Literature DB >> 20387139

RNA modifications: a mechanism that modulates gene expression.

John Karijolich1, Athena Kantartzis, Yi-Tao Yu.   

Abstract

Accuracy in the flow of genetic information from DNA to protein, or gene expression, is essential to the viability of an organisms. Pre-mRNA splicing and protein translation are two major steps in eukaryotic gene expression that necessitate the production of accurate gene products. Both processes occur in large complexes, consisting of both proteins and noncoding RNAs. Interestingly, the RNA components contain a large number of posttranscriptional modifications, including 2'-O-methylation and pseudouridylation, which are functionally important. In this chapter, we highlight the functional aspects of the modifications of spliceosomal snRNA and rRNA and provide a framework for understanding how posttranscriptional modifications are capable of influencing gene expression.

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Year:  2010        PMID: 20387139      PMCID: PMC4154353          DOI: 10.1007/978-1-60761-657-3_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  85 in total

1.  Mutations at U2555, a tRNA-protected base in 23S rRNA, affect translational fidelity.

Authors:  M O'Connor; A E Dahlberg
Journal:  Proc Natl Acad Sci U S A       Date:  1993-10-01       Impact factor: 11.205

2.  Functional reconstitution of U6 snRNA in nematode cis- and trans-splicing: U6 can serve as both a branch acceptor and a 5' exon.

Authors:  Y T Yu; P A Maroney; T W Nilsen
Journal:  Cell       Date:  1993-12-17       Impact factor: 41.582

3.  Splicing function of mammalian U6 small nuclear RNA: conserved positions in central domain and helix I are essential during the first and second step of pre-mRNA splicing.

Authors:  T Wolff; R Menssen; J Hammel; A Bindereif
Journal:  Proc Natl Acad Sci U S A       Date:  1994-02-01       Impact factor: 11.205

4.  Conformational changes of U6 RNA during the spliceosome cycle: an intramolecular helix is essential both for initiating the U4-U6 interaction and for the first step of slicing.

Authors:  T Wolff; A Bindereif
Journal:  Genes Dev       Date:  1993-07       Impact factor: 11.361

5.  Ribonucleoprotein particle assembly and modification of U2 small nuclear RNA containing 5-fluorouridine.

Authors:  J R Patton
Journal:  Biochemistry       Date:  1993-08-31       Impact factor: 3.162

6.  Multiple pseudouridine synthase activities for small nuclear RNAs.

Authors:  J R Patton
Journal:  Biochem J       Date:  1993-03-01       Impact factor: 3.857

7.  Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure.

Authors:  J G Arnez; T A Steitz
Journal:  Biochemistry       Date:  1994-06-21       Impact factor: 3.162

8.  The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles.

Authors:  J A Kowalak; J J Dalluge; J A McCloskey; K O Stetter
Journal:  Biochemistry       Date:  1994-06-28       Impact factor: 3.162

9.  Mutational analysis of human U6 RNA: stabilizing the intramolecular helix blocks the spliceosomal assembly pathway.

Authors:  T Wolff; A Bindereif
Journal:  Biochim Biophys Acta       Date:  1995-07-25

10.  In vitro reconstitution of mammalian U2 and U5 snRNPs active in splicing: Sm proteins are functionally interchangeable and are essential for the formation of functional U2 and U5 snRNPs.

Authors:  V Ségault; C L Will; B S Sproat; R Lührmann
Journal:  EMBO J       Date:  1995-08-15       Impact factor: 11.598

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  18 in total

1.  Development and validation of a generic fluorescent methyltransferase activity assay based on the transcreener AMP/GMP assay.

Authors:  Tony A Klink; Matt Staeben; Kim Twesten; Andrew L Kopp; Meera Kumar; Rebecca Schall Dunn; Cori A Pinchard; Karen M Kleman-Leyer; Martin Klumpp; Robert G Lowery
Journal:  J Biomol Screen       Date:  2011-09-28

Review 2.  Intersections of post-transcriptional gene regulatory mechanisms with intermediary metabolism.

Authors:  Waqar Arif; Gandhar Datar; Auinash Kalsotra
Journal:  Biochim Biophys Acta Gene Regul Mech       Date:  2017-01-11       Impact factor: 4.490

Review 3.  RNA modifications and structures cooperate to guide RNA-protein interactions.

Authors:  Cole J T Lewis; Tao Pan; Auinash Kalsotra
Journal:  Nat Rev Mol Cell Biol       Date:  2017-02-01       Impact factor: 94.444

4.  An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.

Authors:  Mohit Chawla; Romina Oliva; Janusz M Bujnicki; Luigi Cavallo
Journal:  Nucleic Acids Res       Date:  2015-06-27       Impact factor: 16.971

5.  Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling.

Authors:  Andrew D Bailey; Jason Talkish; Hongxu Ding; Haller Igel; Alejandra Duran; Shreya Mantripragada; Benedict Paten; Manuel Ares
Journal:  Elife       Date:  2022-04-06       Impact factor: 8.713

6.  Pre-ribosomal RNA reorganizes DNA damage repair factors in nucleus during meiotic prophase and DNA damage response.

Authors:  Xiaochen Gai; Di Xin; Duo Wu; Xin Wang; Linlin Chen; Yiqing Wang; Kai Ma; Qilin Li; Peng Li; Xiaochun Yu
Journal:  Cell Res       Date:  2022-01-04       Impact factor: 46.297

Review 7.  Transcriptome-wide dynamics of RNA pseudouridylation.

Authors:  John Karijolich; Chengqi Yi; Yi-Tao Yu
Journal:  Nat Rev Mol Cell Biol       Date:  2015-08-19       Impact factor: 94.444

8.  HSP90-dependent PUS7 overexpression facilitates the metastasis of colorectal cancer cells by regulating LASP1 abundance.

Authors:  Dan Song; Ming Guo; Shuai Xu; Xiaotian Song; Bin Bai; Zhengyan Li; Jie Chen; Yanxin An; Yongzhan Nie; Kaichun Wu; Shiqi Wang; Qingchuan Zhao
Journal:  J Exp Clin Cancer Res       Date:  2021-05-14

9.  2'-O methylation of internal adenosine by flavivirus NS5 methyltransferase.

Authors:  Hongping Dong; David C Chang; Maggie Ho Chia Hua; Siew Pheng Lim; Yok Hian Chionh; Fabian Hia; Yie Hou Lee; Petra Kukkaro; Shee-Mei Lok; Peter C Dedon; Pei-Yong Shi
Journal:  PLoS Pathog       Date:  2012-04-05       Impact factor: 6.823

10.  Age-dependent decrease and alternative splicing of methionine synthase mRNA in human cerebral cortex and an accelerated decrease in autism.

Authors:  Christina R Muratore; Nathaniel W Hodgson; Malav S Trivedi; Hamid M Abdolmaleky; Antonio M Persico; Carla Lintas; Suzanne De la Monte; Richard C Deth
Journal:  PLoS One       Date:  2013-02-20       Impact factor: 3.240

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