Abstract

Gene expression in eukaryotes requires synthesis of pre-mRNA by RNA polymerase II (Pol II) and processing to produce mature mRNA. During splicing, introns are removed in a co-transcriptional manner as the nascent RNA emerges from the Pol II surface. Using cryo-electron microscopy (cryo-EM), we determined the structure of a mammalian transcribing Pol II-U1 snRNP complex that revealed the molecular basis of a direct interaction between the transcription and splicing machineries. Furthermore, we identified that transcription elongation factor SPT6 facilitates the recruitment of U1 snRNP to elongating Pol II. This multivalent interaction between U1 snRNP and the transcription elongation complex may both allow efficient spliceosome assembly and ensure transcription processivity. Beyond co-transcriptional recruitment of splicing factors, transcription elongation rate also affects co-transcriptional processes, yet the mechanism of transcription braking remains unclear. Here we report cryo-EM structures of a DNA helicase RECQL5 bound to multiple transcription elongation complexes. Combined with biochemical analysis, we identify a RECQL5 helix responsible for Pol II interaction and slowdown of transcription elongation. We further reveal that the transcription-coupled DNA repair (TCR) complex allows Pol II to overcome RECQL5 -induced transcription braking. Our results suggest a model in which RECQL5 and the TCR complex coordinately regulate the transcription elongation rate to ensure transcription efficiency while maintaining genome stability.