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Related Concept Videos

Master Transcription Regulators02:23

Master Transcription Regulators

6.9K
Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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Combinatorial Gene Control02:33

Combinatorial Gene Control

8.3K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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Related Experiment Video

Updated: Jun 23, 2025

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
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BIT: Bayesian Identification of Transcriptional Regulators from Epigenomics-Based Query Region Sets.

Zeyu Lu1,2, Lin Xu3,4, Xinlei Wang2,5

  • 1Department of Statistics and Data Science, Moody School of Graduate and Advanced Studies, Southern Methodist University, Dallas, TX, USA.

Biorxiv : the Preprint Server for Biology
|June 19, 2024
PubMed
Summary

We developed BIT, a new Bayesian model to identify transcriptional regulators (TRs) controlling gene expression. BIT accurately pinpoints critical TRs using epigenomic data, offering interpretable insights into gene regulation in development and disease.

Keywords:
ATAC-seqBayesian hierarchical modelJaccard indexPólya-Gamma data augmentationchromatin accessibility profilingepigenomics

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Last Updated: Jun 23, 2025

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
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Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
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Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Transcriptional regulators (TRs) are crucial for gene expression, impacting development and disease.
  • Current computational methods for TR identification have limitations in specificity, interpretability, and confidence measures.

Purpose of the Study:

  • To introduce BIT, a novel Bayesian hierarchical model for *in-silico* TR identification.
  • To provide a more accurate and interpretable method for identifying TRs regulating specific biological processes.

Main Methods:

  • Developed BIT, a Bayesian hierarchical model integrating TR ChIP-seq data with user-provided epigenomic profiling.
  • Assessed genome-wide consistency between epigenomic data and TR binding libraries using a fully integrated Bayesian approach.
  • Avoided sequential estimation and isolated statistical tests for enhanced accuracy and interpretability.

Main Results:

  • BIT successfully identified critical TRs in perturbation experiments.
  • Demonstrated BIT's ability to find functionally essential TRs in various cancer types.
  • Showcased BIT's utility in identifying cell-type-specific TRs within heterogeneous cell populations.

Conclusions:

  • BIT offers a robust and interpretable *in-silico* approach for TR identification.
  • The model provides deeper biological insights into transcriptional regulation.
  • BIT quantifies uncertainty, enhancing confidence in identified TRs.