Biology subjects

Sikder, S.

Publications and source records attributed to Sikder, S..

5 recordsLinked to original sources

bioRxiv2025

T13F2.2 of C. elegans is Critical for Chromatin Organization, Autophagy, and Longevity

Intricately modulated by a spectrum of proteins, Chromatin structure governs gene expression and cellular homeostasis. In Caenorhabditis elegans, critical components like the TATA-binding protein tbp-1 play pivotal roles in orchestrating chromatin dynamics. While the function of many of the interacting partners of tbp-1 is well-understood, our study brings into focus a lesser-known entity, T13F2.2, an unexplored tbp-1 interacting protein and a putative RNA polymerase II transcriptional coactivator. Employing reverse genetics, we found that RNAi-induced depletion of T13F2.2 resulted in pronounced disruptions to nuclear architecture, evidenced by nuclear staining and transmission electron microscopy. Accompanying these structural anomalies, we observed increased autophagy, pointing to cellular stress and a hyperacetylation of the core histones, suggesting potential chromatin decompaction. Notably, multifaceted functional alterations, upon the partial knockdown of the T13F2.2, culminated in a substantial reduction in the worms lifespan. Intriguingly, interventions such as administering ROS scavengers and autophagy modulators offered a reprieve from this life-shortening effect. Transcriptomic analysis upon T13F2.2 knockdown revealed upregulation of genes related to autophagy and chromatin remodelling, alongside downregulation of genes involved in longevity pathways and oxidative stress response. This study, thus, not only puts forward the functional implication of an uncharacterized gene in C. elegans biology, but also further emphasizes the role of chromatin organization in aging at the organismal level.

genetics↗

bioRxiv2025

Oncogenic lncRNA transgene transcription modulates epigenetic memory at a naive chromosomal locus.

Maintaining genome integrity is crucial for the proper functioning and development of organisms. One intriguing aspect of genome integrity is the formation and function of neocentromeres at non-centromeric sites. CENP-A, a centromere-specific protein, is essential for centromere identification and function. However, in many cancers, CENP-A is often found to be ectopically misplaced when overexpressed. Moreover, CENP-A deposition at the centromere depends on the transcription of centromeric non-coding RNAs. Consequently, ectopic CENP-A is found at transcriptionally active and frequent breakpoint regions. To further explore ectopic CENP-A localization, we previously engineered a stable ectopic CENP-A site on a naive chromosome by overexpressing a non-centromeric oncogenic lncRNA, PCAT2, which was capable of recruiting CENP-A to its transcription site. In this work, we tracked cells carrying this stable transgene to understand the longevity of the induced ectopic CENP-A site at the chromosome that harbors it. Our findings revealed that the induced epigenetic memory was eventually lost due to the suppression of the transgene through competing epigenetic silencing mechanisms. This epigenetic restoration naturally reversed the ectopic CENP-A level to its previous levels at the engineered site. These data suggest that cells may have evolved failsafe mechanisms to prevent neocentromere formation at ectopic sites by suppressing transcription, unless otherwise favored by selection involving multiple components.

genetics↗

bioRxiv2024

KAT5 Acetylates Human Chromatin Protein PC4 to promote DNA Repair

Human positive coactivator 4 (PC4), is a highly abundant non-histone chromatin protein involved in diverse cellular processes, including transcription regulation, genome organization, DNA repair, etc. The majority of PC4 exists in a phosphorylated state in cells, which impinges its acetylation by p300 and thereby inhibits its double-stranded DNA binding ability and transcriptional co-activator function. Recently, we have shown that PC4 interacts with linker histone H1 in its phosphorylated state, and this interaction is important for PC4- mediated chromatin compaction. PC4 was also found to be an activator of non-homologous end joining and DSB repair activity. Knockdown of PC4 causes drastic decompaction and enhanced autophagy in the cells. Mechanistically, in the absence of PC4, the genome becomes highly vulnerable to DNA damage with an altered epigenetic landscape. Here, we report that other than p300, PC4 also gets acetylated by DNA repair facilitating lysine acetyltransferase KAT5 (Tip60), at K80 residue when the cells are subjected to DNA damage. The vulnerability of DNA in PC4 devoid cells could be substantially reduced by reintroducing wild-type PC4 to the cells but not the mutant PC4 (K80R PC4), defective in KAT5-mediated acetylation. Presumably, KAT5-mediated acetylation of PC4 at K80 residue facilitates the DNA repair machinery at the damage site and thus contributes to DNA damage repair, a process that could be of high significance both in cancer and in aging.

molecular biology↗

bioRxiv2023

Unraveling the mechanism of centromere inactivation in human aging

Aging involves a range of genetic, epigenetic, and physiological alterations. A key characteristic of aged cells is the loss of global heterochromatin, accompanied by a reduction in canonical histone levels. In this study, we track the fate of centromeres during aging in human cells. Our findings reveal that the centromeric histone H3 variant CENP-A is downregulated in aged cells, in a p53-dependent manner. We observe repression of centromeric noncoding transcription through an epigenetic mechanism via recruitment of a lysine-specific demethylase 1 (LSD1/KDM1A) to centromeres. This suppression results in defective de novo CENP-A loading at aging centromeres. By dual inhibition of p53 and LSD1/KDM1A in aged cells, we mitigate the reduction in centromeric proteins and centromeric transcripts, leading to mitotic rejuvenation of these cells. These results offer insights into a novel mechanism for centromeric inactivation during aging and provide potential strategies to reactivate centromeres.

molecular biology↗

bioRxiv2018

Non-histone human chromatin protein, PC4 is critical for genomic integrity and negatively regulates autophagy

Multifunctional human transcriptional positive co-activator 4 (PC4) is a bonafide non-histone component of the chromatin and plays a pivotal role in the process of chromatin compaction and functional genome organization. Knockdown of PC4 expression leads to a drastic open conformation of the chromatin and thereby altered nuclear architecture, defects in chromosome segregation and changed epigenetic landscape. Interestingly, these defects do not induce cellular death but result in enhanced cellular proliferation possibly through enhanced autophagic activity. PC4 depletion confers significant resistance to gamma irradiation. Exposure to gamma irradiation further induced autophagy in these cells. Inhibition of autophagy by small molecule inhibitors as well as by silencing of a critical autophagy gene drastically reduces the survivability PC4 knockdown cells. On the contrary, complementation with wild type PC4 could reverse this phenomenon, confirming the process of autophagy as the key mechanism for radiation resistance in absence of PC4. These data connect the unexplored role of chromatin architecture in regulating autophagy during a stress condition such as radiation.

molecular biology↗