DRP000087
Survey of short RNA expression after interference of RNAs expressed from             retrotransposons
Here, we report in detail the first use of RNA interference against             LINE-1 transposed element RNAs, in an effort to ascertain their functional significance.             Using mouse myoblasts as a model system, we observed clear phenotypic consequences post             knock-down of LINE-1 transcription. Deep sequencing of capped mRNAs and short RNAs was             then used to survey transcriptional activity in wild-type and LINE-1 knock-down             myoblasts, revealing strong expression changes within the gene networks that govern             muscle cell differentiation, thousands of differentially expressed LINE-1 copies and             evidence for a global mechanism by which LINE-1 RNAs may regulate protein-coding gene             expression.
To assess the regulatory role of LINE-1 teRNAs in myogenesis - and its             disruption by LINE-1 RNAi - we generated genome-wide maps of transcriptional activity in             C2C12 muscle cells (myoblasts) poised for differentiation. 18 million Cap Analysis Gene             Expression (CAGE) tags were sequenced using an updated protocol that incorporated             massively parallel sequencing and tags extended to an average length of             27nt.