Genome-wide identification of enhancer elements

• Sarah Tulin ^[2] ; Julius C. Barsi ^[1] ; Carlo Bocconcelli ^[2] ; Joel Smith ^[2]
  1. [1] California Institute of Technology

     California Institute of Technology

     Estados Unidos

     
  2. [2] Eugene Bell Center for Regenerative Biology and Tissue Engineering, USA
• Localización: International journal of developmental biology, ISSN 0214-6282, Vol. 60, Nº. 4-6, 2016, págs. 141-150
• Idioma: inglés
• Texto completo no disponible (Saber más ...)
• Resumen

  • 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.