scholarly journals The Winged Helix Domain of CSB Regulates RNAPII Occupancy at Promoter Proximal Pause Sites

2021 ◽  
Vol 22 (7) ◽  
pp. 3379 ◽  
Author(s):  
Nicole L. Batenburg ◽  
Shixin Cui ◽  
John R. Walker ◽  
Herb E. Schellhorn ◽  
Xu-Dong Zhu
Keyword(s):  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Binding Pocket ◽  
Binding Activity ◽  
Response To Treatment ◽  
Regulation Of Transcription ◽  
Winged Helix ◽  
Ubiquitin Binding ◽  
Group B ◽  
Winged Helix Domain

Cockayne syndrome group B protein (CSB), a member of the SWI/SNF superfamily, resides in an elongating RNA polymerase II (RNAPII) complex and regulates transcription elongation. CSB contains a C-terminal winged helix domain (WHD) that binds to ubiquitin and plays an important role in DNA repair. However, little is known about the role of the CSB-WHD in transcription regulation. Here, we report that CSB is dependent upon its WHD to regulate RNAPII abundance at promoter proximal pause (PPP) sites of several actively transcribed genes, a key step in the regulation of transcription elongation. We show that two ubiquitin binding-defective mutations in the CSB-WHD, which impair CSB’s ability to promote cell survival in response to treatment with cisplatin, have little impact on its ability to stimulate RNAPII occupancy at PPP sites. In addition, we demonstrate that two cancer-associated CSB mutations, which are located on the opposite side of the CSB-WHD away from its ubiquitin-binding pocket, impair CSB’s ability to promote RNAPII occupancy at PPP sites. Taken together, these results suggest that CSB promotes RNAPII association with PPP sites in a manner requiring the CSB-WHD but independent of its ubiquitin-binding activity. These results further imply that CSB-mediated RNAPII occupancy at PPP sites is mechanistically separable from CSB-mediated repair of cisplatin-induced DNA damage.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

scholarly journals PPM1G Binds 7SK RNA and Hexim1 To Block P-TEFb Assembly into the 7SK snRNP and Sustain Transcription Elongation

2015 ◽  
Vol 35 (22) ◽  
pp. 3810-3828 ◽  
Author(s):  
Swapna Aravind Gudipaty ◽  
Ryan P. McNamara ◽  
Emily L. Morton ◽  
Iván D'Orso
Keyword(s):  
Rna Polymerase Ii ◽  
Noncoding Rna ◽  
Kinase Inhibitor ◽  
Transcription Elongation ◽  
Nuclear Factor Κb ◽  
Binding Activity ◽  
New Paradigm ◽  
Pol Ii ◽  
Small Nuclear Ribonucleoprotein ◽  
Rna Interaction

Transcription elongation programs are vital for the precise regulation of several biological processes. One key regulator of such programs is the P-TEFb kinase, which phosphorylates RNA polymerase II (Pol II) once released from the inhibitory 7SK small nuclear ribonucleoprotein (snRNP) complex. Although mechanisms of P-TEFb release from the snRNP are becoming clearer, how P-TEFb remains in the 7SK-unbound state to sustain transcription elongation programs remains unknown. Here we report that the PPM1G phosphatase (inducibly recruited by nuclear factor κB [NF-κB] to target promoters) directly binds 7SK RNA and the kinase inhibitor Hexim1 once P-TEFb has been released from the 7SK snRNP. This dual binding activity of PPM1G blocks P-TEFb reassembly onto the snRNP to sustain NF-κB-mediated Pol II transcription in response to DNA damage. Notably, the PPM1G-7SK RNA interaction is direct, kinetically follows the recruitment of PPM1G to promoters to activate NF-κB transcription, and is reversible, since the complex disassembles before resolution of the program. Strikingly, we found that the ataxia telangiectasia mutated (ATM) kinase regulates the interaction between PPM1G and the 7SK snRNP through site-specific PPM1G phosphorylation. The precise and temporally regulated interaction of a cellular enzyme and a noncoding RNA provides a new paradigm for simultaneously controlling the activation and maintenance of inducible transcription elongation programs.

scholarly journals Structural basis of ubiquitin recognition by the winged-helix domain of Cockayne syndrome group B protein

2019 ◽  
Vol 47 (7) ◽  
pp. 3784-3794 ◽  
Author(s):  
Tomio S Takahashi ◽  
Yusuke Sato ◽  
Atsushi Yamagata ◽  
Sakurako Goto-Ito ◽  
Masafumi Saijo ◽  
...  
Keyword(s):  
Cockayne Syndrome ◽  
Structural Basis ◽  
Winged Helix ◽  
Group B ◽  
Winged Helix Domain

scholarly journals Cell-cycle-specific transcription termination within the human histone H3.3 gene is correlated with specific protein–DNA interactions

1997 ◽  
Vol 69 (2) ◽  
pp. 101-110 ◽  
Author(s):  
ALAN TAYLOR ◽  
LIQUN ZHANG ◽  
JOHN HERRMANN ◽  
BEI WU ◽  
LARRY KEDES ◽  
...  
Keyword(s):  
Protein Binding ◽  
Rna Polymerase Ii ◽  
Transcription Termination ◽  
Transcription Elongation ◽  
Specific Protein ◽  
Binding Activity ◽  
Mobility Shift ◽  
Nuclear Extracts

In vitro studies using highly purified calf thymus RNA polymerase II and a fragment spanning the first intron of H3.3 as template DNA have demonstrated the existence of a strong transcription termination site consisting of thymidine stretches. In this study, nuclear run-on experiments have been performed to assess the extent to which transcription elongation is blocked in vivo using DNA probes corresponding to regions 5′ and 3′ of the in vitro termination sites. These studies suggest that H3.3 expression is stimulated following the inhibition of DNA synthesis through the elimination of the transcription elongation block. Interestingly, both the in vivo and in vitro experiments have revealed that the transcriptional block/termination sites are positioned immediately downstream of a 73 bp region that has been over 90% conserved between the chicken and human H3.3 genes. The extreme conservation of this intronic region suggests a possible role in maintaining cis-acting function. Electrophoretic mobility shift experiments show that HeLa cell nuclear extracts contain protein factors that bind specifically to the region of transcription elongation block. Furthermore, we demonstrate a correlation between the protein binding activity and the transcriptional block in cells that have been either arrested at the initiation of S phase or were replication-interrupted by hydroxyurea. DNA footprinting experiments indicate that the region of protein binding is at the 3′ end of the conserved region and overlaps with one of the three in-vitro-mapped termination sites.

scholarly journals Regulation of transcription elongation by the XPG-TFIIH complex is implicated in Cockayne syndrome

2015 ◽  
pp. MCB.01401-14 ◽  
Author(s):  
Takashi Narita ◽  
Keiko Narita ◽  
Arato Takedachi ◽  
Masafumi Saijo ◽  
Kiyoji Tanaka
Keyword(s):  
Rna Polymerase Ii ◽  
Excision Repair ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Cockayne Syndrome ◽  
Regulation Of Transcription ◽  
Causative Gene ◽  
Coding Regions ◽  
Epidermal Growth ◽  
Xeroderma Pigmentosum Group G

XPGis a causative gene underlying the photosensitive disorder, xeroderma pigmentosum group G, and is involved in nucleotide excision repair. Here, we show that XPG knockdown represses epidermal growth factor (EGF)-inducedFOStranscription at the level of transcription elongation with little effect on EGF signal transduction. XPG interacted with transcription elongation factors in concert with TFIIH, suggesting that the XPG-TFIIH complex serves as a transcription elongation factor. The XPG-TFIIH complex was recruited to promoter and coding regions of both EGF-induced (FOS) and housekeeping (EEF1A1) genes. Further, EGF-induced recruitment of RNA polymerase II and TFIIH toFOSwas reduced by XPG knockdown. Importantly, EGF-inducedFOStranscription was markedly lower in XP-G/CS cells expressing truncated XPG than in control cells expressing wild-type (WT) XPG, with less significant decreases in XP-G cells with XPG nuclease domain mutations. In corroboration of this finding, both WT XPG and a missense XPG mutant from an XP-G patient were recruited toFOSupon EGF stimulation, but an XPG mutant mimicking a C-terminal truncation from an XP-G/CS patient was not. These results suggest that the XPG-TFIIH complex is involved in transcription elongation, and that defects in this association may partly account for Cockayne syndrome in XP-G/CS patients.

scholarly journals Poly(ADP-ribose) polymerase 1 (PARP1) promotes oxidative stress–induced association of Cockayne syndrome group B protein with chromatin

2018 ◽  
Vol 293 (46) ◽  
pp. 17863-17874 ◽  
Author(s):  
Erica L. Boetefuer ◽  
Robert J. Lake ◽  
Kostiantyn Dreval ◽  
Hua-Ying Fan
Keyword(s):  
Oxidative Stress ◽  
Dna Repair ◽  
Rna Polymerase Ii ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Transcription Elongation ◽  
Cockayne Syndrome ◽  
Base Excision ◽  
Group B ◽  
Genomic Regions

Cockayne syndrome protein B (CSB) is an ATP-dependent chromatin remodeler that relieves oxidative stress by regulating DNA repair and transcription. CSB is proposed to participate in base-excision repair (BER), the primary pathway for repairing oxidative DNA damage, but exactly how CSB participates in this process is unknown. It is also unclear whether CSB contributes to other repair pathways during oxidative stress. Here, using a patient-derived CS1AN-sv cell line, we examined how CSB is targeted to chromatin in response to menadione-induced oxidative stress, both globally and locus-specifically. We found that menadione-induced, global CSB–chromatin association does not require CSB's ATPase activity and is, therefore, mechanistically distinct from UV-induced CSB–chromatin association. Importantly, poly(ADP-ribose) polymerase 1 (PARP1) enhanced the kinetics of global menadione-induced CSB–chromatin association. We found that the major BER enzymes, 8-oxoguanine DNA glycosylase (OGG1) and apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1), do not influence this association. Additionally, the level of γ-H2A histone family member X (γ-H2AX), a marker for dsDNA breaks, was not increased in menadione-treated cells. Therefore, our results support a model whereby PARP1 localizes to ssDNA breaks and recruits CSB to participate in DNA repair. Furthermore, this global CSB–chromatin association occurred independently of RNA polymerase II–mediated transcription elongation. However, unlike global CSB–chromatin association, both PARP1 knockdown and inhibition of transcription elongation interfered with menadione-induced CSB recruitment to specific genomic regions. This observation supports the hypothesis that CSB is also targeted to specific genomic loci to participate in transcriptional regulation in response to oxidative stress.

scholarly journals The Rate of c-fos Transcription in Vivo Is Continuously Regulated at the Level of Elongation by Dynamic Stimulus-coupled Recruitment of Positive Transcription Elongation Factor b

2006 ◽  
Vol 282 (7) ◽  
pp. 5075-5084 ◽  
Author(s):  
Stephan Ryser ◽  
Toshitsugu Fujita ◽  
Silvia Tortola ◽  
Isabelle Piuz ◽  
Werner Schlegel
Keyword(s):  
Rna Polymerase Ii ◽  
Mammalian Cells ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Thyrotropin Releasing Hormone ◽  
Early Gene ◽  
Regulation Of Transcription ◽  
Dependent Manner ◽  
Tight Coupling ◽  
Releasing Hormone

In mammalian cells, multiple stimuli induce the expression of the immediate early gene c-fos. The specificity of c-fos transcriptional response depends on the activation of signaling protein kinases, transcription factors, and chromatin-modifying complexes but also on a regulated block to elongation in the first intron. Here we show by chromatin immunoprecipitation that finely tuned control of c-fos gene expression by distinct stimuli is associated with a dynamic regulation of transcription elongation and differential phosphorylation of the C-terminal domain of RNA polymerase II. Comparison of two stimuli of c-fos expression in the pituitary cell line GH4C1, namely the thyrotropin-releasing hormone versus depolarizing KCl, shows that both stimuli increase initiation, but only thyrotropin-releasing hormone is efficient to stimulate elongation and thus produce high transcription rates. To control elongation, the elongation factor P-TEFb is recruited to the 5′-end of the gene in a stimuli and time-dependent manner. Transition from initiation to elongation depends also on the dynamic recruitment of the initiation factors TFIIB and TFIIE but not TFIID, which remains constitutively bound on the promoter. It thus appears that tight coupling of signaling input to transcriptional output rate is achieved by c-fos gene-specific mechanisms, which control post-initiation steps rather than pre-initiation complex assembly.

scholarly journals Human Spt6 Stimulates Transcription Elongation by RNA Polymerase II In Vitro

2004 ◽  
Vol 24 (8) ◽  
pp. 3324-3336 ◽  
Author(s):  
Masaki Endoh ◽  
Wenyan Zhu ◽  
Jun Hasegawa ◽  
Hajime Watanabe ◽  
Dong-Ki Kim ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Underlying Mechanism ◽  
Regulation Of Transcription ◽  
Mrna Synthesis ◽  
Transcription Machinery

ABSTRACT Recent studies have suggested that Spt6 participates in the regulation of transcription by RNA polymerase II (RNAPII). However, its underlying mechanism remains largely unknown. One possibility, which is supported by genetic and biochemical studies of Saccharomyces cerevisiae, is that Spt6 affects chromatin structure. Alternatively, Spt6 directly controls transcription by binding to the transcription machinery. In this study, we establish that human Spt6 (hSpt6) is a classic transcription elongation factor that enhances the rate of RNAPII elongation. hSpt6 is capable of stimulating transcription elongation both individually and in concert with DRB sensitivity-inducing factor (DSIF), comprising human Spt5 and human Spt4. We also provide evidence showing that hSpt6 interacts with RNAPII and DSIF in human cells. Thus, in vivo, hSpt6 may regulate multiple steps of mRNA synthesis through its interaction with histones, elongating RNAPII, and possibly other components of the transcription machinery.

scholarly journals Dynamics of transcription elongation are finely tuned by dozens of regulatory factors

2021 ◽  
Author(s):  
Mary Couvillion ◽  
Kevin M Harlen ◽  
Kate C Lachance ◽  
Kristine Trotta ◽  
Erin Smtih ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Rna Processing ◽  
Transcription Elongation ◽  
Antisense Transcription ◽  
Regulation Of Transcription ◽  
Pol Ii ◽  
Density Peaks ◽  
Large Numbers ◽  
Key Points ◽  
Opposing Effects

Understanding the complex network and dynamics that regulate transcription elongation requires the quantitative analysis of RNA polymerase II (Pol II) activity in a wide variety of regulatory environments. We performed native elongating transcript sequencing (NET-seq) in 41 strains of S. cerevisiae lacking known elongation regulators, including RNA processing factors, transcription elongation factors, chromatin modifiers, and remodelers. We found that the opposing effects of these factors balance transcription elongation dynamics. Different sets of factors tightly regulate Pol II progression across gene bodies so that Pol II density peaks at key points of RNA processing. These regulators control where Pol II pauses with each obscuring large numbers of potential pause sites that are primarily determined by DNA sequence and shape. Genes that are sensitive to disruptions in transcription elongation tend to couple changes in Pol II pausing and antisense transcription to transcription output. Our findings collectively show that the regulation of transcription elongation by a diverse array of factors affects gene expression levels and co-transcriptional processing by precisely balancing Pol II activity.

scholarly journals Evidence that the Transcription Elongation Function of Rpb9 Is Involved in Transcription-Coupled DNA Repair in Saccharomyces cerevisiae

2006 ◽  
Vol 26 (24) ◽  
pp. 9430-9441 ◽  
Author(s):  
Shisheng Li ◽  
Baojin Ding ◽  
Runqiang Chen ◽  
Christine Ruggiero ◽  
Xuefeng Chen
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Repair ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Complementation Group ◽  
Cockayne Syndrome ◽  
Transcription Repression ◽  
Group B

ABSTRACT Rpb9, a small nonessential subunit of RNA polymerase II, has been shown to have multiple transcription-related functions in Saccharomyces cerevisiae. These functions include promoting transcription elongation and mediating a subpathway of transcription-coupled repair (TCR) that is independent of Rad26, the homologue of human Cockayne syndrome complementation group B protein. Rpb9 is composed of three distinct domains: the N-terminal Zn1, the C-terminal Zn2, and the central linker. Here we show that the Zn1 and linker domains are essential, whereas the Zn2 domain is almost dispensable, for both transcription elongation and TCR functions. Impairment of transcription elongation, which does not dramatically compromise Rad26-mediated TCR, completely abolishes Rpb9-mediated TCR. Furthermore, Rpb9 appears to be dispensable for TCR if its transcription elongation function is compensated for by removing a transcription repression/elongation factor. Our data suggest that the transcription elongation function of Rpb9 is involved in TCR.

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