Results 1 to 10 of about 216,058 (206)

3D polymer simulations of genome organization and transcription across different chromosomes and cell types [PDF]

, 2022
We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways to regulate transcription: it is shown that the transcriptional activity profile can be regulated and controlled ...
arxiv   +1 more source

Coding limits on the number of transcription factors [PDF]

BMC Genomics 2006, 7:239, 2010
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of transcription factors encoded in a genome increases with the number of genes in the genome. Here, we examined the number
arxiv   +1 more source

Functional Characteristics of Gene Expression Motifs with Single and Dual Strategies of Regulation [PDF]

Biomed. Phys. Eng. Express, 2 , 025009(2016), 2016
Transcriptional regulation by transcription factors and post-transcriptional regulation by microRNAs constitute two major modes of regulation of gene expression. While gene expression motifs incorporating solely transcriptional regulation are well investigated, the dynamics of motifs with dual strategies of regulation, i.e., both transcriptional and ...
arxiv   +1 more source

Extending the dynamic range of transcription factor action by translational regulation [PDF]

Phys. Rev. E 93, 022404 (2016), 2015
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation.
arxiv   +1 more source

A role for ATP-dependent chromatin remodeling in the hierarchical cooperativity between noninteracting transcription factors [PDF]

J. Theor. Biol. 287, 74-81 (2011), 2015
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the influence of nucleosome position on the regulation of gene expression is generally envisioned under the quasi ...
arxiv   +1 more source

How the DNA sequence affects the Hill curve of transcriptional response [PDF]

Phys. Biol. 9 (2012) 056006, 2011
The Hill coefficient is often used as a direct measure of the cooperativity of binding processes. It is an essential tool for probing properties of reactions in many biochemical systems. Here we analyze existing experimental data and demonstrate that the Hill coefficient characterizing the binding of transcription factors to their cognate sites can in ...
arxiv   +1 more source

Control of noise in gene expression by transcriptional reinitiation [PDF]

, 2019
Gene expression is a random or noisy process. The process consists of several random events among which the reinitiation of transcription by RNAP is an important one. The RNAP molecules can bind the gene only after the promoter gets activated by transcription factors.
arxiv   +1 more source

The role of master regulators in gene regulatory networks [PDF]

Papers in Physics 7, 070011 (2015), 2015
Gene regulatory networks present a wide variety of dynamical responses to intrinsic and extrinsic perturbations. Arguably, one of the most important of such coordinated responses is the one of amplification cascades, in which activation of a few key-responsive transcription factors (termed master regulators, MRs) lead to a large series of ...
arxiv   +1 more source

Dynamics of gene expression and the regulatory inference problem [PDF]

, 2007
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding of transcription factor molecules to regulatory DNA.
arxiv   +1 more source

A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting [PDF]

, 2020
Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours; however, state-of-the-art measurements have revealed that many of the molecular processes that underlie bursting, such as transcription factor binding to DNA, unfold on timescales of seconds.
arxiv   +1 more source