treatment of hepatitis C virus (HCV) infection by combination of direct acting antivirals (DAA), with different mode of action, has made substantial progress in the past few years. However, appearance of resistance and high cost of the therapy is still an obstacle in the achievement of the therapy, more specifically in developing countries. In this context, search for affordable antivirals with new mechanisms of action is still needed. Tea, after water, is the most popular drink worldwide. Polyphenols extracted from green tea have already shown anti-HCV activity as entry inhibitors. Here, three different theaflavins, theaflavin (TF1), theaflavin-3-monogallate (TF2), and theaflavin-3-3-digallate (TF3), which are major polyphenols from black tea, were tested against HCV in cell culture. The results showed that all theaflavins inhibit HCV infection in a dose-dependent manner in an early step of infection. Results obtained with HCV pseudotyped virions confirmed their activity on HCV entry and demonstrated their pan-genotypic action. No effect on HCV replication was observed by using HCV replicon. Investigation on the mechanism of action of black tea theaflavins showed that they act directly on the virus particle and are able to inhibit cell-to-cell spread. Combination study with inhibitors most widely used in anti-HCV treatment regimen demonstrated that TF3 exerts additive effect. In conclusion, theaflavins, that are present in high quantity in black tea, are new inhibitors of HCV entry and hold promise for developing in therapeutic arsenal for HCV infection.

microbiology↗