The yeast transcription elongation factor Spt4/5 is a sequence‐specific RNA binding protein

Abstract

The heterodimeric transcription elongation factor Spt4/Spt5 (Spt4/5) tightly associates with RNAPII to regulate both transcriptional elongation and co-transcriptional pre-mRNA processing; however, the mechanisms by which Spt4/5 acts are poorly understood. Recent studies of the human and Drosophila Spt4/5 complexes indicate that they can bind nucleic acids in vitro. We demonstrate here that yeast Spt4/5 can bind in a sequence-specific manner to single stranded RNA containing AAN repeats. Furthermore, we show that the major protein determinants for RNA-binding are Spt4 together with the NGN domain of Spt5 and that the KOW domains are not required for RNA recognition. These findings attribute a new function to a domain of Spt4/5 that associates directly with RNAPII, making significant steps towards elucidating the mechanism behind transcriptional control by Spt4/5.

Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila

“…Indeed, there is increasing evidence that RNArelated activities are important for processes occurring on chromatin templates [45,46]. For example, RNA-binding activity has been recently demonstrated for the DSIF (Spt4/Spt5) factor of RNA polymerase II pausing [47].…”

Spt4 Promotes Pol I Processivity and Transcription Elongation

“…These findings suggested that the Spt4/5 complex may play a distinct role from Spt6 in transcription by Pol II. Since these early studies, many additional studies have characterized the role of the Spt4/5 complex in transcription by Pol II, and the most widely accepted hypothesis is that this complex may help the polymerase to overcome pausing (especially promoter-proximal pausing), traverse nucleosomes, and aid in nascent RNA processing [ 25 , 26 , 27 , 28 ]. Interestingly, Spt4/5 is the only known transcription factor that is conserved throughout all domains of life (with the bacterial homolog of SPT5 being nusG ), emphasizing the importance of this factor in transcription in potentially all organisms [ 29 ].…”

Targeting Spt5-Pol II by Small-Molecule Inhibitors Uncouples Distinct Activities and Reveals Additional Regulatory Roles

“…Genes known to be highly susceptible to inhibition via promoter-proximal pausing are those that are immediately activated in response to stress and extracellular signals such as heat shock and proinflammatory genes (Boehm et al, 2003;Diamant and Dikstein, 2013;Missra and Gilmour, 2010;Rougvie and Lis, 1990;Wu et al, 2003). During elongation, Spt5 has the ability to stabilize Pol II on the DNA template by interacting with upstream sequences and with RNA (Bernecky et al, 2016;Blythe et al, 2016;Crickard et al, 2016;Hirtreiter et al, 2010;Klein et al, 2011;Martinez-Rucobo et al, 2011). This activity was recently implicated in maintaining high transcriptional speed on long mRNAs (Fitz et al, 2018).…”