PUBLICATION
Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation
- Authors
- Clément, Y., Torbey, P., Gilardi-Hebenstreit, P., Crollius, H.R.
- ID
- ZDB-PUB-200118-4
- Date
- 2020
- Source
- Nucleic acids research 48(5): 2357-2371 (Journal)
- Registered Authors
- Gilardi-Hebenstreit, Pascale
- Keywords
- none
- MeSH Terms
-
- Embryo, Nonmammalian
- Enhancer Elements, Genetic*
- Synteny
- Conserved Sequence
- Genetic Linkage*
- Humans
- Chromosome Mapping
- Zebrafish
- Gene Expression Regulation, Developmental*
- Animals
- Base Sequence
- Genome Size
- Computational Biology/methods
- Biological Evolution
- Transcription Factors/genetics*
- Transcription Factors/metabolism
- PubMed
- 31943068 Full text @ Nucleic Acids Res.
Citation
Clément, Y., Torbey, P., Gilardi-Hebenstreit, P., Crollius, H.R. (2020) Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation. Nucleic acids research. 48(5):2357-2371.
Abstract
The spatiotemporal expression of genes is controlled by enhancer sequences that bind transcription factors. Identifying the target genes of enhancers remains difficult because enhancers regulate gene expression over long genomic distances. To address this, we used an evolutionary approach to build two genome-wide maps of predicted enhancer-gene associations in the human and zebrafish genomes. Evolutionary conserved sequences were linked to their predicted target genes using PEGASUS, a bioinformatics method that relies on evolutionary conservation of synteny. The analysis of these maps revealed that the number of predicted enhancers linked to a gene correlate with its expression breadth. Comparison of both maps identified hundreds of putative vertebrate ancestral regulatory relationships from which we could determine that predicted enhancer-gene distances scale with genome size despite strong positional conservation. The two maps represent a resource for further studies, including the prioritization of sequence variants in whole genome sequence of patients affected by genetic diseases.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping