Search for endogenous small RNAs affecting alternative splicing by TGS

MARIANO ALLÓ, PAOLA BERTUCCI, ENERITZ AGIRRE, EDUARDO EYRAS, JUAN VALCARCEL Y ALBERTO R. KORNBLIHTT

San Miguel de Tucuman, Tucuman, Argentina

Congreso; SAIB; 2009

Small 21- to 25-nucleotide RNAs have diverse biological roles in eukaryotes, including the silencing of repetitive sequences, antiviral defense by small interfering RNAs (siRNAs) and developmental gene regulation by microRNAs (miRNAs). When these small RNAs are fully complementary to their targets can cause specific mRNA cleavage, whereas those with mismatches can mediate translational inhibition. More recently another pathway has emerged: siRNA-induced transcriptional gene silencing (TGS), where small double stranded RNA molecules have been implicated in gene silencing at the level of transcription through DNA methylation, modifications in histone tails and chromatin structure. We have found that exogenous siRNAs are able to affect alternative splicing (AS) events located closely to their target sites by means of the TGS process. In the search for endogenous examples of this process we performed ChIP-seq (deep sequencing) against AGO proteins (key players of TGS) and we’ve analyzed these data in connection with different small RNA population databases available on “Gene Expression Omnibus” from NCBI. Moreover, we’ve used deep sequencing databases from ChIP-seq experiments against histone tail modifications and Pol II and filter our previous data with this information. This analysis will allow us to find endogenous small RNAs that could be affecting AS in different genes.