Improved regulatory element prediction based on tissue-specific local epigenomic signatures.
Proc Natl Acad Sci U S A
; 114(9): E1633-E1640, 2017 02 28.
Article
em En
| MEDLINE
| ID: mdl-28193886
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/.
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Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Regulação da Expressão Gênica
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Elementos Facilitadores Genéticos
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Epigênese Genética
Idioma:
En
Ano de publicação:
2017
Tipo de documento:
Article