Ensembl regulation resources.

Daniel R Zerbino,Simon Brent,Dan Sheppard,Quentin Raffaillac-Desfosses,Ilias Lavidas,Rhoda Kinsella,Ewan Birney,Michael Nuhn,Ian Dunham,Damian Keefe,Emily Perry,Bethan Pritchard,Thomas Juetteman,Steven P Wilder,Anne Parker,Ikhlak Ahmed,Daniel Sobral,Paul Flicek,Stefan Gräf,Nathan Johnson,Ridwan M Amode ,Stephen J Trevanion

doi:10.1093/database/bav119

Daniel R Zerbino, Simon Brent + Show 20 more

Open Access

https://doi.org/10.1093/database/bav119

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Abstract

New experimental techniques in epigenomics allow researchers to assay a diversity of highly dynamic features such as histone marks, DNA modifications or chromatin structure. The study of their fluctuations should provide insights into gene expression regulation, cell differentiation and disease. The Ensembl project collects and maintains the Ensembl regulation data resources on epigenetic marks, transcription factor binding and DNA methylation for human and mouse, as well as microarray probe mappings and annotations for a variety of chordate genomes. From this data, we produce a functional annotation of the regulatory elements along the human and mouse genomes with plans to expand to other species as data becomes available. Starting from well-studied cell lines, we will progressively expand our library of measurements to a greater variety of samples. Ensembl’s regulation resources provide a central and easy-to-query repository for reference epigenomes. As with all Ensembl data, it is freely available at http://www.ensembl.org, from the Perl and REST APIs and from the public Ensembl MySQL database server at ensembldb.ensembl.org.Database URL: http://www.ensembl.org

Highlights

In addition to providing long-term storage of genetic information across cell divisions, DNA is a physical molecule with dynamic biochemical activity
Histone modifications and transcription factors (TF) binding locations previously identified with chromatin immunoprecipitation followed by microarray hybridisation (ChIP-chip) [12] generally employ high-throughput sequencing (ChIP-seq) [13, 14]; DNA methylation is assayed with MeDIP [15] or bisulphite sequencing [16]; regions of open chromatin are identified with Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) [17], DNase-seq [18] or ATAC-seq [19]
The Ensembl Variant Effect Predictor (VEP) [50] has recently added regulatory features to its set of predicted consequences that can be associated with single nucleotide polymorphisms (SNP) or de novo variants

Summary

Introduction

In addition to providing long-term storage of genetic information across cell divisions, DNA is a physical molecule with dynamic biochemical activity. Histone modifications and TF binding locations previously identified with chromatin immunoprecipitation followed by microarray hybridisation (ChIP-chip) [12] generally employ high-throughput sequencing (ChIP-seq) [13, 14]; DNA methylation is assayed with MeDIP [15] or bisulphite sequencing [16]; regions of open chromatin are identified with Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) [17], DNase-seq [18] or ATAC-seq [19] These measurements can be used to identify regulatory elements [20,21,22], and characterise disease [23]. Large consortia have already produced vast reference datasets [24,25,26]

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