High-Resolution Protein−DNA Contacts for the Yeast RNA Polymerase II General Transcription Machinery†

Biochemistry ◽  
2004 ◽  
Vol 43 (40) ◽  
pp. 12741-12749 ◽  
Author(s):  
Bo-Shiun Chen ◽  
Subhrangsu S. Mandal ◽  
Michael Hampsey
Keyword(s):  
High Resolution ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Machinery ◽  
General Transcription Machinery

scholarly journals PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription

2019 ◽  
Vol 47 (11) ◽  
pp. 5573-5586 ◽  
Author(s):  
Nicole Steinbach ◽  
Dan Hasson ◽  
Deepti Mathur ◽  
Elias E Stratikopoulos ◽  
Ravi Sachidanandam ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Machinery

scholarly journals Recruitment of TREX to the Transcription Machinery by Its Direct Binding to the Phospho-CTD of RNA Polymerase II

PLoS Genetics ◽  
2013 ◽  
Vol 9 (11) ◽  
pp. e1003914 ◽  
Author(s):  
Dominik M. Meinel ◽  
Cornelia Burkert-Kautzsch ◽  
Anja Kieser ◽  
Eoghan O'Duibhir ◽  
Matthias Siebert ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Machinery ◽  
Direct Binding

scholarly journals Simultaneous CUT&Tag profiling of the accessible and silenced regulome in single cells

2021 ◽  
Author(s):  
Derek H Janssens ◽  
Dominik J. Otto ◽  
Manu Setty ◽  
Kami Ahmad ◽  
Steven Henikoff
Keyword(s):  
High Resolution ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
High Throughput ◽  
Single Cells ◽  
Regulatory Elements ◽  
Small Samples ◽  
Signal Deconvolution ◽  
Chromatin Profiling

Cleavage Under Targets & Tagmentation (CUT&Tag) is an antibody-directed transposase tethering strategy for in situ chromatin profiling in small samples and single cells. We describe a modified CUT&Tag protocol using a mixture of an antibody to the initiation form of RNA Polymerase II (Pol2 Serine-5 phosphate) and an antibody to repressive Polycomb domains (H3K27me3) followed by computational signal deconvolution to produce high-resolution maps of both the active and repressive regulomes in single cells. The ability to seamlessly map active promoters, enhancers and repressive regulatory elements using a single workflow provides a complete regulome profiling strategy suitable for high-throughput single-cell platforms.

scholarly journals Therapeutic Targeting of the General RNA Polymerase II Transcription Machinery

2020 ◽  
Vol 21 (9) ◽  
pp. 3354 ◽  
Author(s):  
Ryan D. Martin ◽  
Terence E. Hébert ◽  
Jason C. Tanny
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Complex Diseases ◽  
Cellular Models ◽  
Transcription Machinery ◽  
Transcription Inhibitors ◽  
Preclinical And Clinical Studies ◽  
Rna Polymerase Ii Transcription ◽  
Rnapii Transcription

Inhibitors targeting the general RNA polymerase II (RNAPII) transcription machinery are candidate therapeutics in cancer and other complex diseases. Here, we review the molecular targets and mechanisms of action of these compounds, framing them within the steps of RNAPII transcription. We discuss the effects of transcription inhibitors in vitro and in cellular models (with an emphasis on cancer), as well as their efficacy in preclinical and clinical studies. We also discuss the rationale for inhibiting broadly acting transcriptional regulators or RNAPII itself in complex diseases.

scholarly journals High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Zhijie Chen ◽  
Ronen Gabizon ◽  
Aidan I Brown ◽  
Antony Lee ◽  
Aixin Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Residence Time ◽  
Base Pair ◽  
High Accuracy ◽  
Control Of Gene Expression ◽  
Pol Ii ◽  
Crossing Time

Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression.

Sign in / Sign up

Export Citation Format

Share Document