ArticleNucleic acids research2013
Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 16 citations in OpenAlex.
- Immunometabolism changes in fibrosis: from mechanisms to therapeutic strategies.Frontiers in pharmacology · 2023Review
- Pathophysiological Role of Genetic Factors Associated With Gestational Diabetes Mellitus.Frontiers in physiology · 2022Review
- Combining artificial intelligence: deep learning with Hi-C data to predict the functional effects of non-coding variants.Bioinformatics (Oxford, England) · 2021Article
- Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.Computational and structural biotechnology journal · 2020Review
- Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.Nature communications · 2018Article
- McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.Genome biology · 2017Article
- Explaining the disease phenotype of intergenic SNP through predicted long range regulation.Nucleic acids research · 2016Article
- PEDLA: predicting enhancers with a deep learning-based algorithmic framework.Scientific reports · 2016Article
- Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome.Protein & cell · 2016Article
- CCSI: a database providing chromatin-chromatin spatial interaction information.Database : the journal of biological databases and curation · 2016Article
- Computational schemes for the prediction and annotation of enhancers from epigenomic assays.Methods (San Diego, Calif.) · 2015Review
- Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.Critical reviews in biochemistry and molecular biology · 2015Review
- Practical aspects of protein co-evolution.Frontiers in cell and developmental biology · 2014Review
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Defining the target genes of distal regulatory elements (DREs), such as enhancer, repressors and insulators, is a challenging task. The recently developed Hi-C technology is designed to capture chromosome conformation structure by high-throughput sequencing, and can be potentially used to determine the target genes of DREs. However, Hi-C data are noisy, making it difficult to directly use Hi-C data to identify DRE-target gene relationships. In this study, we show that DREs-gene pairs that are confirmed by Hi-C data are strongly phylogenetic correlated, and have thus developed a method that combines Hi-C read counts with phylogenetic correlation to predict long-range DRE-target gene relationships. Analysis of predicted DRE-target gene pairs shows that genes regulated by large number of DREs tend to have essential functions, and genes regulated by the same DREs tend to be functionally related and co-expressed. In addition, we show with a couple of examples that the predicted target genes of DREs can help explain the causal roles of disease-associated single-nucleotide polymorphisms located in the DREs. As such, these predictions will be of importance not only for our understanding of the function of DREs but also for elucidating the causal roles of disease-associated noncoding single-nucleotide polymorphisms.
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