Related Experiment Video
Updated: Jun 9, 2026
11:41
Mapping Mammalian 3D Genome Interactions with Micro-C-XL
Published on: November 3, 2023
Coordinated expression domains in mammalian genomes.
Yong H Woo1, Michael Walker, Gary A Churchill
1The Jackson Laboratory, Center for Genome Dynamics, Bar Harbor, Maine, United States of America.
Plos One
|September 1, 2010
Summary
Gene coexpression clusters across mammalian genomes at multiple scales. Chromosome structure and gene density influence these domains, potentially impacting diseases like Alzheimer's.
Area of Science:
- Genomics
- Molecular Biology
- Systems Biology
Background:
- Gene order in eukaryotic genomes is non-random.
- Coexpressed genes are frequently clustered along the genome.
- Understanding coexpression clustering mechanisms is crucial.
Purpose of the Study:
- Characterize coexpression clustering in mammalian genomes.
- Investigate the underlying mechanisms of coexpression domains.
- Explore the relationship between gene clustering and genome organization.
Main Methods:
- Analysis of gene expression patterns across mammalian genomes.
- Identification and characterization of coexpression domains at various genomic scales.
- Correlation analysis between coexpression domains, gene density, and chromosomal organization.
Main Results:
- Coexpressed genes cluster across multiple scales, from neighboring genes to megabase-spanning domains and entire chromosomes.
- Coexpression domains exhibit positive or negative correlations within and between chromosomes.
- Long-range coexpression domains correlate with gene density and physical chromosome organization in the nucleus.
- Gene expression changes in disease are linked to gene density.
Conclusions:
- Coexpression domains are prevalent across multiple genomic scales.
- Mechanisms for both short-range and long-range coexpression have been identified.
- The 3D architecture of chromosomes likely underlies long-range coexpression domains.
- Chromosome territory reorganization may contribute to diseases like Alzheimer's and psoriasis.
Related Concept Videos
01:30General 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...
02:26Conservation of Protein Domains Over Different Proteins
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 form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:02Cis-regulatory Sequences
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...
02:02Cis-regulatory Sequences
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...
01:23Regulation 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...
02:24Regulation 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...
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...