Genome wide exon trapping

We report the result of testing the splicing potential of random human genomic sequences. We used randomly fragmented HEK293 DNA in a splicing reporter assay to survey the genome for genomic sequences capable of splicing autonomously as a typical internal exon. From ~10 billion sequenced reads we obtained millions of sequences in the human genome capable of splicing autonomously. A read threshold of 100 yields ~1.25 million exons while also capturing most human mRNA exons. Overall design: Randomly fragmented HEK293 gDNA was assembled into exon trapping reporter assay plasmids. Reporter assays were transiently transfected in HEK293 cells. RNA was extracted and RT-PCR was performed to isolate trapped exons and attach Illumina sequencing platform sequences. Trapped exons were mapped back to the genome to recover the genomic coordinates, and associated read counts, of exons autonomously trapped from the random HEK293 DNA fragments.