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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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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...
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Updated: Aug 6, 2025

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Toward a comprehensive catalog of regulatory elements.

Kaili Fan1,2, Edith Pfister1, Zhiping Weng3

  • 1Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA.

Human Genetics
|March 20, 2023
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Summary
This summary is machine-generated.

Understanding gene regulation requires identifying genomic regulatory elements. This review covers assays and computational methods for cataloging these elements, crucial for cell-type-specific gene expression.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Regulatory elements control cell-type-specific gene expression by interacting with transcription factors.
  • A comprehensive catalog of human genome functional elements is essential for understanding gene regulation.
  • Current annotation methods need refinement for precision and completeness.

Purpose of the Study:

  • To review the current state of regulatory element annotation in the human genome.
  • To provide an overview of experimental and computational approaches for identifying functional genomic elements.
  • To highlight existing high-quality regulatory element annotations and suggest future research directions.

Main Methods:

  • Overview of experimental assays: genome, epigenome, transcriptome, 3D chromatin interactions, and functional validation.
  • Discussion of computational methods: peak-calling and statistical modeling for element definition.
  • Introduction to curated lists of regulatory element annotations.

Main Results:

  • Various assays provide complementary data for characterizing functional elements.
  • Computational methods enable the definition and annotation of regulatory regions.
  • Several reliable resources for regulatory element annotations are available.

Conclusions:

  • Accurate annotation of regulatory elements is critical for deciphering gene regulation.
  • Integrating diverse assay data with advanced computational tools improves annotation quality.
  • Future efforts should focus on refining annotation strategies and expanding functional element catalogs.