scholarly journals Determination of lysine residues affinity labeled in the active site of yeast RNA polymerase II(B) by mutagenesis

1992 ◽  
Vol 20 (18) ◽  
pp. 4721-4725 ◽  
Author(s):  
Isabelle Treich ◽  
Christophe Carles ◽  
André Sentenac ◽  
Michel Riva
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site ◽  
Lysine Residues

Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations

2008 ◽  
Vol 120 (4-6) ◽  
pp. 479-489 ◽  
Author(s):  
Rui Zhu ◽  
Florian Janetzko ◽  
Yue Zhang ◽  
Adri C. T. van Duin ◽  
William A. Goddard ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site

Structural Biology of RNA Polymerase II Transcription: 20 Years On

2020 ◽  
Vol 36 (1) ◽  
pp. 1-34 ◽  
Author(s):  
Sara Osman ◽  
Patrick Cramer
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Focal Point ◽  
Dna Lesions ◽  
Cellular Regulation ◽  
Pol Ii ◽  
Associated Proteins ◽  
Rna Polymerase Ii Transcription

Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.

scholarly journals The Non-Coding B2 RNA Binds to the DNA Cleft and Active-Site Region of RNA Polymerase II

2013 ◽  
Vol 425 (19) ◽  
pp. 3625-3638 ◽  
Author(s):  
Steven L. Ponicsan ◽  
Stephane Houel ◽  
William M. Old ◽  
Natalie G. Ahn ◽  
James A. Goodrich ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site ◽  
B2 Rna ◽  
Active Site Region

NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases

2005 ◽  
Vol 83 (4) ◽  
pp. 486-496 ◽  
Author(s):  
Zachary F Burton ◽  
Michael Feig ◽  
Xue Q Gong ◽  
Chunfen Zhang ◽  
Yuri A Nedialkov ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site ◽  
Binding Sites ◽  
Rna Synthesis ◽  
Rna Polymerases ◽  
Phosphoryl Transfer ◽  
Elongation Complex ◽  
Detailed Model ◽  
Loop 2

Multi-subunit RNA polymerases bind nucleotide triphosphate (NTP) substrates in the pretranslocated state and carry the dNMP–NTP base pair into the active site for phosphoryl transfer. NTP-driven translocation requires that NTP substrates enter the main-enzyme channel before loading into the active site. Based on this model, a new view of fidelity and efficiency of RNA synthesis is proposed. The model predicts that, during processive elongation, NTP-driven translocation is coupled to a protein conformational change that allows pyrophosphate release: coupling the end of one bond-addition cycle to substrate loading and translocation for the next. We present a detailed model of the RNA polymerase II elongation complex based on 2 low-affinity NTP binding sites located in the main-enzyme channel. This model posits that NTP substrates, elongation factors, and the conserved Rpb2 subunit fork loop 2 cooperate to regulate opening of the downstream transcription bubble.Key words: RNA polymerase, NTP-driven translocation, transcriptional fidelity, transcriptional efficiency, α-amanitin.

scholarly journals Author response: Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells

2015 ◽  
Author(s):  
João D Dias ◽  
Tiago Rito ◽  
Elena Torlai Triglia ◽  
Alexander Kukalev ◽  
Carmelo Ferrai ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Mammalian Cells ◽  
Author Response ◽  
Lysine Residues ◽  
Early Transcription

Out or decay: fate determination of nuclear RNAs

2020 ◽  
Vol 64 (6) ◽  
pp. 895-905 ◽  
Author(s):  
Jianshu Wang ◽  
Hong Cheng
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Fate Determination ◽  
Biological Relevance ◽  
Nuclear Rna ◽  
Nuclear Degradation ◽  
Processing Steps ◽  
Mammalian System

Abstract In eukaryotes, RNAs newly synthesized by RNA polymerase II (RNAPII) undergo several processing steps prior to transport to the cytoplasm. It has long been known that RNAs with defects in processing or export are removed in the nucleus. Recent studies revealed that RNAs without apparent defects are also subjected to nuclear degradation, indicating that nuclear RNA fate is determined in a more complex and dynamic way than previously thought. Nuclear RNA sorting directly determines the quality and quantity of RNA pools for future translation and thus is of significant importance. In this essay, we will summarize recent studies on this topic, mainly focusing on findings in mammalian system, and discuss about important remaining questions and possible biological relevance for nuclear RNA fate determination.

scholarly journals Transient Reversal of RNA Polymerase II Active Site Closing Controls Fidelity of Transcription Elongation

2008 ◽  
Vol 30 (5) ◽  
pp. 557-566 ◽  
Author(s):  
Maria L. Kireeva ◽  
Yuri A. Nedialkov ◽  
Gina H. Cremona ◽  
Yuri A. Purtov ◽  
Lucyna Lubkowska ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Active Site ◽  
Transcription Elongation
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