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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Conservation of Protein Domains Over Different Proteins02:26

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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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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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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Updated: May 29, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Epigene functional diversity: isoform usage, disordered domain content, and variable binding partners.

Leroy Bondhus1,2,3, Aileen A Nava1,2,3, Isabelle S Liu1,2,3

  • 1Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.

Epigenetics & Chromatin
|February 1, 2025
PubMed
Summary
This summary is machine-generated.

Epigenes, crucial for development and disease, exhibit unique structural features like larger size, more exons, and intrinsically disordered regions, enabling diverse functions. These findings aid in developing targeted therapies for epigene-related disorders and cancers.

Keywords:
Chromatin modifiersEpigenesEpigeneticsRare diseasesTranscriptomics

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Area of Science:

  • Epigenetics and Molecular Biology
  • Genomics and Bioinformatics

Background:

  • Epigenes are proteins controlling chromatin structure, essential for cell-type-specific development.
  • Mutations in epigenes are linked to pediatric disorders and cancer.
  • A systematic analysis of epigene functional diversity sources is lacking.

Purpose of the Study:

  • To systematically analyze the sources of functional diversity in human epigenes.
  • To identify structural and functional differences between epigenes and non-epigenes.
  • To explore potential therapeutic targets for epigene-related diseases.

Main Methods:

  • Comparative analysis of gene structure, isoforms, and protein domains using functional genomics datasets (Ensembl, ENCODE, GTEx, HPO, LINCS L1000, BrainSpan).
  • Assessment of protein complex formation and intrinsically disordered regions (IDRs).
  • Analysis of gene expression profiles and identification of drug modulators using the L1000 dataset.

Main Results:

  • Epigenes are larger, possess more exons, and exhibit greater isoform diversity than non-epigenes.
  • Epigenes participate in more multimeric complexes and have significantly larger intrinsically disordered regions (IDRs).
  • Epigenes show ubiquitous expression patterns and potential drug modulators were identified.

Conclusions:

  • Significant differences in isoform usage, disordered domain content, and binding partners distinguish human epigenes from non-epigenes.
  • These findings advance understanding of epigene function in development and disease.
  • The study provides a foundation for developing targeted therapies for chromatinopathies and cancers.