Related Experiment Video
Updated: Jun 12, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Characterisation of conserved non-coding sequences in vertebrate genomes using bioinformatics, statistics and
Yvonne J K Edwards1, Klaudia Walter, Gayle McEwen
1School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London, E1 4NS, UK.
Summary
Researchers identified ~1400 conserved non-coding elements (CNEs) in fugu and human genomes linked to vertebrate development. Functional assays confirmed over 90% of tested CNEs enhance gene expression, highlighting their regulatory roles.
Area of Science:
- Genomics
- Developmental Biology
- Bioinformatics
Background:
- Conserved non-coding elements (CNEs) are genomic regions shared across species.
- Approximately 1400 CNEs were identified between fugu (Takifugu rubripes) and human genomes.
- These CNEs are hypothesized to play roles in vertebrate developmental regulation.
Purpose of the Study:
- To review research characterizing vertebrate- and human-conserved non-coding sequences.
- To present ongoing research, including phylogenomics and sequence conservation patterns.
- To explore the potential of CNEs in correlating genetic variation with health and disease.
Main Methods:
- Bioinformatics and statistical analyses for CNE identification.
- In vivo enhancer assays using GFP expression to test CNE function.
- Phylogenomic analysis and examination of sequence conservation patterns.
Main Results:
- Over 90% of tested CNEs demonstrated tissue-specific gene upregulation (GFP expression).
- Analysis of sequence conservation patterns across vertebrates was performed.
- Distribution of human single nucleotide polymorphisms (SNPs) within CNEs was investigated.
Conclusions:
- CNEs are functionally validated as enhancers of tissue-specific gene expression.
- The CNE dataset offers a valuable resource for understanding genetic variation in health and disease.
- Public access to CNEs and associated annotations is now available.
Related Concept Videos
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
01:49Conserved Binding Sites
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 analyses the...
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 analyses the...
01:49Conserved Binding Sites
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 analyses the...
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 analyses the...
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...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...