A trimeric USP11-USP7-TCEAL1 complex stabilizes paused RNAPII to sustain oncogenic transcription [RNA-seq]

During early transcription, RNA polymerase II (RNAPII) undergoes a series of structural transitions controlled by cyclin-dependent kinases. Whether protein ubiquitylation and proteasomal degradation affect the fate of RNAPII at core promoters is less well understood. Here we show that the deubiquitinating enzyme USP11 and its heterodimeric partner USP7 form a trimeric complex with TCEAL1, a member of the poorly understood TCEAL (TCEA/TFIIS-like) protein family. TCEAL1 shares sequence homology with the RNAPII interaction domain of the TCEA/TFIIS elongation factor, which controls the fate of backtracked RNAPII. TCEAL1 stabilizes complexes of USP11 with USP7 and with RNAPII. TCEAL1 is recruited to core promoters upon RNAPII pausing and globally enhances the chromatin association of paused RNAPII. Mechanistically, the USP11/USP7/TCEAL1 complex competes with TFIIS for binding to core promoters and protects RPB8, an essential subunit of RNAPII, from degradation, likely preventing TFIIS-mediated transcript cleavage and RNAPII disassembly. In neuroblastoma and other tumors, TCEAL1-dependent genes define a TGF-beta-dependent gene expression program that is characteristic of mesenchymal and invasive tumor cell types, suggesting that the USP11/USP7/TCEAL1 trimer stabilizes paused RNAPII to support a critical oncogenic gene expression program. Overall design: Using ChIP-sequencing, we assessed changes in the binding of TCEAL1, TFIIS, total RNA Polymerase II and Ser2-phophorylated RNA Polymerase II to chromatin in SHEP cells under control conditions and after exogenous expression of an OHT-activated MYCN-ER construct. The SHEP cells used in the various different experiments further contained either a Dox-inducible shRNA targeting TCEAL1 or an constitutive exogenous overexpression of HA-tagged TCEAL1 (either wild-type or mutant). In some experiments, SHEP cells were also treated with the CDK7 or CDK9 inhibitors THZ1 or NVP-2, respectively. In addition, poly(A)-RNA-sequencing was used for differential gene expression analysis in SHEP cells with an OHT-activated MYCN transgene and a Dox-inducible shRNA targeting TCEAL1.