Review
. 2015 Nov; 17(6):980-995.
doi: 10.1093/bib/bbv097.

In the loop: promoter-enhancer interactions and bioinformatics

Antonio Mora  Geir Kjetil Sandve  Odd Stokke Gabrielsen  Ragnhild Eskeland  
  • PMID: 26586731
  •     162 References
  •     42 citations

Abstract

Enhancer-promoter regulation is a fundamental mechanism underlying differential transcriptional regulation. Spatial chromatin organization brings remote enhancers in contact with target promoters in cis to regulate gene expression. There is considerable evidence for promoter-enhancer interactions (PEIs). In the recent years, genome-wide analyses have identified signatures and mapped novel enhancers; however, being able to precisely identify their target gene(s) requires massive biological and bioinformatics efforts. In this review, we give a short overview of the chromatin landscape and transcriptional regulation. We discuss some key concepts and problems related to chromatin interaction detection technologies, and emerging knowledge from genome-wide chromatin interaction data sets. Then, we critically review different types of bioinformatics analysis methods and tools related to representation and visualization of PEI data, raw data processing and PEI prediction. Lastly, we provide specific examples of how PEIs have been used to elucidate a functional role of non-coding single-nucleotide polymorphisms. The topic is at the forefront of epigenetic research, and by highlighting some future bioinformatics challenges in the field, this review provides a comprehensive background for future PEI studies.

Keywords: CTCF; Chromatin loops; SNPs; chromosome conformation capture; enhancer prediction; histone modifications; promoter–enhancer interactions; transcription factories.

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Nucleic Acids Res, 2010 Oct 30; 38(22). PMID: 21030438    Free PMC article.
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Curr Opin Cell Biol, 2012 Feb 18; 24(3). PMID: 22336329
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Nat Genet, 2011 Oct 18; 43(11). PMID: 22001755
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CREB, NF-Y and MEIS1 conserved binding sites are essential to balance Myostatin promoter/enhancer activity during early myogenesis.
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Mol Biol Rep, 2017 Sep 29; 44(5). PMID: 28956216
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BMC Genomics, 2018 Jun 20; 19(1). PMID: 29914364    Free PMC article.
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Plant Physiol, 2018 Oct 12; 178(4). PMID: 30305372    Free PMC article.
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A New Risk Variant for Multiple Sclerosis at 11q23.3 Locus Is Associated with Expansion of CXCR5+ Circulating Regulatory T Cells.
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Infect Drug Resist, 2019 Jun 14; 12. PMID: 31190910    Free PMC article.
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iEnhancer-GAN: A Deep Learning Framework in Combination with Word Embedding and Sequence Generative Adversarial Net to Identify Enhancers and Their Strength.
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