Improved Regulatory Element Prediction Based on Tissue-specific Local Epigenomic Signatures

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2017 Feb 15

PMID 28193886

Citations 42

Authors

Yupeng He

David U Gorkin

Diane E Dickel

Joseph R Nery

Rosa G Castanon

Ah Young Lee

Yin Shen

Axel Visel

Len A Pennacchio

Bing Ren

Joseph R Ecker

Affiliations

Soon will be listed here.

Abstract

Accurate enhancer identification is critical for understanding the spatiotemporal transcriptional regulation during development as well as the functional impact of disease-related noncoding genetic variants. Computational methods have been developed to predict the genomic locations of active enhancers based on histone modifications, but the accuracy and resolution of these methods remain limited. Here, we present an algorithm, regulatory element prediction based on tissue-specific local epigenetic marks (REPTILE), which integrates histone modification and whole-genome cytosine DNA methylation profiles to identify the precise location of enhancers. We tested the ability of REPTILE to identify enhancers previously validated in reporter assays. Compared with existing methods, REPTILE shows consistently superior performance across diverse cell and tissue types, and the enhancer locations are significantly more refined. We show that, by incorporating base-resolution methylation data, REPTILE greatly improves upon current methods for annotation of enhancers across a variety of cell and tissue types. REPTILE is available at https://github.com/yupenghe/REPTILE/.

Citing Articles

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Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes.

Xie F, Armand E, Yao Z, Liu H, Bartlett A, Margarita Behrens M Cell Genom. 2023; 3(7):100342.

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