Barsi Julius C.

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Julius C.

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  • Dataset
    GRIPseq data for S. Purpuratus 24 hpf
    ( 2015-01-19) Tulin, Sarah ; Barsi, Julius C. ; Bocconcelli, Carlo ; Smith, Joel
    This dataset is the result of a new method for identifying putative cis-regulatory elements genome wide, termed GRIPseq for Genome-wide Regulatory element Immunoprecipitation. Our protocol combines elements of chromatin conformation capture (e.g., 3C, 4C, Hi-C), chromatin immunoprecipitation, and paired-end high-throughput sequencing with molecular tools that enrich for active cis-regulatory elements across the genome. Our pioneer dataset, available to the community, derives from the purple sea urchin, Stronglyocentrotus purpuratus, mesenchyme blastula embryos collected at 24 hpf. We benchmark our results against independent findings, i.e., rigorously tested cis-elements previously identified and find good congruence at the loci we have investigated, and in particular we find a strong signal-to-noise ratio for known distal elements, marking an improvement over existing methods. A corollary of this approach is the ability, in many cases, to link cis-regulatory elements to the genes they regulate.
  • Article
    Genome-wide identification of enhancer elements
    (UPV/EHU Press, 2016-06) Tulin, Sarah ; Barsi, Julius C. ; Bocconcelli, Carlo ; Smith, Joel
    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.