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.

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

“…p300, Mediator, BRG1) or their enzymatic products (e.g. H3K27ac, catalyzed by p300/CBP or H3K4me1, catalyzed by MLL3/4) can be mapped using ChIP-seq (for reviews on enhancer chromatin signatures and epigenomic annotation strategies see (Calo and Wysocka, 2013; Sakabe and Nobrega, 2013; Whitaker et al, 2015)).…”

In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences

“…have developed an SVM model to predict enhancers by integrating various data, such as evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA sequence motifs. Recently, Whitaker et al 25. have reviewed current progress in terms of the prediction and annotation of enhancers.…”

(Epi)Genomics approaches and their applications

“…Wei Wang and colleagues in this issue review genome-wide assays and analysis schemes that have been used to predict and annotate enhancers. In addition to the identification, they also discuss the how cell-type-specific activity can be determined, and how enhancers are linked to their target genes [28].…”