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General Transcription Factors01:30

General Transcription Factors

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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...
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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...
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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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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.
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Updated: Jan 10, 2026

Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue
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TSProm: Deciphering the Genomic Context of Tissue Specificity.

Pallavi Surana1, Pratik Dutta1, Nimisha Papineni1

  • 1Department of Biomedical Informatics, Stony Brook University, USA.

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|November 24, 2025
PubMed
Summary

TSProm deciphers tissue-specific (TSp) gene regulation by analyzing DNA sequences near promoters. This AI framework identifies key regulatory elements and transcription factors, advancing our understanding of gene expression in health and disease.

Keywords:
DNA Language ModelsExplainable AIInterpretable genomics Frameworktissue specificity

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Area of Science:

  • Genomics
  • Computational Biology
  • Epigenetics

Background:

  • Tissue-specific (TSp) gene expression is vital for development and disease.
  • Traditional methods miss regulatory information in non-coding DNA.
  • Distal promoter regions contain crucial regulatory grammar.

Purpose of the Study:

  • Introduce TSProm, a framework using DNA foundation models (DNABERT2) to decode TSp promoter regulatory logic.
  • Isolate sequence motifs defining tissue identity using comparative model training.
  • Provide interpretable AI (xAI) for robust feature interpretation.

Main Methods:

  • Specialized DNA foundation model (DNABERT2) for TSp promoter analysis.
  • Comparative training of two models: general promoter biology (A) and TSp regulation (B).
  • Integrated xAI module with attention-based discovery and SHAP analysis.

Main Results:

  • Identified clinically relevant transcription factors (TFs) in brain promoters (SP1, MYC, HES6).
  • Validated TF roles in brain-related diseases like gliomas and neuroblastomas.
  • Revealed C2H2 Zinc Finger proteins as dominant in TSp gene regulation.

Conclusions:

  • TSProm offers a novel, interpretable framework for identifying TSp gene regulatory elements.
  • Provides powerful computational tools for studying TSp gene regulation in normal and disease states.
  • Advances understanding of the regulatory grammar in non-coding DNA.