scholarly journals A Functional Role for the Switch 2 Region of Yeast RNA Polymerase II in Transcription Start Site Utilization and Abortive Initiation

2005 ◽  
Vol 280 (41) ◽  
pp. 34917-34923 ◽  
Author(s):  
Robert C. Majovski ◽  
Denys A. Khaperskyy ◽  
Mohamed A. Ghazy ◽  
Alfred S. Ponticelli
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Start Site ◽  
Functional Role ◽  
Start Site ◽  
Transcription Start ◽  
Abortive Initiation

scholarly journals The sua8 suppressors of Saccharomyces cerevisiae encode replacements of conserved residues within the largest subunit of RNA polymerase II and affect transcription start site selection similarly to sua7 (TFIIB) mutations.

1994 ◽  
Vol 14 (1) ◽  
pp. 226-237 ◽  
Author(s):  
R W Berroteran ◽  
D E Ware ◽  
M Hampsey
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Start Site ◽  
Site Selection ◽  
Synthetic Lethality ◽  
Single Amino Acid ◽  
Start Site ◽  
Transcription Start ◽  
Conserved Residues

Mutations in the Saccharomyces cerevisiae sua8 gene were found to be suppressors of an aberrant ATG translation initiation codon in the leader region of the cyc1 gene. Analysis of cyc1 transcripts from sua8 mutants revealed that suppression is a consequence of diminished transcription initiation at the normal start sites in favor of initiation at downstream sites, including a site between the aberrant and normal ATG start codons. This effect is not cyc1 gene specific since initiation at other genes, including ADH1, CYC7, and HIS4, was similarly affected, although initiation at HIS3 and SPT15 was unaffected. The SUA8 gene was cloned and partially sequenced, revealing identity to RPB1, which encodes the largest subunit of RNA polymerase II. The sua8 suppressors are the result of single amino acid replacements of highly conserved residues. Three replacements were found either within or immediately preceding homology block D, and a fourth was found adjacent to homology block H, indicating that these regions play a role in defining start sites in vivo. Nearly identical effects on start site selection were observed for sua7 suppressors, which encode altered forms of TFIIB. Synthetic lethality was associated with double sua7 sua8 suppressor mutations, and recessive sua7 mutants failed to fully complement recessive sua8 mutants in heterozygous diploids (nonallelic noncomplementation). These data indicate that the largest subunit of RNA polymerase II and TFIIB are important determinants of transcription start site selection in S. cerevisiae and suggest that this function might be conferred by interaction between these two proteins.

scholarly journals Histone modifications at the transcription start site of non-coding RNA revealed regulatory patterns of activation in Caenorhabditis elegans embryo

2020 ◽  
Author(s):  
Megan A. Bandeira ◽  
Max E. Boeck
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Start Site ◽  
Histone Modifications ◽  
Principal Component ◽  
Integrated Analysis ◽  
Regulation Of Transcription ◽  
Start Site ◽  
Transcription Start ◽  
Non Coding Rna

AbstractHistone modifications play an essential role in regulating recruitment of RNA polymerase II and through this regulation of transcription itself. Which modifications are essential for regulating the transcription of non-coding RNA (ncRNA) species and how these patterns differ between the different types of ncRNA remains less studied compared to mRNA. We performed a principal component analysis (PCA) of histone modifications patterns surrounding the transcription start site (TSS) of ncRNA in an attempt to understand how histone modifications predict polymerase recruitment and transcription of ncRNA in early C. elegans development We found that our first PCA axis was a better predictor of polymerase recruitment and expression than any single histone modification for ncRNA and miRNA. This indicates an integrated analysis of many histone modifications is essential for predicting expression based on histone modifications and that each ncRNA species have unique regulation of RNA polymerase recruitment through histone modifications.

scholarly journals Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution

2020 ◽  
Vol 3 (10) ◽  
pp. e202000762
Author(s):  
Oscar D Villarreal ◽  
Sofiane Y Mersaoui ◽  
Zhenbao Yu ◽  
Jean-Yves Masson ◽  
Stéphane Richard
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Start Site ◽  
Transcription Initiation ◽  
Transcription Termination ◽  
Start Site ◽  
Loop Gain ◽  
Transcription Start ◽  
Genome Wide ◽  
Rna Polymerase Ii Transcription

DDX5, XRN2, and PRMT5 have been shown to resolve DNA/RNA hybrids (R-loops) at RNA polymerase II transcription termination sites at few genomic loci. Herein, we perform genome-wide R-loop mapping using classical DNA/RNA immunoprecipitation and high-throughput sequencing (DRIP-seq) of loci regulated by DDX5, XRN2, and PRMT5. We observed hundreds to thousands of R-loop gains and losses at transcribed loci in DDX5-, XRN2-, and PRMT5-deficient U2OS cells. R-loop gains were characteristic of highly transcribed genes located at gene-rich regions, whereas R-loop losses were observed in low-density gene areas. DDX5, XRN2, and PRMT5 shared many R-loop gain loci at transcription termination sites, consistent with their coordinated role in RNA polymerase II transcription termination. DDX5-depleted cells had unique R-loop gain peaks near the transcription start site that did not overlap with those of siXRN2 and siPRMT5 cells, suggesting a role for DDX5 in transcription initiation independent of XRN2 and PRMT5. Moreover, we observed that the accumulated R-loops at certain loci in siDDX5, siXRN2, and siPRMT5 cells near the transcription start site of genes led to antisense intergenic transcription. Our findings define unique and shared roles of DDX5, XRN2, and PRMT5 in DNA/RNA hybrid regulation.

The sua8 suppressors of Saccharomyces cerevisiae encode replacements of conserved residues within the largest subunit of RNA polymerase II and affect transcription start site selection similarly to sua7 (TFIIB) mutations

1994 ◽  
Vol 14 (1) ◽  
pp. 226-237
Author(s):  
R W Berroteran ◽  
D E Ware ◽  
M Hampsey
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Start Site ◽  
Site Selection ◽  
Synthetic Lethality ◽  
Single Amino Acid ◽  
Start Site ◽  
Transcription Start ◽  
Conserved Residues

Mutations in the Saccharomyces cerevisiae sua8 gene were found to be suppressors of an aberrant ATG translation initiation codon in the leader region of the cyc1 gene. Analysis of cyc1 transcripts from sua8 mutants revealed that suppression is a consequence of diminished transcription initiation at the normal start sites in favor of initiation at downstream sites, including a site between the aberrant and normal ATG start codons. This effect is not cyc1 gene specific since initiation at other genes, including ADH1, CYC7, and HIS4, was similarly affected, although initiation at HIS3 and SPT15 was unaffected. The SUA8 gene was cloned and partially sequenced, revealing identity to RPB1, which encodes the largest subunit of RNA polymerase II. The sua8 suppressors are the result of single amino acid replacements of highly conserved residues. Three replacements were found either within or immediately preceding homology block D, and a fourth was found adjacent to homology block H, indicating that these regions play a role in defining start sites in vivo. Nearly identical effects on start site selection were observed for sua7 suppressors, which encode altered forms of TFIIB. Synthetic lethality was associated with double sua7 sua8 suppressor mutations, and recessive sua7 mutants failed to fully complement recessive sua8 mutants in heterozygous diploids (nonallelic noncomplementation). These data indicate that the largest subunit of RNA polymerase II and TFIIB are important determinants of transcription start site selection in S. cerevisiae and suggest that this function might be conferred by interaction between these two proteins.

scholarly journals Wdr82 Is a C-Terminal Domain-Binding Protein That Recruits the Setd1A Histone H3-Lys4 Methyltransferase Complex to Transcription Start Sites of Transcribed Human Genes

2007 ◽  
Vol 28 (2) ◽  
pp. 609-618 ◽  
Author(s):  
Jeong-Heon Lee ◽  
David G. Skalnik
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Start Site ◽  
Histone H3 ◽  
Rna Recognition Motif ◽  
Start Site ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Terminal Domain ◽  
Rnap Ii

ABSTRACT Histone H3-Lys4 trimethylation is associated with the transcription start site of transcribed genes, but the molecular mechanisms that control this distribution in mammals are unclear. The human Setd1A histone H3-Lys4 methyltransferase complex was found to physically associate with the RNA polymerase II large subunit. The Wdr82 component of the Setd1A complex interacts with the RNA recognition motif of Setd1A and additionally binds to the Ser5-phosphorylated C-terminal domain of RNA polymerase II, which is involved in initiation of transcription, but does not bind to an unphosphorylated or Ser2-phosphorylated C-terminal domain. Chromatin immunoprecipitation analysis revealed that Setd1A is localized near the transcription start site of expressed genes. Small interfering RNA-mediated depletion of Wdr82 leads to decreased Setd1A expression and occupancy at transcription start sites and reduced histone H3-Lys4 trimethylation at these sites. However, neither RNA polymerase II (RNAP II) occupancy nor target gene expression levels are altered following Wdr82 depletion. Hence, Wdr82 is required for the targeting of Setd1A-mediated histone H3-Lys4 trimethylation near transcription start sites via tethering to RNA polymerase II, an event that is a consequence of transcription initiation. These results suggest a model for how the mammalian RNAP II machinery is linked with histone H3-Lys4 histone methyltransferase complexes at transcriptionally active genes.

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