scholarly journals Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription initiation in Saccharomyces cerevisiae

2020 ◽  
Author(s):  
Margaret K. Shirra ◽  
Rachel A. Kocik ◽  
Mitchell A. Ellison ◽  
Karen M. Arndt
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Histone Deacetylase ◽  
Chromatin Structure ◽  
Histone Deacetylases ◽  
Transcription Initiation ◽  
Transcription Elongation ◽  
Chromatin Accessibility ◽  
Elongation Complex ◽  
Gene Encoding ◽  
Cryptic Transcription

ABSTRACTMaintenance of chromatin structure under the disruptive force of transcription requires cooperation among numerous chromatin regulatory factors. Histone post-translational modifications can regulate nucleosome stability and influence the disassembly and reassembly of nucleosomes during transcription elongation. The Paf1 transcription elongation complex, Paf1C, is required for several transcription-coupled histone modifications, including the mono-ubiquitylation of H2B. In Saccharomyces cerevisiae, amino acid substitutions in the Rtf1 subunit of Paf1C greatly diminish H2B ubiquitylation and cause transcription to initiate at a cryptic promoter within a coding gene, an indicator of chromatin disruption. In a genetic screen to identify factors that functionally interact with Paf1C, we identified a mutation in HDA3, a gene encoding a subunit of the Hda1C histone deacetylase, as a suppressor of an rtf1 mutation. Absence of Hda1C also suppresses the cryptic initiation phenotype of other mutants defective in H2B ubiquitylation. The genetic interactions between Hda1C and the H2B ubiquitylation pathway appear specific: loss of Hda1C does not suppress the cryptic initiation phenotypes of other chromatin mutants and absence of other histone deacetylases does not suppress the absence of H2B ubiquitylation. Providing further support for an appropriate balance of histone acetylation in regulating cryptic initiation, we find that deletion of the Sas3 histone acetyltransferase elevates cryptic initiation in rtf1 mutants. Our data suggest a coordination between two epigenetic modifiers, the H2B ubiquitylation pathway and Hda1C, in regulating chromatin structure during transcription elongation and reveal an unexpected role for a histone deacetylase in supporting chromatin accessibility.

scholarly journals Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Margaret K Shirra ◽  
Rachel A Kocik ◽  
Mitchell A Ellison ◽  
Karen M Arndt
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Histone Deacetylase ◽  
Chromatin Structure ◽  
Histone Deacetylases ◽  
Transcription Elongation ◽  
Chromatin Accessibility ◽  
Coding Region ◽  
Elongation Complex ◽  
Gene Encoding ◽  
Cryptic Transcription

Abstract Maintenance of chromatin structure under the disruptive force of transcription requires cooperation among numerous regulatory factors. Histone post-translational modifications can regulate nucleosome stability and influence the disassembly and reassembly of nucleosomes during transcription elongation. The Paf1 transcription elongation complex, Paf1C, is required for several transcription-coupled histone modifications, including the mono-ubiquitylation of H2B. In Saccharomyces cerevisiae, amino acid substitutions in the Rtf1 subunit of Paf1C greatly diminish H2B ubiquitylation and cause transcription to initiate at a cryptic promoter within the coding region of the FLO8 gene, an indicator of chromatin disruption. In a genetic screen to identify factors that functionally interact with Paf1C, we identified mutations in HDA3, a gene encoding a subunit of the Hda1C histone deacetylase, as suppressors of an rtf1 mutation. Absence of Hda1C also suppresses the cryptic initiation phenotype of other mutants defective in H2B ubiquitylation. The genetic interactions between Hda1C and the H2B ubiquitylation pathway appear specific: loss of Hda1C does not suppress the cryptic initiation phenotypes of other chromatin mutants and absence of other histone deacetylases does not suppress the absence of H2B ubiquitylation. Providing further support for an appropriate balance of histone acetylation in regulating cryptic initiation, absence of the Sas3 histone acetyltransferase elevates cryptic initiation in rtf1 mutants. Our data suggest that the H2B ubiquitylation pathway and Hda1C coordinately regulate chromatin structure during transcription elongation and point to a potential role for a histone deacetylase in supporting chromatin accessibility.

scholarly journals In Vitro Targeting Reveals Intrinsic Histone Tail Specificity of the Sin3/Histone Deacetylase and N-CoR/SMRT Corepressor Complexes

2004 ◽  
Vol 24 (6) ◽  
pp. 2364-2372 ◽  
Author(s):  
Michiel Vermeulen ◽  
Michael J. Carrozza ◽  
Edwin Lasonder ◽  
Jerry L. Workman ◽  
Colin Logie ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
Chromatin Structure ◽  
Histone Deacetylases ◽  
Histone H3 ◽  
Histone Code ◽  
Histone Acetyltransferases ◽  
Histone Tail ◽  
In Vitro System ◽  
Selective Targeting

ABSTRACT The histone code is among others established via differential acetylation catalyzed by histone acetyltransferases (HATs) and histone deacetylases (HDACs). To unambiguously determine the histone tail specificity of HDAC-containing complexes, we have established an in vitro system consisting of nucleosomal templates reconstituted with hyperacetylated histones or recombinant histones followed by acetylation with native SAGA or NuA4. Selective targeting of the mammalian Sin3/HDAC and N-CoR/SMRT corepressor complexes by using specific chimeric repressors created a near physiological setting to assess their histone tail specificity. Recruitment of the Sin3/HDAC complex to nucleosomal templates preacetylated with SAGA or NuA4 resulted in deacetylation of histones H3 and H4, whereas recruitment of N-CoR/SMRT resulted in deacetylation of histone H3 only. These results provide solid evidence that HDAC-containing complexes display distinct, intrinsic histone tail specificities and hence may function differently to regulate chromatin structure and transcription.

scholarly journals Promoter-proximal elongation regulates transcription in archaea

2020 ◽  
Author(s):  
Fabian Blombach ◽  
Thomas Fouqueau ◽  
Dorota Matelska ◽  
Katherine Louise Smollett ◽  
Finn Werner
Keyword(s):  
Transcription Initiation ◽  
Transcription Elongation ◽  
Sulfolobus Solfataricus ◽  
Transcription Activation ◽  
Rna Polymerases ◽  
Promoter Strength ◽  
Elongation Complex ◽  
Initiation Factors ◽  
Elongation Phase ◽  
Rate Limiting

Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.

scholarly journals Kidney cell type specific changes in the chromatin and transcriptome landscapes following epithelial Hdac1and Hdac2 knockdown

2021 ◽  
Author(s):  
Kelly A. Hyndman ◽  
David K Crossman
Keyword(s):  
Chromatin Structure ◽  
Kidney Cell ◽  
Histone Deacetylases ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Electrolyte Balance ◽  
Transcript Expression ◽  
Single Nucleus ◽  
Cell Type Specific

Recent studies have identified at least 20 different kidney cell types based upon chromatin structure and gene expression. Histone deacetylases (HDACs) are epigenetic transcriptional repressors via deacetylation of histone lysines resulting in inaccessible chromatin. We reported that kidney epithelial HDAC1 and HDAC2 activity is critical for maintaining a healthy kidney and preventing fluid-electrolyte abnormalities. However, to what extent does Hdac1/Hdac2 knockdown affect chromatin structure and subsequent transcript expression in the kidney? To answer this question, we used single nucleus Assay for Transposase-Accessible Chromatin-sequencing (snATAC-seq) and snRNA-seq to profile kidney nuclei from male and female, control and littermate kidney epithelial Hdac1/Hdac2 knockdown mice. Hdac1/Hdac2 knockdown resulted in significant changes in the chromatin structure predominantly within the promoter region of gene loci involved in fluid-electrolyte balance such as the aquaporins, with both increased and decreased accessibility captured. Moreover, Hdac1/Hdac2 knockdown resulted different gene loci being accessible with a corresponding increased transcript number in the kidney, but among all mice only 24-30% of chromatin accessibility agreed with transcript expression (e.g. open chromatin, increased transcript). To conclude, although chromatin structure does affect transcription, ~70% of the differentially expressed genes cannot be explained by changes in chromatin accessibility and HDAC1/HDAC2 had a minimal effect on these global patterns. Yet, the genes that are targets of HDAC1 and HDAC2 are critically important for maintaining kidney function.

scholarly journals The Double-Strand Break Landscape of Meiotic Chromosomes Is Shaped by the Paf1 Transcription Elongation Complex in Saccharomyces cerevisiae

Genetics ◽  
2015 ◽  
Vol 202 (2) ◽  
pp. 497-512 ◽  
Author(s):  
Santosh K. Gothwal ◽  
Neem J. Patel ◽  
Meaghan M. Colletti ◽  
Hiroyuki Sasanuma ◽  
Miki Shinohara ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Elongation ◽  
Strand Break ◽  
Double Strand Break ◽  
Elongation Complex ◽  
Meiotic Chromosomes

scholarly journals Promoter-proximal elongation regulates transcription in archaea

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fabian Blombach ◽  
Thomas Fouqueau ◽  
Dorota Matelska ◽  
Katherine Smollett ◽  
Finn Werner
Keyword(s):  
Transcription Initiation ◽  
Transcription Elongation ◽  
Transcription Activation ◽  
Rna Polymerases ◽  
Promoter Strength ◽  
Elongation Complex ◽  
Termination Factor ◽  
Initiation Factors ◽  
Elongation Phase ◽  
Rate Limiting

AbstractRecruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.

scholarly journals Spt6 is required for the fidelity of promoter selection

2018 ◽  
Author(s):  
Stephen M. Doris ◽  
James Chuang ◽  
Olga Viktorovskaya ◽  
Magdalena Murawska ◽  
Dan Spatt ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromatin Structure ◽  
Genetic Information ◽  
Transcription Initiation ◽  
Elongation Factor ◽  
Initiation Site ◽  
Sequence Features ◽  
Coding Regions ◽  
Genome Wide ◽  
Site Competition

SUMMARYSpt6 is a conserved factor that controls transcription and chromatin structure across the genome. Although Spt6 is viewed as an elongation factor, spt6 mutations in Saccharomyces cerevisiae allow elevated levels of transcripts from within coding regions, suggesting that Spt6 also controls initiation. To address the requirements for Spt6 in transcription and chromatin structure, we have combined four genome-wide approaches. Our results demonstrate that Spt6 represses transcription initiation at thousands of intragenic promoters. We characterize these intragenic promoters, and find sequence features conserved with genic promoters. Finally, we show that Spt6 also regulates transcription initiation at most genic promoters and propose a model of initiation-site competition to account for this. Together, our results demonstrate that Spt6 controls the fidelity of transcription initiation throughout the genome and reveal the magnitude of the potential for expressing alternative genetic information via intragenic promoters.

scholarly journals Evidence that the Elongation Factor TFIIS Plays a Role in Transcription Initiation at GAL1 in Saccharomyces cerevisiae

2005 ◽  
Vol 25 (7) ◽  
pp. 2650-2659 ◽  
Author(s):  
Donald M. Prather ◽  
Erica Larschan ◽  
Fred Winston
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Pol Ii ◽  
Upstream Activating Sequence ◽  
Transcript Cleavage

ABSTRACT TFIIS is a transcription elongation factor that has been extensively studied biochemically. Although the in vitro mechanisms by which TFIIS stimulates RNA transcript cleavage and polymerase read-through have been well characterized, its in vivo roles remain unclear. To better understand TFIIS function in vivo, we have examined its role during Gal4-mediated activation of the Saccharomyces cerevisiae GAL1 gene. Surprisingly, TFIIS is strongly associated with the GAL1 upstream activating sequence. In addition, TFIIS recruitment to Gal4-binding sites is dependent on Gal4, SAGA, and Mediator but not on RNA polymerase II (Pol II). The association of TFIIS is also necessary for the optimal recruitment of TATA-binding protein and Pol II to the GAL1 promoter. These results provide strong evidence that TFIIS plays an important role in the initiation of transcription at GAL1 in addition to its well-characterized roles in transcription elongation.

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