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https://www.readbyqxmd.com/read/27863397/targeting-gli-by-gant61-involves-mechanisms-dependent-on-inhibition-of-both-transcription-and-dna-licensing
#1
Ruowen Zhang, Jiahui Wu, Sylvain Ferrandon, Katie J Glowacki, Janet A Houghton
The GLI genes are transcription factors and in cancers are oncogenes, aberrantly and constitutively activated. GANT61, a specific GLI inhibitor, has induced extensive cytotoxicity in human models of colon cancer. The FOXM1 promoter was determined to be a transcriptional target of GLI1. In HT29 cells, inhibition of GLI1 binding at the GLI consensus sequence by GANT61 led to inhibited binding of Pol II, the pause-release factors DSIF, NELF and p-TEFb. The formation of R-loops (RNA:DNA hybrids, ssDNA), were reduced by GANT61 at the FOXM1 promoter...
November 15, 2016: Oncotarget
https://www.readbyqxmd.com/read/27833949/the-emerging-picture-of-cdk9-p-tefb-more-than-20-years-of-advances-since-pitalre
#2
REVIEW
Nikolas Ferreira Dos Santos Paparidis, Maxwell Castro Durvale, Fernanda Canduri
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation...
November 11, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27716820/gdown1-associates-efficiently-with-rna-polymerase-ii-after-promoter-clearance-and-displaces-tfiif-during-transcript-elongation
#3
Elizabeth DeLaney, Donal S Luse
Pausing during the earliest stage of transcript elongation by RNA polymerase II (Pol II) is a nearly universal control point in metazoan gene expression. The substoichiometric Pol II subunit Gdown1 facilitates promoter proximal pausing in vitro in extract-based transcription reactions, out-competes the initiation/elongation factor TFIIF for binding to free Pol II and co-localizes with paused Pol II in vivo. However, we have shown that Gdown1 cannot functionally associate with the Pol II preinitiation complex (PIC), which contains TFIIF...
2016: PloS One
https://www.readbyqxmd.com/read/27353326/multiple-p-tefbs-cooperatively-regulate-the-release-of-promoter-proximally-paused-rna-polymerase-ii
#4
Xiaodong Lu, Xinxing Zhu, You Li, Min Liu, Bin Yu, Yu Wang, Muhua Rao, Haiyang Yang, Kai Zhou, Yao Wang, Yanheng Chen, Meihua Chen, Songkuan Zhuang, Lin-Feng Chen, Runzhong Liu, Ruichuan Chen
The association of DSIF and NELF with initiated RNA Polymerase II (Pol II) is the general mechanism for inducing promoter-proximal pausing of Pol II. However, it remains largely unclear how the paused Pol II is released in response to stimulation. Here, we show that the release of the paused Pol II is cooperatively regulated by multiple P-TEFbs which are recruited by bromodomain-containing protein Brd4 and super elongation complex (SEC) via different recruitment mechanisms. Upon stimulation, Brd4 recruits P-TEFb to Spt5/DSIF via a recruitment pathway consisting of Med1, Med23 and Tat-SF1, whereas SEC recruits P-TEFb to NELF-A and NELF-E via Paf1c and Med26, respectively...
August 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/26789250/structure-of-transcribing-mammalian-rna-polymerase-ii
#5
Carrie Bernecky, Franz Herzog, Wolfgang Baumeister, Jürgen M Plitzko, Patrick Cramer
RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript...
January 28, 2016: Nature
https://www.readbyqxmd.com/read/26257281/thz1-reveals-roles-for-cdk7-in-co-transcriptional-capping-and-pausing
#6
Kyle A Nilson, Jiannan Guo, Michael E Turek, John E Brogie, Elizabeth Delaney, Donal S Luse, David H Price
The Cdk7 subunit of TFIIH phosphorylates RNA polymerase II (Pol II) during initiation, and, while recent studies show that inhibition of human Cdk7 negatively influences transcription, the mechanisms involved are unclear. Using in vitro transcription with nuclear extract, we demonstrate that THZ1, a covalent Cdk7 inhibitor, causes defects in Pol II phosphorylation, co-transcriptional capping, promoter proximal pausing, and productive elongation. THZ1 does not affect initiation but blocks essentially all Pol II large subunit C-terminal domain (CTD) phosphorylation...
August 20, 2015: Molecular Cell
https://www.readbyqxmd.com/read/26217014/characterization-of-the-human-transcription-elongation-factor-rtf1-evidence-for-nonoverlapping-functions-of-rtf1-and-the-paf1-complex
#7
Qing-Fu Cao, Junichi Yamamoto, Tomoyasu Isobe, Shumpei Tateno, Yuki Murase, Yexi Chen, Hiroshi Handa, Yuki Yamaguchi
Restores TBP function 1 (Rtf1) is generally considered to be a subunit of the Paf1 complex (PAF1C), a multifunctional protein complex involved in histone modification and transcriptional or posttranscriptional regulation. Rtf1, however, is not stably associated with the PAF1C in most species except Saccharomyces cerevisiae, and its biochemical functions are not well understood. Here, we show that human Rtf1 is a transcription elongation factor that may function independently of the PAF1C. Rtf1 requires "Rtf1 coactivator" activity, which is most likely unrelated to the PAF1C or DSIF, for transcriptional activation in vitro...
October 2015: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/25675981/the-integrator-complex-controls-the-termination-of-transcription-at-diverse-classes-of-gene-targets
#8
Jeffrey R Skaar, Andrea L Ferris, Xiaolin Wu, Anita Saraf, Kum Kum Khanna, Laurence Florens, Michael P Washburn, Stephen H Hughes, Michele Pagano
Complexes containing INTS3 and either NABP1 or NABP2 were initially characterized in DNA damage responses, but their biochemical function remained unknown. Using affinity purifications and HIV Integration targeting-sequencing (HIT-Seq), we find that these complexes are part of the Integrator complex, which binds RNA Polymerase II and regulates specific target genes. Integrator cleaves snRNAs as part of their processing to their mature form in a mechanism that is intimately coupled with transcription termination...
March 2015: Cell Research
https://www.readbyqxmd.com/read/24972996/characteristic-bimodal-profiles-of-rna-polymerase-ii-at-thousands-of-active-mammalian-promoters
#9
Mathieu Quinodoz, Cédric Gobet, Felix Naef, Kyle B Gustafson
BACKGROUND: In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of PolII through sequential promoter states. RESULTS: Here, we analyze PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans...
2014: Genome Biology
https://www.readbyqxmd.com/read/24968874/dsif-and-nelf-interact-with-integrator-to-specify-the-correct-post-transcriptional-fate-of-snrna-genes
#10
Junichi Yamamoto, Yuri Hagiwara, Kunitoshi Chiba, Tomoyasu Isobe, Takashi Narita, Hiroshi Handa, Yuki Yamaguchi
The elongation factors DSIF and NELF are responsible for promoter-proximal RNA polymerase II (Pol II) pausing. NELF is also involved in 3' processing of replication-dependent histone genes, which produce non-polyadenylated mRNAs. Here we show that DSIF and NELF contribute to the synthesis of small nuclear RNAs (snRNAs) through their association with Integrator, the large multisubunit complex responsible for 3' processing of pre-snRNAs. In HeLa cells, Pol II, Integrator, DSIF and NELF accumulate at the 3' end of the U1 snRNA gene...
2014: Nature Communications
https://www.readbyqxmd.com/read/24050178/control-of-transcriptional-elongation
#11
REVIEW
Hojoong Kwak, John T Lis
Elongation is becoming increasingly recognized as a critical step in eukaryotic transcriptional regulation. Although traditional genetic and biochemical studies have identified major players of transcriptional elongation, our understanding of the importance and roles of these factors is evolving rapidly through the recent advances in genome-wide and single-molecule technologies. Here, we focus on how elongation can modulate the transcriptional outcome through the rate-liming step of RNA polymerase II (Pol II) pausing near promoters and how the participating factors were identified...
2013: Annual Review of Genetics
https://www.readbyqxmd.com/read/23921639/chromatin-loop-organization-of-the-junb-locus-in-mouse-dendritic-cells
#12
Tamara Salem, Tiphanie Gomard, Franck Court, Gabriel Moquet-Torcy, Frédérique Brockly, Thierry Forné, Marc Piechaczyk
The junb gene behaves as an immediate early gene in bacterial lipopolysaccharide (LPS)-stimulated dendritic cells (DCs), where its transient transcriptional activation is necessary for the induction of inflammatory cytokines. junb is a short gene and its transcriptional activation by LPS depends on the binding of NF-κB to an enhancer located just downstream of its 3' UTR. Here, we have addressed the mechanisms underlying the transcriptional hyper-reactivity of junb. Using transfection and pharmacological assays to complement chromatin immunoprecipitation analyses addressing the localization of histones, polymerase II, negative elongation factor (NELF)-, DRB sensitivity-inducing factor (DSIF)- and Positive Transcription Factor b complexes, we demonstrate that junb is a RNA Pol II-paused gene where Pol II is loaded in the transcription start site domain but poorly active...
October 2013: Nucleic Acids Research
https://www.readbyqxmd.com/read/23624258/transcriptional-control-by-nf-%C3%AE%C2%BAb-elongation-in-focus
#13
REVIEW
Gil Diamant, Rivka Dikstein
The NF-κB family of transcription factors governs the cellular reaction to a variety of extracellular signals. Following stimulation, NF-κB activates genes involved in inflammation, cell survival, cell cycle, immune cell homeostasis and more. This review focuses on studies of the past decade that uncover the transcription elongation process as a key regulatory stage in the activation pathway of NF-κB. Of interest are studies that point to the elongation phase as central to the selectivity of target gene activation by NF-κB...
September 2013: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/23589332/brd4-coordinates-recruitment-of-pause-release-factor-p-tefb-and-the-pausing-complex-nelf-dsif-to-regulate-transcription-elongation-of-interferon-stimulated-genes
#14
Mira C Patel, Maxime Debrosse, Matthew Smith, Anup Dey, Walter Huynh, Naoyuki Sarai, Tom D Heightman, Tomohiko Tamura, Keiko Ozato
RNA polymerase II (Pol II) and the pausing complex, NELF and DSIF, are detected near the transcription start site (TSS) of many active and silent genes. Active transcription starts when the pause release factor P-TEFb is recruited to initiate productive elongation. However, the mechanism of P-TEFb recruitment and regulation of NELF/DSIF during transcription is not fully understood. We investigated this question in interferon (IFN)-stimulated transcription, focusing on BRD4, a BET family protein that interacts with P-TEFb...
June 2013: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/23340209/mediator-med23-regulates-basal-transcription-in-vivo-via-an-interaction-with-p-tefb
#15
Wei Wang, Xiao Yao, Yan Huang, Xiangming Hu, Runzhong Liu, Dongming Hou, Ruichuan Chen, Gang Wang
The Mediator is a multi-subunit complex that transduces regulatory information from transcription regulators to the RNA polymerase II apparatus. Growing evidence suggests that Mediator plays roles in multiple stages of eukaryotic transcription, including elongation. However, the detailed mechanism by which Mediator regulates elongation remains elusive. In this study, we demonstrate that Mediator MED23 subunit controls a basal level of transcription by recruiting elongation factor P-TEFb, via an interaction with its CDK9 subunit...
January 2013: Transcription
https://www.readbyqxmd.com/read/23202475/transcription-elongation-factors-dsif-and-nelf-promoter-proximal-pausing-and-beyond
#16
REVIEW
Yuki Yamaguchi, Hirotaka Shibata, Hiroshi Handa
DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF) were originally identified as factors responsible for transcriptional inhibition by 5,6-dichloro-1-beta-d-ribofuranosyl-benzimidazole (DRB) and were later found to control transcription elongation, together with P-TEFb, at the promoter-proximal region. Although there is ample evidence that these factors play roles throughout the genome, other data also suggest gene- or tissue-specific roles for these factors. In this review, we discuss how these apparently conflicting data can be reconciled...
January 2013: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/23064645/cyclin-dependent-kinase-control-of-the-initiation-to-elongation-switch-of-rna-polymerase-ii
#17
Stéphane Larochelle, Ramon Amat, Kira Glover-Cutter, Miriam Sansó, Chao Zhang, Jasmina J Allen, Kevan M Shokat, David L Bentley, Robert P Fisher
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...
November 2012: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/23041311/dsif-restricts-nf-%C3%AE%C2%BAb-signaling-by-coordinating-elongation-with-mrna-processing-of-negative-feedback-genes
#18
Gil Diamant, Liat Amir-Zilberstein, Yuki Yamaguchi, Hiroshi Handa, Rivka Dikstein
NF-κB is central for immune response and cell survival, and its deregulation is linked to chronic inflammation and cancer through poorly defined mechanisms. IκBα and A20 are NF-κB target genes and negative feedback regulators. Upon their activation by NF-κB, DSIF is recruited, P-TEFb is released, and their elongating polymerase II (Pol II) C-terminal domain (CTD) remains hypophosphorylated. We show that upon DSIF knockdown, mRNA levels of a subset of NF-κB targets are not diminished; yet much less IκBα and A20 protein are synthesized, and NF-κB activation is abnormally prolonged...
October 25, 2012: Cell Reports
https://www.readbyqxmd.com/read/22570620/the-dsif-subunits-spt4-and-spt5-have-distinct-roles-at-various-phases-of-immunoglobulin-class-switch-recombination
#19
Andre Stanlie, Nasim A Begum, Hideo Akiyama, Tasuku Honjo
Class-switch recombination (CSR), induced by activation-induced cytidine deaminase (AID), can be divided into two phases: DNA cleavage of the switch (S) regions and the joining of the cleaved ends of the different S regions. Here, we show that the DSIF complex (Spt4 and Spt5), a transcription elongation factor, is required for CSR in a switch-proficient B cell line CH12F3-2A cells, and Spt4 and Spt5 carry out independent functions in CSR. While neither Spt4 nor Spt5 is required for transcription of S regions and AID, expression array analysis suggests that Spt4 and Spt5 regulate a distinct subset of transcripts in CH12F3-2A cells...
2012: PLoS Genetics
https://www.readbyqxmd.com/read/22244331/functional-association-of-gdown1-with-rna-polymerase-ii-poised-on-human-genes
#20
Bo Cheng, Tiandao Li, Peter B Rahl, Todd E Adamson, Nicholas B Loudas, Jiannan Guo, Katayoun Varzavand, Jeffrey J Cooper, Xiaopeng Hu, Averell Gnatt, Richard A Young, David H Price
Most human genes are loaded with promoter-proximally paused RNA polymerase II (Pol II) molecules that are poised for release into productive elongation by P-TEFb. We present evidence that Gdown1, the product of the POLR2M gene that renders Pol II responsive to Mediator, is involved in Pol II elongation control. During in vitro transcription, Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme...
January 13, 2012: Molecular Cell
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