MPI Campus Seminar: Growing intron loop model – structural basis for initiating spliceosome assembly on transcribing RNA polymerase II

Gene expression in eukaryotes requires synthesis of precursor messenger RNA (pre-mRNA) by RNA polymerase II (Pol II) and processing such as splicing to produce mature mRNA. During splicing, non-coding introns are generally removed from the pre-mRNA in a co-transcriptional manner as the nascent RNA emerges from Pol II. Co-transcriptional splicing enhances the efficiency and accuracy of pre-mRNA processing and begins with recruitment of the U1 small nuclear ribonucleoprotein (U1 snRNP) to the 5’ splice site in the nascent pre-mRNA. Here, we report the cryo-electron microscopy structure of a mammalian transcribing Pol II-U1 snRNP complex. The structure reveals that Pol II and U1 snRNP interact directly. This interaction positions the 5’ splice site of the pre-mRNA near the RNA exit site of Pol II. Our biochemical and structural data showed that extension of the pre-mRNA retains the 5′ splice site, leading to formation of a “growing intron loop.” Loop formation may facilitate scanning of the nascent pre-mRNA for the 3′ splice site, functional pairing of distant intron ends, and prespliceosome assembly. Our results provide a starting point for a mechanistic analysis of co-transcriptional spliceosome assembly and the biogenesis of mRNA isoforms by alternative splicing.