Genome-wide identification of enhancer elements
Abstract
We present a prospective genome-wide regulatory element database for the sea urchin embryo and the modified chromosome capture-related methodology used to create it. The method we developed is termed GRIP-seq for genome-wide regulatory element immunoprecipitation and combines features of chromosome conformation capture, chromatin immunoprecipitation, and paired-end next-generation sequencing with molecular steps that enrich for active cis-regulatory elements associated with basal transcriptional machinery. The first GRIP-seq database, available to the community, comes from S. purpuratus 24 hpf embryos and takes advantage of the extremely well-characterized cis-regulatory elements in this system for validation. In addition, using the GRIP-seq database, we identify and experimentally validate a novel, intronic cis-regulatory element at the onecut locus. We find GRIP-seq signal sensitively identifies active cis-regulatory elements with a high signal-to-noise ratio for both distal and intronic elements. This promising GRIP-seq protocol has the potential to address a rate-limiting step in resolving comprehensive, predictive network models in all systems.
Additional Information
© 2016 UPV/EHU Press. Accepted: 14 June 2016. Accession Numbers: GRIP-seq data and peak calling files available at ArrayExpress, accession number E-MTAB-3607. Authors' contributions: ST participated in protocol development, creating the dataset, data analysis, and drafting the manuscript. JCB performed all experiments involving the onecut gene, participated in data analysis and drafting the manuscript. CB participated in the design of the study, performed experiments to develop the method and create the GRIP-seq dataset. JS conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.Attached Files
Published - ft141.pdf
Supplemental Material - IntJDevBiol-160108jb-SuppMaterial.pdf
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Additional details
- Eprint ID
- 69571
- Resolver ID
- CaltechAUTHORS:20160811-123716884
- Created
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2016-08-11Created from EPrint's datestamp field
- Updated
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2021-11-11Created from EPrint's last_modified field