RNA polymerase II (pol II) frequently pauses in the promoter-proximal region to ensure gene-specific regulation and RNA quality control. New research demonstrates that the cyclin-dependent kinase Cdk7 can act to establish the promoter-proximal pause, through its control of the TFIIE-DSIF switch, and to release Pol II from the pause, through its ability to activate Cdk9. Promoter-proximal pausing by RNA polymerase II (Pol II) ensures gene-specific regulation and RNA quality control. Structural considerations suggested a requirement for initiation-factor eviction in elongation-factor engagement and pausing of transcription complexes. Here we show that selective inhibition of Cdk7—part of TFIIH—increases TFIIE retention, prevents DRB sensitivity–inducing factor (DSIF) recruitment and attenuates pausing in human cells. Pause release depends on Cdk9–cyclin T1 (P-TEFb); Cdk7 is also required for Cdk9-activating phosphorylation and Cdk9-dependent downstream events—Pol II C-terminal domain Ser2 phosphorylation and histone H2B ubiquitylation—in vivo. Cdk7 inhibition, moreover, impairs Pol II transcript 3′-end formation. Cdk7 thus acts through TFIIE and DSIF to establish, and through P-TEFb to relieve, barriers to elongation: incoherent feedforward that might create a window to recruit RNA-processing machinery. Therefore, cyclin-dependent kinases govern Pol II handoff from initiation to elongation factors and cotranscriptional RNA maturation.

Peroxisome proliferator activated receptor-gamma co-activator-1alpha (PGC-1alpha) is a transcriptional co-activator that coordinately regulates the expression of distinct sets of metabolism-related genes in different tissues. Here we show that PGC-1alpha expression is reduced in skeletal muscles from mice lacking the sirtuin family deacetylase SIRT1. Conversely, SIRT1 activation or overexpression in differentiated C2C12 myotubes increased PGC-1alpha mRNA expression. The transcription-promoting effects of SIRT1 occurred through stimulation of PGC-1alpha promoter activity and were enhanced by co-transfection of myogenic factors, such as myocyte enhancer factor 2 (MEF2) and, especially, myogenic determining factor (MyoD). SIRT1 bound to the proximal promoter region of the PGC-1alpha gene, an interaction potentiated by MEF2C or MyoD, which also interact with this region. In the presence of MyoD, SIRT1 promoted a positive autoregulatory PGC-1alpha expression loop, such that overexpression of PGC-1alpha increased PGC-1alpha promoter activity in the presence of co-expressed MyoD and SIRT1. Chromatin immunoprecipitation showed that SIRT1 interacts with PGC-1alpha promoter and increases PGC-1alpha recruitment to its own promoter region. Immunoprecipitation assays further showed that SIRT1-PGC-1alpha interactions are enhanced by MyoD. Collectively, these data indicate that SIRT1 controls PGC-1alpha gene expression in skeletal muscle and that MyoD is a key mediator of this action. The involvement of MyoD in SIRT1-dependent PGC-1alpha expression may help to explain the ability of SIRT1 to drive muscle-specific gene expression and metabolism. Autoregulatory control of PGC-1alpha gene transcription seems to be a pivotal mechanism for conferring a transcription-activating response to SIRT1 in skeletal muscle.

Immunotherapy resistance in non–small cell lung cancer (NSCLC) may be mediated by an immunosuppressive microenvironment, which can be shaped by the mutational landscape of the tumor. Here, we observed genetic alterations in the PTEN/PI3K/AKT/mTOR pathway and/or loss of PTEN expression in >25% of patients with NSCLC, with higher frequency in lung squamous carcinomas (LUSC). Patients with PTEN-low tumors had higher levels of PD-L1 and PD-L2 and showed worse progression-free survival when treated with immunotherapy. Development of a Pten-null LUSC mouse model revealed that tumors with PTEN loss were refractory to antiprogrammed cell death protein 1 (anti–PD-1), highly metastatic and fibrotic, and secreted TGFβ/CXCL10 to promote conversion of CD4+ lymphocytes into regulatory T cells (Treg). Human and mouse PTEN-low tumors were enriched in Tregs and expressed higher levels of immunosuppressive genes. Importantly, treatment of mice bearing Pten-null tumors with TLR agonists and anti-TGFβ antibody aimed to alter this immunosuppressive microenvironment and led to tumor rejection and immunologic memory in 100% of mice. These results demonstrate that lack of PTEN causes immunotherapy resistance in LUSCs by establishing an immunosuppressive tumor microenvironment that can be reversed therapeutically. Significance: PTEN loss leads to the development of an immunosuppressive microenvironment in lung cancer that confers resistance to anti–PD-1 therapy, which can be overcome by targeting PTEN loss–mediated immunosuppression.

UCP3 (uncoupling protein-3) is a mitochondrial membrane transporter expressed preferentially in skeletal muscle. UCP3 lowers mitochondrial membrane potential and protects muscle cells against an overload of fatty acids, and it probably reduces excessive production of reactive oxygen species. Accordingly, ucp3 gene transcription is highly sensitive to fatty acid-dependent stimulation and also to other unrelated stress signals. In this study, glucocorticoids are identified as major inducers of ucp3 gene transcription in muscle. Glucocorticoids activate the transcription of the ucp3 gene through a glucocorticoid receptor-binding site in the promoter region. Glucocorticoids are capable of inducing ucp3 gene transcription independently from the myogenic regulatory factor MyoD, in contrast with the transcriptional activation of the ucp3 gene through other nuclear hormone receptors. An interplay of regulatory factors modulates positively (p300) or negatively (histone deacetylases) the action of glucocorticoids on ucp3 gene transcription via histone acetylation or deacetylation processes, respectively. Among them, SIRT1 acts as a major repressor of ucp3 gene expression in response to glucocorticoids. The action of SIRT1 requires its deacetylase activity and results in histone deacetylation in the ucp3 promoter. Moreover, it involves a specific impairment of association of p300 with the glucocorticoid receptor. Agents activating SIRT1, such as resveratrol, repress ucp3 gene expression. The control of SIRT1 activity via the metabolic redox status of the cell points to a novel regulatory pathway of ucp3 gene transcription in response to metabolic and stress signaling in muscle cells.

Cdk7, the CDK-activating kinase and transcription factor IIH component, is a target of inhibitors that kill cancer cells by exploiting tumor-specific transcriptional dependencies. However, whereas selective inhibition of analog-sensitive (AS) Cdk7 in colon cancer-derived cells arrests division and disrupts transcription, it does not by itself trigger apoptosis efficiently. Here, we show that p53 activation by 5-fluorouracil or nutlin-3 synergizes with a reversible Cdk7as inhibitor to induce cell death. Synthetic lethality was recapitulated with covalent inhibitors of wild-type Cdk7, THZ1, or the more selective YKL-1-116. The effects were allele specific; a CDK7as mutation conferred both sensitivity to bulky adenine analogs and resistance to covalent inhibitors. Non-transformed colon epithelial cells were resistant to these combinations, as were cancer-derived cells with p53-inactivating mutations. Apoptosis was dependent on death receptor DR5, a p53 transcriptional target whose expression was refractory to Cdk7 inhibition. Therefore, p53 activation induces transcriptional dependency to sensitize cancer cells to Cdk7 inhibition.