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 GRIPseq 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.

Genome-wide analysis of chromatin accessibility using ATAC-seq

“…Shashikant et al (2018b) used ATAC-seq for the high-throughput identification of cisregulatory modules that are components of a transcriptional network deployed in skeletogenic cells of Strongylocentrotus purpuratus (Shashikant et al, 2018a). In related work, Tulin, Barsi, Bocconcelli, and Smith (2016) used a different, immunoprecipitationbased approach, termed GRIP-seq, to produce a database of putative, active enhancers from whole, 24-h S. purpuratus embryos.…”