MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

Baluapuri, Apoorva; Hofstetter, Julia; Stanković, Nevenka Dudvarski; Endres, Theresa; Bhandare, Pranjali; Vos, Seychelle M.; Adhikari, Bikash; Schwarz, Jessica Denise; Narain, Ashwin; Vogt, Markus; Wang, Shuangyan; Düster, Robert; Jung, Lisa Anna; Vanselow, Jens T.; Wiegering, Armin; Geyer, Matthias; Maric, Hans Michael; Gallant, Peter; Walz, Susanne; Schlösser, Andreas; Cramer, Patrick; Eilers, Martin; Wolf, Elmar

doi:10.1016/j.molcel.2019.02.031

Cited by 103 publications

(115 citation statements)

References 67 publications

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“…Unlike activated genes, those down-regulated by either MycER WT or MycER HEA recruited the transcription factor with the lowest efficiency and lacked enrichment of the cognate binding motif (Fig. EV5A,B): hence, as previously proposed (Baluapuri et al, 2019, de Pretis et al, 2017, repression by either MycER WT or MycER HEA may be largely indirect. Moreover, MycER HEArepressed loci included known Myc-dependent genes (Lorenzin et al, 2016, Muhar et al, 2018, Perna et al, 2012, Tesi et al, 2019 (Fig.…”

Section: Sequence Recognition Determines Transcriptional Activationsupporting

confidence: 52%

Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription

Pellanda

Dalsass

Filipuzzi

et al. 2020

Preprint

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Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity: how these binding modes are integrated to determine select transcriptional outputs remains unresolved. We designed mutants of the MYC transcription factor bearing substitutions in residues that contact either the DNA backbone or specific bases within the consensus binding motif (E-box), and profiled their DNA-binding and gene-regulatory activities in murine cells. Our data reveal that non-specific DNA binding is required for MYC to engage onto active regulatory elements in the genome, preceding sequence recognition; beyond merely stabilizing MYC onto select target loci, sequence-specific binding contributes to its precise positioning and -most unexpectedly -to transcriptional activation per se. In particular, at any given binding intensity, promoters targeted via the cognate DNA motif were more frequently activated by MYC. Hence, seemingly promiscuous chromatin interaction profiles actually encompass diverse DNA-binding modalities, driving defined, sequencedependent transcriptional responses.

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Section: Sequence Recognition Determines Transcriptional Activationsupporting

confidence: 52%

Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription

Pellanda

Dalsass

Filipuzzi

et al. 2020

Preprint

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“…This pause is established within the first ~100 nucleotides (nt) downstream of the transcription start site (TSS) by recruitment of the DRB-sensitivity inducing factor (DSIF)—a heterodimer of Spt4 and Spt5 subunits conserved in all eukaryotes—and a metazoan-specific negative elongation factor (NELF) 12 . In human cells, DSIF and NELF recruitment (and thus, pause establishment) depends on activity of Cdk7, a component of transcription initiation factor TFIIH 13–16 , whereas pause release depends on the Cdk9/cyclin T1 complex, also known as positive transcription elongation factor b (P-TEFb) 17 , which phosphorylates residues in Pol II, Spt5, NELF and other components of the paused complex, to convert it into an active elongation complex from which NELF is displaced 18,19 . P-TEFb and its orthologs in yeast are the major CDKs active during the elongation phase of Pol II transcription, phosphorylating Spt5 to enable its function as a processivity factor 20 , and stimulating elongation rate by 3-4-fold 21,22 .…”

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confidence: 99%

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

Parua

Kalan

Benjamin

et al. 2020

Preprint

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Reversible phosphorylation of Pol II and accessory factors helps order the 12 transcription cycle. Here we define two kinase-phosphatase switches that operate 13 at different points in human transcription. Cdk9/cyclin T1 (P-TEFb) catalyzes 14 inhibitory phosphorylation of PP1 and PP4 complexes that localize to 3' and 5' 15 ends of genes, respectively, and have overlapping but distinct specificities for 16Cdk9-dependent phosphorylations of Spt5, a factor instrumental in promoter-17 proximal pausing and elongation-rate control. PP1 dephosphorylates an Spt5 18 carboxy-terminal repeat (CTR), but not Spt5-Ser666, a site between KOW motifs 4 19 and 5, whereas PP4 can target both sites. In vivo, Spt5-CTR phosphorylation 20 decreases as transcription complexes pass the cleavage and polyadenylation 21 signal (CPS) and increases upon PP1 depletion, consistent with a PP1 function in 22In fission yeast, chemical-genetic inhibition of Cdk9 led to rapid, nearly complete 130 dephosphorylation of the Spt5 CTD (T1/2 ~20 sec); the rate of decay decreased ~4-fold in 131 dis2 mutant strains, suggesting that the fast kinetics in dis2 + cells were partly due to the 132 concomitant activation of Dis2 (PP1) when Cdk9 is inactivated 27 . In HCT116 cells, both 133 pThr806 and a phosphorylation outside the CTRs, pSer666, were lost rapidly upon 134 treatment with 250 nM NVP-2 (T1/2 ~10 min), consistent with a similar, reinforcing effect 135 of kinase inhibition and phosphatase activation (Fig. 1d). 136 137

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“…The p21-luc reporter contains a short, truncated core promoter with binding sites for SP1, MIZ1, and MYC (Wu et al, 2003), and also for MXDs. Thus, analysis of (Baluapuri et al, 2019;Kress et al, 2015;Poole and van Riggelen, 2017;Tu et al, 2018). The conditions and mechanisms specifying MYC as either (general) activator or repressor of particular genes are only partly understood.…”

Section: Discussionmentioning

confidence: 99%

“…Elevated expression or activation of MYC is associated with uncontrolled cellular growth and proliferation and supports the development of cancer, and MYC or its homologues are overexpressed, amplified or deregulated in many cancer types (Dang, 2012;Kalkat et al, 2017). MYC has been reported to function as a regulator of specific target genes (Kress et al, 2015;Muhar et al, 2018;Sabo et al, 2014;Walz et al, 2014) and/or as a general amplifier of transcription of active genes on a genome-wide scale (Baluapuri et al, 2019;Gerlach et al, 2017;Lin et al, 2012;Nie et al, 2012). MYC interacts with several coactivators and RNA-polymerase II (Pol II) associated factors including chromatin modifiers, transcription initiation and elongation factors that are implicated in transcription activation, but also with several complexes and assemblies involved in transcriptional repression (Baluapuri et al, 2019;Kress et al, 2015;Poole and van Riggelen, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…MYC has been shown to facilitate the release of promoter-proximally paused Pol II (Rahl et al, 2010), enhance mRNA capping (Cowling and Cole, 2010), facilitate the transfers PAF1 to Pol II (Gerlach et al, 2017;Jaenicke et al, 2016), and enhance rate and processivity of transcription elongation by loading SPT5 onto Pol II (Baluapuri et al, 2019), and thereby support transcription of most active genes. In contrast, rapid depletion of MYC in leukemia and colon cancer cell lines affects transcription of a small subset of genes, suggesting that expression of a rather limited set of activated genes might depend on the presence of MYC (Muhar et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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MXD/MIZ1 complexes activate transcription of MYC-repressed genes

Shostak

Schermann

Diernfellner

et al. 2019

Preprint

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MXD proteins are transcription repressors that antagonize the E-box dependent activation of genes by MYC. MYC together with MIZ1 acts also as a repressor of a subset of genes, including cell cycle inhibitor genes such as p15 and p21. A role of MXDs in regulation of MYC-repressed genes is not known. Here we report that MXDs are functionally expressed in U2OS cells and activate transcription of p15 and p21, and other MYC-repressed genes. Activation of transcription was dependent on the interaction of MXDs with MIZ1, and on an intact DNA binding domain. MIZ1-binding deficient MXD mutants interacted with MAX and were active as repressors of MYC-activated genes but failed to activate MYC-repressed genes. Mutant MXDs with reduced DNA binding affinity interacted with MAX and MIZ1 but neither repressed nor activated transcription. Overexpression of MXDs attenuated proliferation of U2OS cells predominantly via MIZ1-dependent induction of p21. Our data show that MXDs and MYC have a reciprocally antagonistic potential to regulate transcription of mutual target genes.

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MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

Cited by 103 publications

References 67 publications

Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription

Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

MXD/MIZ1 complexes activate transcription of MYC-repressed genes

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