Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.

PubWeight™: 0.76‹?›

🔗 View Article (PMID 27782844)

Published in Genome Biol on October 25, 2016

Authors

Mansoureh Tajaddod1, Andrea Tanzer2, Konstantin Licht3, Michael T Wolfinger3,2, Stefan Badelt2, Florian Huber1,4, Oliver Pusch3, Sandy Schopoff1, Michael Janisiw3, Ivo Hofacker2, Michael F Jantsch5,6

Author Affiliations

1: Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, Vienna, A-1030, Austria.
2: Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, Vienna, A-1090, Austria.
3: Department of Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, A-1090, Austria.
4: Present address: Center for molecular biology of the University Heidelberg, Im Neuenheimer Feld 282, Heidelberg, D-69120, Germany.
5: Department of Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, A-1090, Austria. Michael.Jantsch@meduniwien.ac.at.
6: Department of Cell and Developmental Biology, Medical University of Vienna, Center of Anatomy and Cell Biology, Schwarzspanierstrasse 17, Vienna, A-1090, Austria. Michael.Jantsch@meduniwien.ac.at.

Articles cited by this

BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23

Landscape of transcription in human cells. Nature (2012) 20.18

GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19

qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol (2007) 16.15

Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol (2004) 7.61

Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol (2004) 6.67

Regulating gene expression through RNA nuclear retention. Cell (2005) 5.58

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature (2011) 5.42

PKR; a sentinel kinase for cellular stress. Oncogene (1999) 5.29

The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science (2003) 5.04

Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell (2008) 4.24

Somatic retrotransposition alters the genetic landscape of the human brain. Nature (2011) 4.16

Active human retrotransposons: variation and disease. Curr Opin Genet Dev (2012) 3.60

Alu element-mediated gene silencing. EMBO J (2008) 3.22

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature (2012) 3.08

Characterization of transgenic mice with targeted disruption of the catalytic domain of the double-stranded RNA-dependent protein kinase, PKR. J Biol Chem (1999) 2.65

Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science (2001) 2.32

Staufen1 regulates diverse classes of mammalian transcripts. EMBO J (2007) 2.18

Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J (2000) 2.01

Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability. Genome Res (2001) 1.97

Inhibiting eukaryotic transcription: Which compound to choose? How to evaluate its activity? Transcription (2011) 1.94

RNAPol-ChIP: a novel application of chromatin immunoprecipitation to the analysis of real-time gene transcription. Nucleic Acids Res (2004) 1.86

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. Elife (2014) 1.82

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Res (2013) 1.81

RNA-editing-mediated exon evolution. Genome Biol (2007) 1.77

RNA editing level in the mouse is determined by the genomic repeat repertoire. RNA (2006) 1.75

C. elegans and H. sapiens mRNAs with edited 3' UTRs are present on polysomes. RNA (2008) 1.70

ADAR editing in double-stranded UTRs and other noncoding RNA sequences. Trends Biochem Sci (2010) 1.63

Specificity of ADAR-mediated RNA editing in newly identified targets. RNA (2008) 1.51

Useful 'junk': Alu RNAs in the human transcriptome. Cell Mol Life Sci (2007) 1.50

Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats. Cell Cycle (2008) 1.42

Activation of the mouse histone deacetylase 1 gene by cooperative histone phosphorylation and acetylation. Mol Cell Biol (2002) 1.36

Intronic Alus influence alternative splicing. PLoS Genet (2008) 1.35

The origins and implications of Aluternative splicing. Trends Genet (2004) 1.35

STAU1 binding 3' UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown. Genes Dev (2013) 1.32

Alu elements and the human genome. Genetica (2000) 1.32

Origin and evolution of SINEs in eukaryotic genomes. Heredity (Edinb) (2011) 1.23

Inverted Alu dsRNA structures do not affect localization but can alter translation efficiency of human mRNAs independent of RNA editing. Nucleic Acids Res (2012) 1.21

Staufen1 senses overall transcript secondary structure to regulate translation. Nat Struct Mol Biol (2013) 1.19

A distant cis acting intronic element induces site-selective RNA editing. Nucleic Acids Res (2012) 1.14

B1 and related SINEs in mammalian genomes. Gene (2003) 1.08

PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator. Genes Dev (2014) 0.99

Molecular mechanisms of transcription through single-molecule experiments. Chem Rev (2014) 0.98

Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus. Genes Dev (2015) 0.97

Alu elements shape the primate transcriptome by cis-regulation of RNA editing. Genome Biol (2014) 0.97

Increased sensitivity and accuracy of a single-stranded DNA splint-mediated ligation assay (sPAT) reveals poly(A) tail length dynamics of developmentally regulated mRNAs. RNA Biol (2014) 0.89

Tandem insertions of Alu elements. Cytogenet Genome Res (2005) 0.88

Structure and origin of a novel dimeric retroposon B1-diD. J Mol Evol (2001) 0.82

Regulation of gene expression via retrotransposon insertions and the noncoding RNA 4.5S RNAH. Genes Cells (2015) 0.77