TY  - JOUR
TI  - Genome-wide identification of enhancer elements
AU  - Tulin, Sarah
AU  - Barsi, JuliusC.
AU  - Bocconcelli, Carlo
AU  - Smith, Joel
T2  - The International Journal of Developmental Biology
AB  - 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.
PY  - 2016
DO  - 10.1387/ijdb.160108jb
VL  - 60
IS  - 4-5-6
SP  - 141
EP  - 150
J2  - Int. J. Dev. Biol.
LA  - en
SN  - 0214-6282
SN  - 1696-3547
UR  - https://ijdb.ehu.eus/article/160108jb
Y2  - 2024/11/21/23:25:31
ER  -