In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF along with other proteins. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns in human cells, we discovered that the nascent 5′ splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. This association functionally corresponds with splicing outcome, involves bona fide 5′ splice sites and cryptic intronic sites, and occurs transcriptome-wide. Overall, our findings reveal that the upstream 5′ splice sites remain attached to the transcriptional machinery during intron synthesis and are thus brought into proximity of the 3′ splice sites; potentially mediating the rapid splicing of long introns.
Bibliographical noteFunding Information:
The research was funded by the Israel Science Foundation [ISF 671/18, ISF 142/13, 1140/ 17]; German-Israel Foundation for R&D [GIF I-1460]; Israel Cancer Association [ICA 20170034]; Israel Cancer Research Foundation [ICRF PG-18-105]; and United States – Israel Binational Science Foundation [BSF 2017086].
© 2021, The Author(s).