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
  • Animals
  • Base Sequence
  • Biological Evolution
  • Chromosome Mapping
  • Computational Biology/methods
  • Conserved Sequence
  • Embryo, Nonmammalian
  • Enhancer Elements, Genetic*
  • Gene Expression Regulation, Developmental*
  • Genetic Linkage*
  • Genome Size
  • Humans
  • Synteny
  • Transcription Factors/genetics*
  • Transcription Factors/metabolism
  • Zebrafish
PubMed
31943068 Full text @ Nucleic Acids Res.
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
Figures
Show all Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping