scholarly journals GENOME‐WIDE DISTRIBUTIONS OF RNA POL II CTD PHOSPHORYLATION AND CTD‐ASSOCIATED TERMINATION FACTORS IN BUDDING YEAST

2010 ◽  
Vol 24 (S1) ◽  
Author(s):  
David Bentley
Keyword(s):  
Budding Yeast ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Genome Wide ◽  
Ctd Phosphorylation

scholarly journals Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq

2010 ◽  
Vol 39 (1) ◽  
pp. 190-201 ◽  
Author(s):  
Hao Sun ◽  
Jiejun Wu ◽  
Priyankara Wickramasinghe ◽  
Sharmistha Pal ◽  
Ravi Gupta ◽  
...  
Keyword(s):  
Rna Pol Ii ◽  
Pol Ii ◽  
Genome Wide ◽  
Mouse Tissues ◽  
Promoter Usage ◽  
Rna Pol Ii Promoter

scholarly journals RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction

2017 ◽  
Vol 66 (4) ◽  
pp. 546-557.e3 ◽  
Author(s):  
Nova Fong ◽  
Tassa Saldi ◽  
Ryan M. Sheridan ◽  
Michael A. Cortazar ◽  
David L. Bentley
Keyword(s):  
Chromatin Modification ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Transcriptional Direction ◽  
Ctd Phosphorylation

scholarly journals NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution

2018 ◽  
Author(s):  
Constantine Mylonas ◽  
Peter Tessarz
Keyword(s):  
Splicing Factors ◽  
Elongation Factors ◽  
Single Nucleotide ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Genome Wide ◽  
Regulatory Complexity ◽  
Pol Ii Pausing ◽  
Nucleotide Resolution ◽  
The Impact

ABSTRACTThe advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. However, little is known, at such high resolution, how transcription factors directly influence RNA Pol II pausing and directionality. To map the impact of transcription/elongation factors on transcription dynamics genome-wide at base pair resolution, we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). Application of NET-prism on elongation factors (Spt6, Ssrp1), splicing factors (Sf1), and components of the pre-initiation complex (PIC) (TFIID, and Mediator) reveals their inherent command on transcription dynamics, with regards to directionality and pausing over promoters, splice sites, and enhancers/super-enhancers. NET-prism will be broadly applicable as it exposes transcription factor/Pol II dependent topographic specificity and thus, a new degree of regulatory complexity during gene expression.

scholarly journals Nutrient-Driven O-GlcNAcylation at Promoters Impacts Genome-Wide RNA Pol II Distribution

2018 ◽  
Vol 9 ◽  
Author(s):  
Michael W. Krause ◽  
Dona C. Love ◽  
Salil K. Ghosh ◽  
Peng Wang ◽  
Sijung Yun ◽  
...  
Keyword(s):  
Rna Pol Ii ◽  
Pol Ii ◽  
Genome Wide

scholarly journals Correction: Transcriptome Kinetics Is Governed by a Genome-Wide Coupling of mRNA Production and Degradation: A Role for RNA Pol II

PLoS Genetics ◽  
2011 ◽  
Vol 7 (9) ◽  
Author(s):  
Ophir Shalem ◽  
Bella Groisman ◽  
Mordechai Choder ◽  
Orna Dahan ◽  
Yitzhak Pilpel
Keyword(s):  
Rna Pol Ii ◽  
Pol Ii ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide RNA pol II initiation and pausing in neural progenitors of the rat

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Adam Scheidegger ◽  
Carissa J. Dunn ◽  
Ann Samarakkody ◽  
Nii Koney-Kwaku Koney ◽  
Danielle Perley ◽  
...  
Keyword(s):  
Neural Progenitors ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Genome Wide

scholarly journals Selective Requirement for SAGA in Hog1-Mediated Gene Expression Depending on the Severity of the External Osmostress Conditions

2007 ◽  
Vol 27 (11) ◽  
pp. 3900-3910 ◽  
Author(s):  
Meritxell Zapater ◽  
Marc Sohrmann ◽  
Matthias Peter ◽  
Francesc Posas ◽  
Eulàlia de Nadal
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Genetic Screening ◽  
Essential Role ◽  
Regulation Of Gene Expression ◽  
Transcriptional Program ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Genome Wide ◽  
Transcriptional Complex

ABSTRACT Regulation of gene expression by the Hog1 stress-activated protein kinase is essential for proper cell adaptation to osmostress. Hog1 coordinates an extensive transcriptional program through the modulation of transcription. To identify systematically novel components of the transcriptional machinery required for osmostress-mediated gene expression, we performed an exhaustive genome-wide genetic screening, searching for mutations that render cells osmosensitive at high osmolarity and that are associated with reduced expression of osmoresponsive genes. The SAGA and Mediator complexes were identified as putative novel regulators of osmostress-mediated transcription. Interestingly, whereas Mediator is essential for osmostress gene expression, the requirement for SAGA is different depending on the strength of the extracellular osmotic conditions. At mild osmolarity, SAGA mutants show only very slight defects on RNA polymerase II (Pol II) recruitment and gene expression, whereas at severe osmotic conditions, SAGA mutants show completely impaired RNA Pol II recruitment and transcription of osmoresponsive genes. Thus, our results define an essential role for Mediator in osmostress gene expression and a selective role for SAGA under severe osmostress. Our results indicate that the requirement for a transcriptional complex to regulate a promoter might be determined by the strength of the stimuli perceived by the cell through the regulation of interactions between transcriptional complexes.

scholarly journals Intronic heterochromatin prevents cryptic transcription initiation in Arabidopsis

2019 ◽  
Author(s):  
Jincong Zhou ◽  
Liangyu Liu ◽  
Qin Li ◽  
Wei Xu ◽  
Kuan Li ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Common Mechanism ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Genome Wide ◽  
Chimeric Transcripts ◽  
Genes Expression ◽  
Cryptic Transcription ◽  
Eukaryotic Genomes ◽  
Host Genes

ABSTRACTIntronic transposable elements (TEs) comprise a large proportion in eukaryotic genomes, but how they regulate the host genes remains to be explored. Our forward genetic screen disclosed the plant specific RNA polymerases IV and V in suppressing intronic TE-mediated cryptic transcription initiation of a chimeric transcripts at FLC (FLCTE). Initiation of FLCTE transcription is blocked by the locally formed intronic heterochromatin, which is directly associated with RNA Pol V to inhibit the entry of RNA Pol II and the occupancy of H3K4 methylation. Genome-wide Pol II Ser5p native elongation transcription sequencing revealed that this is a common mechanism among intronic heterochromatin-containing genes. This study sheds light on deeply understanding the function of intronic heterochromatin on host genes expression in eukaryotic genome.

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