Related Experiment Video
Updated: Jul 15, 2026
06:59
A Reverse Genetic Approach to Test Functional Redundancy During Embryogenesis
Published on: August 11, 2010
Comparative genomics using Fugu reveals insights into regulatory subfunctionalization
1School of Biological Sciences, Queen Mary, University of London, London, UK. woolfea@mail.nih.gov
Genome Biology
|April 13, 2007
Summary
Regulatory subfunctionalization preserves gene duplicates by modifying cis-regulatory elements. This study analyzed conserved non-coding elements (CNEs) in fish-mammal genomes, revealing patterns of element loss and retention in duplicated genes.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Gene duplication is a key driver of evolutionary innovation.
- Regulatory subfunctionalization, the modification of cis-regulatory elements in gene duplicates, is a major preservation mechanism.
- Previous studies lacked comprehensive analysis of distal cis-regulatory modules in this process.
Purpose of the Study:
- To comprehensively analyze regulatory subfunctionalization at the level of distal cis-regulatory modules.
- To investigate the role of conserved non-coding elements (CNEs) in the evolution of duplicated genes.
Main Methods:
- Exploited fish-mammal genomic alignments to identify and compare over 800 CNEs.
- Utilized multiple alignments of orthologous regions between mammalian and Fugu duplicated genes.
- Focused on seven pairs of teleost-specific paralogs involved in early vertebrate development.
Main Results:
- Identified patterns of CNE retention and loss between paralogs, indicative of subfunctionalization.
- Observed varying degrees of subfunctionalization across different duplicate gene pairs.
- Found evidence of both complete CNE loss and sequence divergence in retained CNEs.
Conclusions:
- Comparative analysis of conserved elements in duplicated genes is a powerful method to study regulatory subfunctionalization.
- This approach allows for the examination of regulatory divergence at the level of individual regulatory elements.
Related Concept Videos
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...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
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...