Biology subjects

Saha, R. N.

Publications and source records attributed to Saha, R. N..

4 recordsLinked to original sources

bioRxiv2023

Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA Polymerase II productive elongation.

Signal-dependent RNA Polymerase II (Pol2) productive elongation is an integral component of gene transcription, including those of immediate early genes (IEGs) induced by neuronal activity. However, it remains unclear how productively elongating Pol2 overcome nucleosomal barriers. Using RNAi, three degraders, and several small molecule inhibitors, we show that the mammalian SWI/SNF complex of neurons (neuronal BAF, or nBAF) is required for activity-induced transcription of neuronal IEGs, including Arc. The nBAF complex facilitates promoter-proximal Pol2 pausing, signal-dependent Pol2 recruitment (loading), and importantly, mediates productive elongation in the gene body via interaction with the elongation complex and elongation-competent Pol2. Mechanistically, Pol2 elongation is mediated by activity-induced nBAF assembly (especially, ARID1A recruitment) and its ATPase activity. Together, our data demonstrate that the nBAF complex regulates several aspects of Pol2 transcription and reveal mechanisms underlying activity-induced Pol2 elongation. These findings may offer insights into human maladies etiologically associated with mutational interdiction of BAF functions.

neuroscience↗

bioRxiv2021

Elucidating the correlation between the number of TTTTGAT heptamer repeats and cholera toxin promoter activity in Vibrio cholerae O1 pandemic strains

A complex regulatory cascade controls expression of the cholera toxin genes (ctxAB) in Vibrio cholerae; which eventually leads to choleragen (CT) production and secretion, resulting in rice watery diarrhoea. The cholera toxin promoter (PctxAB) contains a series of heptad repeats (5-TTTTGAT-3); which have been previously shown to play crucial role in ctxAB transcriptional regulation by recruiting the transcriptional activators ToxT, ToxR, and the nucleoid-associated protein H-NS along the ctx promoter. The numbers of these repeats vary between the two biotypes of V. cholerae O1 strains, and even among strains of the same biotype. In this study, we examined PctxAB activation of V. cholerae O1 pandemic strains to understand the significance of the distal heptad repeats in regulating ctx expression. Interestingly, we found that ctx activation may depend on the number of TTTTGAT heptad repeats within PctxAB, and we posit that the occupation of the distal repeats by H-NS could further prevent transcriptional activation of ctx genes in V. cholerae. We hypothesize that ToxT-dependent transcriptional activation may not require entire displacement of H-NS and propose a revision in the currently accepted model of ToxT dependent PctxAB transcriptional activation. IMPORTANCECT production by pathogenic V. cholerae O1 strains is regulated through the transcriptional silencing of CTX promoter by H-NS and counter repression by ToxT. The highly AT rich PctxAB is composed of the tandem repeats 5{square} TTTTGAT 3{square}; the numbers of which differ among the classical and El Tor biotypes. However, it is still not very clear whether the numbers of these repeats could be correlated with promoter activation of the ctx operon. Here we report the role of the distal repeats in ctxAB expression levels. We demonstrate that PctxAB activation changes with the number of the heptad repats within the core promoter element, thereby suggesting a model for ctx regulation in the toxigenic strains of V. cholerae.

microbiology↗

bioRxiv2020

Mild membrane depolarization in neurons induces immediate early gene transcription and acutely subdues responses to successive stimulus.

The transcriptional profile of immediate early genes (IEGs) is indicative of the duration of neuronal activity, but it is unknown whether it affected by the strength of depolarization. Also unknown is whether an activity history of graded potential changes influences further neuronal activity. In this work with dissociated rat cortical neurons, we found mild depolarization - mediated by elevated extracellular KCl - not only induces a wide array of rapid IEGs, but also transiently depresses transcriptional and signaling responses to a successive stimulus. This latter effect was independent of de novo transcription, translation, calcineurin (CaN) signaling, and MAPK signaling downstream of PKC. Furthermore, as measured by multiple electrode arrays, mild depolarization acutely subdues subsequent spontaneous and bicuculline-evoked activity. Collectively, this work suggests that a recent history of graded potential changes acutely depresses neuronal intrinsic properties and subsequent responses. Such effects may have several potential downstream implications, including reducing signal-to-noise ratio during Hebbian plasticity processes.

neuroscience↗

bioRxiv2017

Distinct neuronal activity patterns induce different gene expression programs

Brief and sustained neuronal activity patterns can have opposite effects on synaptic strength that both require activity-regulated gene (ARG) expression. However, whether distinct patterns of activity induce different sets of ARGs is unknown. In genome-scale experiments, we reveal that a neurons activity-pattern history can be predicted from the ARGs it expresses. Surprisingly, brief activity selectively induces a small subset of the ARG program that that corresponds precisely to the first of three temporal waves of genes induced by sustained activity. These first-wave genes are distinguished by an open chromatin state, proximity to rapidly activated enhancers, and a requirement for MAPK/ERK signaling for their induction. MAPK/ERK mediates rapid RNA polymerase recruitment to promoters, as well as enhancer RNA induction but not histone acetylation at enhancers. Thus, the same mechanisms that establish the multi-wave temporal structure of ARG induction also enable different sets of genes to be induced by distinct activity patterns.

neuroscience↗