The upstream 5′ splice site remains associated to the transcription machinery during intron synthesis

Yodfat Leader, Galit Lev Maor*, Matan Sorek, Ronna Shayevitch, Maram Hussein, Ofir Hameiri, Luna Tammer, Jonathan Zonszain, Ifat Keydar, Dror Hollander, Eran Meshorer, Gil Ast*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number4545
JournalNature Communications
Issue number1
StatePublished - 1 Dec 2021


FundersFunder number
German-Israel foundation for R&DGIF I-1460
Israel Cancer Research FundPG-18-105
United States - Israel Binational Science FoundationBSF 2017086
German-Israeli Foundation for Scientific Research and DevelopmentI-1460
Israel Cancer AssociationICA 20170034
Israel Science Foundation1140/ 17, ISF 671/18, ISF 142/13


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