The super elongation complex (SEC) mediates phase transition of SPT5 during transcriptional pause release

Abstract

Release of promoter‐proximally paused RNA Pol II into elongation is a tightly regulated and rate‐limiting step in metazoan gene transcription. However, the biophysical mechanism underlying pause release remains unclear. Here, we demonstrate that the pausing and elongation regulator SPT5 undergoes phase transition during transcriptional pause release. SPT5 per se is prone to form clusters. The disordered domain in SPT5 is required for pause release and gene activation. During early elongation, the super elongation complex (SEC) induces SPT5 transition into elongation droplets. Depletion of SEC increases SPT5 pausing clusters. Furthermore, disease‐associated SEC mutations impair phase properties of elongation droplets and transcription. Our study suggests that SEC‐mediated SPT5 phase transition might be essential for pause release and early elongation and that aberrant phase properties could contribute to transcription abnormality in diseases.

SPTing across condensates: SEC‐mediated translocation of SPT complex from pausing condensates to elongation condensates

“…The second model suggests a change in the concentrations of condensate components, such as the mediator complex or splicing machinery in Pol II containing condensates. Both models remain probable for DSIF, in line with findings reported here (Guo et al , 2023). Additionally, it is possible that insulator complexes function in preventing the mixing of components from different transcriptional condensates.…”

“…These results align with published biochemical evidence on pause release and transcription elongation (Cramer, 2019). Thus, the results reported by Guo et al (2023) provide a first biochemical glimpse into the dynamics of transcription regulators within condensates when transitioning from one stage to another. Interestingly, the authors find that diseaseassociated mutations alter the properties of transcription condensates and their functional outcome.…”

“…As a first step to address these questions, Guo et al (2023) characterized the propensity of the DSIF complex to undergo condensation in the context of transcriptional pausing and the subsequent step of transcriptional elongation. The DSIF complex consists of two proteins SPT4 and SPT5.…”

Variant-specific pathophysiological mechanisms ofAFF3differently influence transcriptome profiles

“…These nuclear proteins function as transcriptional activators, promoting RNA elongation 1–3 . They share conserved N-terminal (NHD) and C-terminal homology domains (CHD) 4 , an AF4-LAF4-FMR2 (ALF) domain 2,3,5 , which contains the degron motif, a Serine-rich transactivation domain (TAD) 6 , and a nuclear/nucleolar localization sequence (NLS) (Figure 1A). AFF proteins are integral components of transcriptional super elongation complexes (SECs) that include positive transcription elongation factor (P-TEFb) 2,3 .…”

“…They share conserved N-terminal (NHD) and C-terminal homology domains (CHD) 4 , an AF4-LAF4-FMR2 (ALF) domain 2,3,5 , which contains the degron motif, a Serine-rich transactivation domain (TAD) 6 , and a nuclear/nucleolar localization sequence (NLS) (Figure 1A). AFF proteins are integral components of transcriptional super elongation complexes (SECs) that include positive transcription elongation factor (P-TEFb) 2,3 . SECs are made of an AFF family member as scaffold, YEATS domain-containing MLLT proteins (myeloid/lymphoid or mixed-lineage leukemia; translocated to), and an ELL (Elongation Factor for RNA Polymerase II) protein 2 .…”