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Related Concept Videos

Master Transcription Regulators02:23

Master Transcription Regulators

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...
Master Transcription Regulators02:23

Master Transcription Regulators

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...
Neural Regulation01:37

Neural Regulation

Digestion begins with a cephalic phase that prepares the digestive system to receive food. When our brain processes visual or olfactory information about food, it triggers impulses in the cranial nerves innervating the salivary glands and stomach to prepare for food.
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

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Related Experiment Video

Updated: Jun 6, 2026

Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets
03:37

Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets

Published on: March 1, 2024

TSProm: deep learning framework to predict tissue-specific regulatory logic.

Pallavi Surana1, Pratik Dutta1, Nimisha Papineni1

  • 1Department of Biomedical Informatics, Stony Brook University, NY 11794, United States.

NAR Genomics and Bioinformatics
|June 5, 2026
PubMed
Summary
This summary is machine-generated.

We developed TSProm, an AI framework using DNABERT2 to decode tissue-specific (TSp) gene promoters. It identifies regulatory grammar in DNA, revealing key transcription factors linked to brain cancers.

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Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Tissue-specific (TSp) gene expression is vital for development and disease research.
  • Traditional methods miss regulatory information in non-coding DNA, especially distal promoters.
  • Understanding TSp promoter logic is key to deciphering gene regulation.

Purpose of the Study:

  • Introduce TSProm, a novel framework to decode TSp promoter regulatory logic at the isoform level.
  • Adapt a DNA foundation model (DNABERT2) for analyzing TSp promoter sequences.
  • Isolate sequence motifs defining tissue identity and identify associated transcription factors.

Main Methods:

  • Developed TSProm, training two specialized DNABERT2 models: one for general promoter biology (Model A) and one for TSp regulation (Model B).
  • Integrated an explainable AI module with attention-based motif discovery and SHAP analysis for feature interpretation.
  • Applied TSProm to human brain, liver, and testis promoters.

Main Results:

  • Identified clinically relevant transcription factors (TFs) in brain promoters, including SP1, MYC, and HES6, linked to gliomas and neuroblastomas.
  • Highlighted C2H2 zinc finger proteins as a dominant family in TSp gene regulation.
  • Discovered sequence motifs that uniquely define tissue identity.

Conclusions:

  • TSProm offers an interpretable and generalizable framework for identifying TSp regulatory elements.
  • Provides powerful computational tools for investigating gene regulation in normal and disease states.
  • Advances the understanding of DNA's regulatory grammar in tissue-specific contexts.