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Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

ABSTRACT: Here, we present PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first.

ORGANISM(S): Mus musculus

PROVIDER: GSE58443 | GEO | 2014/06/13

SECONDARY ACCESSION(S): PRJNA252694

REPOSITORIES: GEO

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Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

Project description:Here, we present PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. High-resolution characterization of PolII at promoters in mouse liver

2014-06-13 | E-GEOD-58443 | biostudies-arrayexpress

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters.

Project description:BACKGROUND: In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of PolII through sequential promoter states. RESULTS: Here, we analyze PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. Using an empirical model that reliably quantifies the spatial PolII signal, gene by gene, we show that the first PolII peak allows for refined positioning of transcription start sites, which is corroborated by mRNA sequencing. This bimodal signature is found both in mouse and humans. Analysis of the pausing-related factors NELF and DSIF suggests that the downstream peak reflects widespread pausing at the +1 nucleosome barrier. Several features of the bimodal pattern are correlated with sequence features such as CpG content and TATA boxes, as well as the histone mark H3K4me3. CONCLUSIONS: We thus show how high coverage DNA sequencing experiments can reveal as-yet unnoticed bimodal spatial features of PolII accumulation that are frequent at individual mammalian genes and reminiscent of transcription initiation and pausing. The initiation-pausing hypothesis is corroborated by evidence from run-on sequencing and immunoprecipitation in other cell types and species.

| S-EPMC4197824 | biostudies-literature

CUT&RUN reveals unique positioning of pre-initiated RNA polymerase II in the steady state of transcription

Project description:CUT&RUN is a powerful tool to study protein-DNA interactions in vivo. DNA fragments cleaved by the targeted micrococcal nuclease identify the footprints of DNA-binding proteins on the chromatin. We performed CUT&RUN on human lung carcinoma cell line A549 maintained in a multi-well cell culture plate to profile RNA polymerase II. Size-fractionation of aligned reads revealed that the collection of long (>270 bp) DNA fragments corresponded to the bimodal peak around the transcription start sites, as previously seen with chromatin immunoprecipitation. However, we found that shorter (<120 bp) fragments identify a well-defined peak localised at the transcription start sites. This distinct DNA footprint of shorter fragments, which constituted only about 5% of the total reads, indicates the unique positioning of the poised RNA polymerase II before transcription initiation, which has not been detected in the steady state of transcription by standard chromatin immunoprecipitation.

2020-10-20 | GSE155666 | GEO

A novel feedback loop that controls bimodal expression of genetic competence

Project description:Gene expression can be highly heterogeneous in clonal cell populations. An extreme type of heterogeneity is the so-called bistable or bimodal expression, whereby a cell can differentiate into two alternative expression states, and consequently a population will be composed of cells that are ‘ON’ and cells that are ‘OFF’. Stochastic fluctuations of protein levels, also referred to as noise, provide the necessary source of heterogeneity that must be amplified by autostimulatory feedback regulation to obtain the bimodal response. A classical model of bistable differentiation is the development of genetic competence in Bacillus subtilis. Noise in expression of the transcription factor ComK ultimately determines the fraction of cells that enter the competent state. Due to its intrinsic random nature, noise is difficult to investigate. We adapted an artificial autostimulatory loop that bypasses all known ComK regulators, to screen for possible factors that affect noise in the bimodal regulation of ComK. This led to the discovery of Kre, a novel factor that controls the bimodal expression of ComK. Kre appears to affect the stability of comK mRNA. Interestingly, ComK itself represses the expression of kre, adding a new double negative feedback loop to the intricate ComK regulation circuit. Our data emphasize that mRNA stability is an important factor in bimodal regulation.

2017-02-10 | GSE61757 | GEO

Multi-omics analysis identifies ALDH7A1 as a key regulator of the visual-olfactory bimodal learning in honeybee

Project description:Specific genes or encoded proteins are involved in regulating various learning models of different species through certain signaling pathways，but whether there are also regulatory genes during bimodal learning and memory is largely unknown. Using a multi-omics approach to examine gene expression changes in bees brain performed with three different learning assays, a general up-regulation of genes and proteins were observed in bimodal learning compared to controls. Protein-protein network predictions of differential proteins together with FISH assays suggest ALDH7A1 may be involved in regulation of bimodal learning and memory. Injecting siRNA-ALDH7A1 to the bee brain results in significant inhibition the expressions of ALDH7A1 and regucalcin, and increase β-alanine content. Interestingly, we found that loss of ALDH7A1 only affect visual-olfactory bimodal learning and memory, but not single visual or olfactory conditioned learning after ALDH7A1-RNAi in bees. Therefore, our data suggests that ALDH7A1 may affect bimodal learning and memory though controlling β-alanine related plasticity mechanisms.

2021-09-13 | PXD017008 | Pride

Different resource allocation in a Bacillus subtilis population displaying bimodal motility

Project description:To cope with sudden changes in their environment, bacteria can use a bet-hedging strategy by dividing the population into cells with different properties. This so called bimodal or bistable cellular differentiation is generally controlled by positive feedback regulation of transcriptional activators. Due to continued turnover of the cytoplasmic content, it is difficult for these activators to reach an activation threshold concentration when cells are growing exponentially. This is one reason why bimodal differentiation is primarily observed from the onset of the stationary phase when exponential growth ceases. An exception is the bimodal induction of motility in Bacillus subtilis, which occurs early during exponential growth. Several mechanisms have been put forward to explain this, including double negative-feedback regulation and the stability of the mRNA molecules involved. In this study, we used fluorescence-assisted cell sorting to compare the transcriptome of motile and non-motile cells and noted that expression of ribosomal genes is lower in motile cells. This was confirmed using an unstable GFP reporter fused to the strong ribosomal rpsD promoter. We propose that the reduction in ribosomal gene expression in motile cells is the result of a diversion of cellular resources to the synthesis of the chemotaxis and motility systems. In agreement, single-cell microscopic analysis indicates that motile cells are slightly shorter than non-motile cells, an indication of slower growth. We speculate that this growth rate reduction can contribute to the bimodal induction of motility during exponential growth.

2021-01-20 | GSE164348 | GEO

Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility [40-K562_ATAC]

Project description:We report a new technology for the parallel bimodal analysis of RNA-seq and ATAC-seq within a single-cell, known as ASTAR (Assay for Single-cell Transcriptome and Accessibility Regions).

2020-06-10 | GSE151734 | GEO

Genome-wide mapping of SPDEF and ESR1 binding in MCF-7 cells (ChIP-seq)

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2013-07-17 | E-GEOD-48930 | biostudies-arrayexpress

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