Literature DB >> 26392149

RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications.

Liang Xu1, Wei Wang1, Jenny Chong1, Ji Hyun Shin1, Jun Xu1, Dong Wang1.   

Abstract

Accurate genetic information transfer is essential for life. As a key enzyme involved in the first step of gene expression, RNA polymerase II (Pol II) must maintain high transcriptional fidelity while it reads along DNA template and synthesizes RNA transcript in a stepwise manner during transcription elongation. DNA lesions or modifications may lead to significant changes in transcriptional fidelity or transcription elongation dynamics. In this review, we will summarize recent progress toward understanding the molecular basis of RNA Pol II transcriptional fidelity control and impacts of DNA lesions and modifications on Pol II transcription elongation.

Entities:  

Keywords:  Chemical biology; DNA damage; RNA polymerase II; computational biology; epigenetic DNA modifications; structural biology; transcription fidelity

Mesh:

Substances:

Year:  2015        PMID: 26392149      PMCID: PMC4891981          DOI: 10.3109/10409238.2015.1087960

Source DB:  PubMed          Journal:  Crit Rev Biochem Mol Biol        ISSN: 1040-9238            Impact factor:   8.250


  202 in total

1.  Transcription elongation factor S-II maintains transcriptional fidelity and confers oxidative stress resistance.

Authors:  Hiroshi Koyama; Takahiro Ito; Toshiyuki Nakanishi; Nobuyuki Kawamura; Kazuhisa Sekimizu
Journal:  Genes Cells       Date:  2003-10       Impact factor: 1.891

Review 2.  DNA sequences that interfere with transcription: implications for genome function and stability.

Authors:  Boris P Belotserkovskii; Sergei M Mirkin; Philip C Hanawalt
Journal:  Chem Rev       Date:  2013-08-23       Impact factor: 60.622

3.  Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.

Authors:  Jasmin F Sydow; Florian Brueckner; Alan C M Cheung; Gerke E Damsma; Stefan Dengl; Elisabeth Lehmann; Dmitry Vassylyev; Patrick Cramer
Journal:  Mol Cell       Date:  2009-06-26       Impact factor: 17.970

4.  RNA polymerase II transcript elongation.

Authors:  Jesper Q Svejstrup
Journal:  Biochim Biophys Acta       Date:  2013-01

5.  RNA polymerase II blockage by cisplatin-damaged DNA. Stability and polyubiquitylation of stalled polymerase.

Authors:  Yongwon Jung; Stephen J Lippard
Journal:  J Biol Chem       Date:  2005-11-07       Impact factor: 5.157

6.  The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes.

Authors:  M D Rudd; M G Izban; D S Luse
Journal:  Proc Natl Acad Sci U S A       Date:  1994-08-16       Impact factor: 11.205

7.  Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase.

Authors:  Vasily Sosunov; Ekaterina Sosunova; Arkady Mustaev; Irina Bass; Vadim Nikiforov; Alex Goldfarb
Journal:  EMBO J       Date:  2003-05-01       Impact factor: 11.598

Review 8.  Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects.

Authors:  Maria Fousteri; Leon H F Mullenders
Journal:  Cell Res       Date:  2008-01       Impact factor: 25.617

9.  Active site opening and closure control translocation of multisubunit RNA polymerase.

Authors:  Anssi M Malinen; Matti Turtola; Marimuthu Parthiban; Lioudmila Vainonen; Mark S Johnson; Georgiy A Belogurov
Journal:  Nucleic Acids Res       Date:  2012-05-08       Impact factor: 16.971

10.  5-Formylcytosine alters the structure of the DNA double helix.

Authors:  Eun-Ang Raiber; Pierre Murat; Dimitri Y Chirgadze; Dario Beraldi; Ben F Luisi; Shankar Balasubramanian
Journal:  Nat Struct Mol Biol       Date:  2014-12-15       Impact factor: 15.369

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  18 in total

1.  Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis.

Authors:  Liang Xu; Wei Wang; Jiabin Wu; Ji Hyun Shin; Pengcheng Wang; Ilona Christy Unarta; Jenny Chong; Yinsheng Wang; Dong Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-07       Impact factor: 11.205

2.  8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II.

Authors:  Kirill A Konovalov; Fátima Pardo-Avila; Carmen Ka Man Tse; Juntaek Oh; Dong Wang; Xuhui Huang
Journal:  J Biol Chem       Date:  2019-02-04       Impact factor: 5.157

3.  RNA polymerase II acts as a selective sensor for DNA lesions and endogenous DNA modifications.

Authors:  Ji Hyun Shin; Liang Xu; Dong Wang
Journal:  Transcription       Date:  2016-04-22

4.  Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.

Authors:  Wei Wang; Liang Xu; Lulu Hu; Jenny Chong; Chuan He; Dong Wang
Journal:  J Am Chem Soc       Date:  2017-10-03       Impact factor: 15.419

Review 5.  Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair.

Authors:  Wei Wang; Jun Xu; Jenny Chong; Dong Wang
Journal:  DNA Repair (Amst)       Date:  2018-08-23

6.  5-Formylcytosine-induced DNA-peptide cross-links reduce transcription efficiency, but do not cause transcription errors in human cells.

Authors:  Shaofei Ji; Daeyoon Park; Konstantin Kropachev; Marina Kolbanovskiy; Iwen Fu; Suse Broyde; Maram Essawy; Nicholas E Geacintov; Natalia Y Tretyakova
Journal:  J Biol Chem       Date:  2019-10-09       Impact factor: 5.157

7.  Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.

Authors:  Candy S Hwang; Liang Xu; Wei Wang; Sébastien Ulrich; Lu Zhang; Jenny Chong; Ji Hyun Shin; Xuhui Huang; Eric T Kool; Charles E McKenna; Dong Wang
Journal:  Nucleic Acids Res       Date:  2016-04-07       Impact factor: 16.971

8.  DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi.

Authors:  Timothy Casselli; Yvonne Tourand; Adam Scheidegger; William K Arnold; Anna Proulx; Brian Stevenson; Catherine A Brissette
Journal:  J Bacteriol       Date:  2018-11-26       Impact factor: 3.490

9.  RNA polymerase I (Pol I) lobe-binding subunit Rpa12.2 promotes RNA cleavage and proofreading.

Authors:  Katrin Schwank; Catharina Schmid; Tobias Fremter; Philipp Milkereit; Joachim Griesenbeck; Herbert Tschochner
Journal:  J Biol Chem       Date:  2022-03-25       Impact factor: 5.486

10.  Cisplatin alters the function and expression of N-type voltage-gated calcium channels in the absence of morphological damage of sensory neurons.

Authors:  Markus Leo; Linda-Isabell Schmitt; Holger Jastrow; Jürgen Thomale; Christoph Kleinschnitz; Tim Hagenacker
Journal:  Mol Pain       Date:  2017-11-22       Impact factor: 3.395

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