title: Computational schemes for the prediction and annotation of enhancers from epigenomic assays.
abstract: Identifying and annotating distal regulatory enhancers is critical to understand the mechanisms that control gene expression and cell-type-specific activities. Next-generation sequencing techniques have provided us an exciting toolkit of genome-wide assays that can be used to predict and annotate enhancers. However, each assay comes with its own specific set of analytical needs if enhancer prediction is to be optimal. Furthermore, integration of multiple genome-wide assays allows for different genomic features to be combined, and can improve predictive performance. Herein, we review the genome-wide assays and analysis schemes that are used to predict and annotate enhancers. In particular, we focus on three key computational topics: predicting enhancer locations, determining the cell-type-specific activity of enhancers, and linking enhancers to their target genes.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, United States.
authors.forename: John W
authors.initials: JW
authors.lastname: Whitaker
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, United States.
authors.forename: Tung T
authors.initials: TT
authors.lastname: Nguyen
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, United States.
authors.forename: Yun
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, United States.
authors.forename: Andre
authors.initials: A
authors.lastname: Wildberg
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, United States. Electronic address: wei-wang@ucsd.edu.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
mesh_terms: D042002:Chromatin Assembly and Disassembly; D019295:Computational Biology / Q000379:methods; D004742:Enhancer Elements, Genetic; D057890:Epigenomics / Q000379:methods*; D005786:Gene Expression Regulation; D008957:Models, Genetic; D058977:Molecular Sequence Annotation
keywords: Enhancer activity; Enhancer prediction; Enhancer–gene linking; Epigenetics; Epigenomics