Biology subjects

Prajapati, H. K.

Publications and source records attributed to Prajapati, H. K..

7 recordsLinked to original sources

bioRxiv2026

Long-read DNA sequencing reveals global hypomethylation and focal hypermethylation in SDHx-deficient pheochromocytoma and paraganglioma

Pheochromocytomas and paragangliomas (PPGL) are highly heritable neuroendocrine tumors of the autonomic ganglia. Genomic DNA in most cancer cells is hypomethylated. However, DNA in PPGLs secondary to mutations in succinate dehydrogenase complex (SDHx) genes is reportedly hypermethylated due to succinate-mediated inhibition of DNA demethylases. We used nanopore long-read sequencing to characterize the methylome of tumor and white blood cell DNA from SDHx and non-SDHx PPGL patients, alongside normal adrenal medulla. We find that both SDHx and non-SDHx PPGLs are globally hypomethylated, particularly at centromeres. In normal adrenal medulla, CpG islands marked by H3K4 methylation are hypomethylated, whereas CpG islands lacking H3K4 methylation are hypermethylated. In SDHx-related PPGL, some H3K4me-marked CpG islands are hypermethylated, but most are not. We propose that DNA methylation in SDHx-related PPGL reflects the global hypomethylation generally observed in tumors, partly offset by succinate-mediated inhibition of TET DNA demethylases. Opposing effects of succinate may alter the balance between DNA methylation (indirect inhibition of the DNMT3A/B DNA methylases via inhibition of H3K4me demethylases) and DNA demethylation (inhibition of TET DNA demethylases) at active CpG islands.

genomics↗

bioRxiv2025

Sir proteins impede, but do not prevent, access to silent chromatin in living Saccharomyces cerevisiae

Gene silencing at the mating type loci in budding yeast (HMRa and HML) depends on the Sir proteins. Sir2, Sir3 and Sir4 are indispensable for silencing, whereas Sir1 has a more limited role. The Sir proteins are also involved in repression at telomeres and ribosomal DNA (rDNA) repeats. Proposed mechanisms for Sir-mediated silencing include limiting access to silenced DNA and inhibition of transcript initiation and/or elongation. Using an inducible M.SssI DNA methyltransferase expression system, we showed previously that the silenced mating type loci are methylated at a much slower rate than the rest of the genome in vivo. Here, we show that, in the absence of Sir2, Sir3 or Sir4, the silenced loci and the telomeric X elements are methylated at a similar rate to the rest of the genome, indicating that these Sir proteins impede access, but do not prevent it. The rDNA repeats are methylated faster in the absence of Sir2 and, to a lesser extent, of Sir3, but not of Sir4. The methylation rates of adjacent rDNA repeats are not strongly correlated in wild-type cells, suggesting that Sir proteins silence rDNA repeats randomly. Loss of Sir1 increases the methylation rate at HMRa but not at HML, telomeres or rDNA. Our data indicate that steric occlusion is unlikely to be the primary mechanism of silencing, since silenced DNA is accessible in vivo, albeit at a slower rate than elsewhere in the genome.

genetics↗

bioRxiv2025

The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells

The budding yeast genome is globally accessible to DNA methyltransferases in living cells, unlike in isolated nuclei, where it is mostly inaccessible. Here, we assess the roles of the RSC, ISW1 and CHD1 ATP-dependent chromatin remodelers in generating nucleosome dynamics in vivo. We compare DNA methylation rates in wild type cells and chromatin remodeler mutants by normalizing nuclear methylation rates to the non-nucleosomal mitochondrial DNA methylation rate in each strain. Depletion of subunits of the RSC, ISW1 or CHD1 ATP-dependent chromatin remodelers has little effect on normalized methylation rate. A decaying sine wave model used to fit nucleosome phasing data shows that nucleosome dynamics decrease with distance from the promoter in an Isw1/Chd1-dependent manner. Depletion of both Isw1 and Chd1 increases the methylation rate, suggesting that these remodelers act together to suppress nucleosome dynamics. Furthermore, the TFIIIB and TFIIIC transcription factors exhibit differential dynamics at tRNA genes. Our analysis provides insight into nucleosome and transcription factor dynamics in vivo. TeaserThe budding yeast ISW1 and CHD1 ATP-dependent remodelers organize chromatin on genes, slowing nucleosome dynamics in living cells.

genomics↗

bioRxiv2024

Nucleosome dynamics render heterochromatin accessible in living human cells

The eukaryotic genome is packaged into chromatin, which is composed of a nucleosomal filament that coils up to form more compact structures. Chromatin exists in two main forms: euchromatin, which is relatively decondensed and enriched in transcriptionally active genes, and heterochromatin, which is condensed and transcriptionally repressed 1-10. It is widely accepted that chromatin architecture modulates DNA accessibility, restricting the access of sequence-specific, gene-regulatory, transcription factors to the genome. Here, we measure genome accessibility at all GATC sites in living human MCF7 and MCF10A cells, using an adenovirus vector to express the sequence-specific dam DNA adenine methyltransferase. We find that the human genome is globally accessible in living cells, unlike in isolated nuclei. Active promoters are methylated somewhat faster than gene bodies and inactive promoters. Remarkably, both constitutive and facultative heterochromatic sites are methylated only marginally more slowly than euchromatic sites. In contrast, sites in centromeric chromatin are methylated slowly and are partly inaccessible. We conclude that all nucleosomes in euchromatin and heterochromatin are highly dynamic in living cells, whereas nucleosomes in centromeric -satellite chromatin are static. A dynamic architecture implies that simple occlusion of transcription factor binding sites by chromatin is unlikely to be critical for gene regulation.

genomics↗

bioRxiv2021

The evolution of regulatory elements in the emerging promoter variant strains of HIV-1

In a multicentric, observational, investigator-blinded, and longitudinal clinical study of 764 ART-naive subjects, we identified nine different promoter-variant strains of HIV-1 subtype C (HIV-1C) emerging in the Indian population, with some of these variants being reported for the first time. Unlike several previous studies, our work here focuses on the evolving viral regulatory elements, not coding sequences. The emerging viral strains contain additional copies of the existing transcription factor binding sites (TFBS), including TCF-1/LEF-1, RBEIII, AP-1, and NF-{kappa}B, created by sequence duplication. The additional TFBS are genetically diverse and may blur the distinction between the modulatory region of the promoter and the viral enhancer. In a follow-up analysis, we found trends, but not significant associations between any specific variant promoter and prognostic markers, probably because the emerging viral strains might not have established mono infections yet. Illumina sequencing of four clinical samples containing a co-infection indicated the domination of one strain over the other and establishing a stable ratio with the second strain at the follow-up time-points. Since a single promoter regulates viral gene expression and constitutes the master regulatory circuit with Tat, the acquisition of additional and variant copies of the TFBS may significantly impact viral latency and latent reservoir characteristics. Further studies are urgently warranted to understand how the diverse TFBS profiles of the viral promoter may modulate the characteristics of the latent reservoir, especially following the initiation of antiretroviral therapy. Significance StatementA unique conglomeration of TFBS enables the HIV-1 promoter to accomplish two diametrically opposite functions - transcriptional activation and transcriptional silencing. The various phases of viral latency -establishment, maintenance, and reversal -collectively determine the replication fitness of individual viral strains. A profound variation in the TFBS composition of the viral promoter may significantly alter the viral latency properties and the latent reservoir characteristics. Although the duplication of certain TFBS remains a quality unique to HIV-1C, the high-level genetic recombination of HIV-1 may promote the transfer of such molecular properties to the other HIV-1 subtypes. The emergence of several promoter-variant viral strains may make the task of a functional cure more challenging in HIV-1C.

microbiology↗

bioRxiv2020

Hitchhiking on condensed chromatin promotes plasmid persistence in yeast without perturbing chromosome function

Equipartitioning by chromosome hitchhiking and copy number correction by DNA amplification are at the heart of the evolutionary success of the selfish yeast 2-micron plasmid. The present analysis reveals plasmid presence near centromeres and telomeres in mitotic cells, with a preference towards the latter. The observed correlation of plasmid missegregation with non-disjunction of rDNA and telomeres under Cdc14 inactivation, higher plasmid missegregation upon induced missegregation of chromosome XII but not chromosome III, requirement of condensin for plasmid stability and the interaction of the condensin subunit Brn1 with the plasmid partitioning system lend functional credence to condensed chromatin being favored for plasmid tethering. By homing to condensed/quiescent chromosome locales, and not over-perturbing genome homeostasis, the plasmid may minimize fitness conflicts with its host. Analogous persistence strategies may be utilized by other extrachromosomal selfish genomes, for example, episomes of mammalian viruses that also hitchhike on host chromosomes for their stable maintenance.

cell biology↗

bioRxiv2019

Meiosis-specific functions of kinesin motors in cohesin removal and maintenance of chromosome integrity in budding yeast

Kinesin motors provide the molecular forces at the kinetochore-microtubule interface and along the spindle to control chromosome segregation. During meiosis with the two rounds of microtubule assembly-disassembly, the roles of motor proteins remain unexplored. We observed that in contrast to mitosis Cin8 (kinesin 5) and Kip3 (kinesin 8) together are indispensable in meiosis. Examining the meiosis in cin8{triangleup} kip3{triangleup} cells, we detected chromosome breakage in the meiosis II cells. The double mutant exhibits delay in the cohesin removal and spindle elongation during anaphase I. Consequently, some cells abrogate meiosis II and form dyads while some, as they progress through meiosis II, cause defect in chromosome integrity. We believe that in the latter cells, an imbalance of spindle mediated force and simultaneous persistent cohesin on the chromosomes cause their breakage. We provide evidence that tension generated by Cin8 and Kip3 through microtubule cross-linking is essential for signaling efficient cohesin removal and maintenance of chromosome integrity during meiosis.\n\nSummaryMolecular motors generate forces that facilitate chromosome segregation. Unlike mitosis, in meiosis, two times chromosome segregation occur with twice microtubule assembly/disassembly. This work reports that the motor mediated forces are crucial for cohesin removal in meiosis and thus maintain genome integrity.

cell biology↗