Biology subjects

Narayanan, I. V.

Publications and source records attributed to Narayanan, I. V..

4 recordsLinked to original sources

bioRxiv2026

Characterizing nascent readthrough transcripts in human cells

Termination of transcription by RNA polymerase II (RNAPII) is critical to appropriately define transcriptome and proteome identity; yet mechanisms of termination regulation are incompletely understood. Current models suggest critical roles for the exonuclease XRN2, which is posited to "torpedo" out RNAPII after degrading uncapped and RNAPII-tethered nascent transcripts and posit an allosteric model wherein elongating RNAPII loses its processivity downstream of the transcription end site (TES) via unknown mechanisms. Here, we used nascent RNA Bru-seq to interrogate transcription termination across 16 human cell lines of distinct lineages, as part of the ENCODE 4 project, to identify key regulatory modes. We find that > 75% of protein-coding genes engage in readthrough transcription under homeostatic conditions. Exposing human cells to oxidative stress or hyperosmotic conditions or splicing inhibitors cause an increase in readthrough transcripts globally. Using an auxin-inducible degradation approach we find that depletion of BRD4, MED14 or XRN2 increases the extent and pervasiveness of readthrough transcripts while depletion of SUPT16H results in shorter readthrough transcripts. Our study provides a comprehensive view of homeostatic readthrough transcripts in human cells and delineates key components regulating transcription termination.

molecular biology↗

bioRxiv2024

Isoform and pathway-specific post-transcriptional RNA processing in human cells

Steady-state levels of RNA transcripts are controlled by their rates of synthesis and degradation. Here we used nascent RNA Bru-seq and BruChase-seq to profile RNA dynamics across 16 human cell lines as part of ENCODE4 Deeply Profiled Cell Lines collection. We show that RNA turnover dynamics differ widely between transcripts of different genes and between different classes of RNA. Gene set enrichment analysis (GSEA) revealed that transcripts encoding proteins belonging to the same pathway often show similar turnover dynamics. Furthermore, transcript isoforms show distinct dynamics suggesting that RNA turnover is important in regulating mRNA isoform choice. Finally, splicing across newly made transcripts appears to be cooperative with either all or none type splicing. These data sets generated as part of ENCODE4 illustrate the intricate and coordinated regulation of RNA dynamics in controlling gene expression to allow for the precise coordination of cellular functions.

molecular biology↗

bioRxiv2021

ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation

Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. The binding of the TCR-specific repair factor CSB triggers DNA damage-induced ubiquitylation of RNA polymerase II (RNAPII) at a single lysine (K1268) by the CRL4CSA ubiquitin ligase. However, how the CRL4CSA ligase is specifically directed toward the K1268 site is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to the K1268 site, revealing ELOF1 as a specificity factor that positions CRL4CSA for optimal RNAPII ubiquitylation. Furthermore, drug-genetic interaction screening reveals an unanticipated compensatory TCR pathway in which ELOF1 together with known factors DOT1L and HIRA protect CSB-deficient cells from collisions between transcription and replication machineries. Our study provides a genetic framework of the transcription stress response and reveals key insights into the molecular mechanism of TCR.

molecular biology↗

bioRxiv2020

KMT2D Links TGF-β Signalling to Non-Canonical Activin Pathway and Regulates Pancreatic Cancer Cell Plasticity

Although KMT2D, also known as MLL2, is known to play an essential role in development, differentiation, and tumor suppression, its role in pancreatic cancer development is not well understood. Here, we discovered a novel signaling axis mediated by KMT2D, which links TGF-{beta} to the activin A pathway. We found that TGF-{beta} upregulates a microRNA, miR-147b, which in turn leads to post-transcriptional silencing of KMT2D. Loss of KMT2D induces the expression and secretion of activin A, which activates a non-canonical p38 MAPK-mediated pathway to modulate cancer cell plasticity, promote a mesenchymal phenotype, and enhance tumor invasion and metastasis in mice. We observed a decreased KMT2D expression in human primary and metastatic pancreatic cancer. Furthermore, inhibition or knockdown of activin A reversed the pro-tumoral role of KMT2D. These findings reveal a tumor-suppressive role of KMT2D and identify miR-147b and activin A as novel therapeutic targets in pancreatic cancer.

cancer biology↗