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Genome-wide identification of enhancer elements

Tulin, Sarah and Barsi, Julius C. and Bocconcelli, Carlo and Smith, Joel (2016) Genome-wide identification of enhancer elements. International Journal of Developmental Biology, 60 . pp. 141-150. ISSN 0214-6282. http://resolver.caltech.edu/CaltechAUTHORS:20160811-123716884

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1387/ijdb.160108jbDOIArticle
http://www.ijdb.ehu.es/web/paper/160108jb/genome-wide-identification-of-enhancer-elementsPublisherArticle
http://www.ijdb.ehu.es/data/16/160108jb/IntJDevBiol-160108jb-SuppMaterial.pdfPublisherSupplemental Material
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.
Subject Keywords:GRIP-seq, chromatin conformation capture, anti-Pol-II, sea urchin development
Record Number:CaltechAUTHORS:20160811-123716884
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20160811-123716884
Official Citation:Genome-wide identification of enhancer elements Sarah Tulin, Julius C. Barsi, Carlo Bocconcelli and Joel Smith Int. J. Dev. Biol. 60: 141 - 150 (2016) doi: 10.1387/ijdb.160108jb
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:69571
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:11 Aug 2016 21:41
Last Modified:11 Aug 2016 21:41

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