Published in Nucleic Acids Res on March 15, 2017
Host noncoding retrotransposons induced by DNA viruses: a SINE of infection? J Virol (2017) 0.75
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
WebLogo: a sequence logo generator. Genome Res (2004) 59.58
BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23
GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol (2004) 6.67
Repeat sequence families derived from mammalian tRNA genes. Nature (1985) 6.10
lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature (2011) 5.42
Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res (2004) 5.14
Psoralens as photoactive probes of nucleic acid structure and function: organic chemistry, photochemistry, and biochemistry. Annu Rev Biochem (1985) 4.83
The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell (2001) 4.72
Alu sequences are processed 7SL RNA genes. Nature (1984) 4.67
Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell (2009) 4.54
Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell (2008) 4.24
Cloning and mutagenesis of the murine gammaherpesvirus 68 genome as an infectious bacterial artificial chromosome. J Virol (2000) 4.09
DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature (2011) 3.90
The noncoding RNA revolution-trashing old rules to forge new ones. Cell (2014) 3.87
Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res (2008) 3.76
Synthesis and characterization of new psoralen derivatives with superior photoreactivity with DNA and RNA. Biochemistry (1977) 3.68
Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands. Cell (1988) 3.54
Mammalian retroelements. Genome Res (2002) 3.49
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell (2012) 3.48
An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell (1980) 3.45
Alu element-mediated gene silencing. EMBO J (2008) 3.22
Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat Struct Mol Biol (2006) 3.21
DICER1 loss and Alu RNA induce age-related macular degeneration via the NLRP3 inflammasome and MyD88. Cell (2012) 2.81
The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol (2004) 2.71
Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science (2007) 2.70
The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc Natl Acad Sci U S A (2003) 2.61
Effects of tRNATyr point mutations on the binding of yeast RNA polymerase III transcription factor C. J Biol Chem (1986) 2.55
Induction of B2 RNA polymerase III transcription by heat shock: enrichment for heat shock induced sequences in rodent cells by hybridization subtraction. Nucleic Acids Res (1986) 2.31
Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol (2010) 2.30
Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res (1995) 2.28
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc (2008) 2.17
Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol (2010) 2.15
Unified mode of centromeric protection by shugoshin in mammalian oocytes and somatic cells. Nat Cell Biol (2007) 2.13
Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet (2007) 2.00
Monoclonal antibodies to double-stranded RNA as probes of RNA structure in crude nucleic acid extracts. Nucleic Acids Res (1991) 1.92
Gene regulation by antisense transcription. Nat Rev Genet (2013) 1.90
Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics (2006) 1.80
REAP: A two minute cell fractionation method. BMC Res Notes (2010) 1.76
Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res (1994) 1.70
RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA. EMBO J (2013) 1.68
RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell (2016) 1.67
B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci U S A (2009) 1.65
Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol (1998) 1.64
Differential stress induction of individual Alu loci: implications for transcription and retrotransposition. Gene (2001) 1.62
Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res (2010) 1.57
Novel small-molecule inhibitors of RNA polymerase III. Eukaryot Cell (2003) 1.56
Shugoshin-2 is essential for the completion of meiosis but not for mitotic cell division in mice. Genes Dev (2008) 1.49
Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J Biol Chem (2003) 1.43
Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res (2014) 1.31
Nucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation. J Biol Chem (1993) 1.30
Activation of RNA polymerase III transcription of human Alu repetitive elements by adenovirus type 5: requirement for the E1b 58-kilodalton protein and the products of E4 open reading frames 3 and 6. Mol Cell Biol (1993) 1.27
Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC Genomics (2007) 1.27
Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells. Nucleic Acids Res (2011) 1.23
Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. Proc Natl Acad Sci U S A (2002) 1.23
Control of myogenesis by rodent SINE-containing lncRNAs. Genes Dev (2013) 1.21
Host shutoff is a conserved phenotype of gammaherpesvirus infection and is orchestrated exclusively from the cytoplasm. J Virol (2009) 1.19
Identification of widespread ultra-edited human RNAs. PLoS Genet (2011) 1.16
Analysis of RNA secondary structure by photochemical reversal of psoralen crosslinks. Nucleic Acids Res (1979) 1.16
Using Alu elements as polyadenylation sites: A case of retroposon exaptation. Mol Biol Evol (2008) 1.16
Heterogeneous nuclear RNA double-stranded regions probed in living HeLa cells by crosslinking with the psoralen derivative aminomethyltrioxsalen. Proc Natl Acad Sci U S A (1979) 1.15
Murine gamma-herpesvirus 68 hijacks MAVS and IKKbeta to initiate lytic replication. PLoS Pathog (2010) 1.14
Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo. Proc Natl Acad Sci U S A (2008) 1.12
Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nat Genet (2011) 1.12
Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch. Genome Res (2011) 1.10
Human retroelements may introduce intragenic polyadenylation signals. Cytogenet Genome Res (2005) 1.06
Sgol2 provides a regulatory platform that coordinates essential cell cycle processes during meiosis I in oocytes. Elife (2013) 1.04
HSV infection induces increased transcription of Alu repeated sequences by RNA polymerase III. FEBS Lett (1989) 1.03
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation. Nat Struct Mol Biol (2012) 1.03
Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs. Genes Genet Syst (2013) 1.02
mRNA-mRNA duplexes that autoelicit Staufen1-mediated mRNA decay. Nat Struct Mol Biol (2013) 1.01
A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver. Genome Res (2012) 1.00
Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput Biol (2009) 0.99
Activation of RNA polymerase III transcription of human Alu elements by herpes simplex virus. Virology (1994) 0.98
Global Mapping of Human RNA-RNA Interactions. Mol Cell (2016) 0.98
Global mRNA degradation during lytic gammaherpesvirus infection contributes to establishment of viral latency. PLoS Pathog (2011) 0.97
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
Evolution of Alu elements toward enhancers. Cell Rep (2014) 0.96
Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development. Genome Res (2011) 0.93
Genome-wide analysis of Alu editability. Nucleic Acids Res (2014) 0.92
In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation. Mol Cell (2016) 0.91
Small B2 RNAs in mouse oocytes, embryos, and somatic tissues. Dev Biol (1988) 0.89
SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nat Commun (2015) 0.87
Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data. Nucleic Acids Res (2014) 0.85
Binding of TFIIIC to sine elements controls the relocation of activity-dependent neuronal genes to transcription factories. PLoS Genet (2013) 0.84
Increased levels of B1 and B2 SINE transcripts in mouse fibroblast cells due to minute virus of mice infection. Virology (2004) 0.83
RNA polymerase III transcriptomes in human embryonic stem cells and induced pluripotent stem cells, and relationships with pluripotency transcription factors. PLoS One (2014) 0.83
Infection-Induced Retrotransposon-Derived Noncoding RNAs Enhance Herpesviral Gene Expression via the NF-κB Pathway. PLoS Pathog (2015) 0.80
Regulation of gene expression via retrotransposon insertions and the noncoding RNA 4.5S RNAH. Genes Cells (2015) 0.77