Transcriptome-wide maps of STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

We report the application of enhanced cross-linking immunoprecipitation (eCLIP) sequencing technology for high-throughput profiling of STRAP-RNA interactions in mouse embryos (E9.5) or embryoid body (EB) cells. Based on the eCLIP-seq data, we computationally identified a transcriptome-wide set of high-confidence peaks (over ten thousands) and most of STRAP-peaks distributed in the murine genome by defining certain exons and introns as well as their intersection. STRAP eCLIP signals in embryos were dramatically enriched at exon/intron and intron/exon borders. Numerous STRAP peaks are significantly enriched on the genes with critical roles in early organ development. Finally, we show two examples of STRAP-RNA binding that link to its regulated genes at the alternative splicing level. Together, we uncover the position- and context- dependent effects of STRAP on splicing regulation during mouse embryonic stem cells lineage commitment. Our studies provide a very useful platform to decipher STRAP's role in the many steps in RNA biogenesis for future studies. Overall design: Examination of STRAP-RNA interactions in mouse embryos and embryoid body cells.