Published in RNA on December 01, 2003
The diversity of LTR retrotransposons. Genome Biol (2004) 1.74
Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae. Nucleic Acids Res (2006) 1.40
Mechanisms and implications of programmed translational frameshifting. Wiley Interdiscip Rev RNA (2012) 1.34
A programmed -1 ribosomal frameshift signal can function as a cis-acting mRNA destabilizing element. Nucleic Acids Res (2004) 1.18
Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast. Nucleic Acids Res (2010) 1.09
Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli. J Bacteriol (2005) 1.00
Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics (2009) 1.00
Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification. BMC Genomics (2012) 0.96
The Sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, interact with a family of proteins related to dynein light chain 8. Plant Physiol (2005) 0.93
The centromeric retrotransposons of rice are transcribed and differentially processed by RNA interference. Genetics (2007) 0.89
Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning. Nat Rev Genet (2015) 0.88
Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? BMC Genomics (2010) 0.87
The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age. Chromosome Res (2009) 0.84
MASiVEdb: the Sirevirus Plant Retrotransposon Database. BMC Genomics (2012) 0.83
A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons. Genetica (2012) 0.82
AtCopeg1, the unique gene originated from AtCopia95 retrotransposon family, is sensitive to external hormones and abiotic stresses. Plant Cell Rep (2008) 0.82
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res (2016) 0.82
Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC). RNA Biol (2011) 0.81
Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algae. J Mol Evol (2007) 0.81
Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world. Mob DNA (2013) 0.79
Experimental evidence for splicing of intron-containing transcripts of plant LTR retrotransposon Ogre. Mol Genet Genomics (2008) 0.78
RNA sociology: group behavioral motifs of RNA consortia. Life (Basel) (2014) 0.78
BARE retrotransposons are translated and replicated via distinct RNA pools. PLoS One (2013) 0.76
Reverse transcriptase domain sequences from tree peony (Paeonia suffruticosa) long terminal repeat retrotransposons: sequence characterization and phylogenetic analysis. Biotechnol Biotechnol Equip (2014) 0.75
Transposable elements in Drosophila. Mob Genet Elements (2017) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene (1988) 42.41
The genome sequence of Schizosaccharomyces pombe. Nature (2002) 14.26
Nested retrotransposons in the intergenic regions of the maize genome. Science (1996) 12.95
Characterization of ribosomal frameshifting in HIV-1 gag-pol expression. Nature (1988) 10.69
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A (1994) 8.06
Murine leukemia virus protease is encoded by the gag-pol gene and is synthesized through suppression of an amber termination codon. Proc Natl Acad Sci U S A (1985) 5.36
Translation of MuLV and MSV RNAs in nuclease-treated reticulocyte extracts: enhancement of the gag-pol polypeptide with yeast suppressor tRNA. Cell (1978) 5.31
Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res (1998) 5.10
A -1 ribosomal frameshift in a double-stranded RNA virus of yeast forms a gag-pol fusion protein. Proc Natl Acad Sci U S A (1991) 4.08
Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell (1990) 3.87
Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme. Cell (1995) 3.64
RNA pseudoknots: translational frameshifting and readthrough on viral RNAs. Virus Genes (1990) 2.82
Overexpression of the HIV-1 gag-pol polyprotein results in intracellular activation of HIV-1 protease and inhibition of assembly and budding of virus-like particles. Virology (1993) 2.81
E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent. New Biol (1989) 2.71
Overexpression of the gag-pol precursor from human immunodeficiency virus type 1 proviral genomes results in efficient proteolytic processing in the absence of virion production. J Virol (1991) 2.65
Mutational analysis of the "slippery-sequence" component of a coronavirus ribosomal frameshifting signal. J Mol Biol (1992) 2.64
Evidence that a downstream pseudoknot is required for translational read-through of the Moloney murine leukemia virus gag stop codon. Proc Natl Acad Sci U S A (1991) 2.39
Maintenance of the Gag/Gag-Pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity. J Virol (2001) 2.16
A novel programed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: frameshifting without tRNA slippage. Cell (1993) 2.00
A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae. Genetics (1993) 1.90
A nascent peptide is required for ribosomal bypass of the coding gap in bacteriophage T4 gene 60. Cell (1990) 1.87
Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs. Nucleic Acids Res (2001) 1.68
Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50%. J Mol Biol (1997) 1.61
The signal for translational readthrough of a UGA codon in Sindbis virus RNA involves a single cytidine residue immediately downstream of the termination codon. J Virol (1993) 1.50
Novel gene expression mechanism in a fission yeast retroelement: Tf1 proteins are derived from a single primary translation product. EMBO J (1993) 1.46
Primary structure and functional organization of Drosophila 1731 retrotransposon. Nucleic Acids Res (1988) 1.45
Evolutionary history of Cer elements and their impact on the C. elegans genome. Genome Res (2001) 1.28
Genes of the Pseudoviridae (Ty1/copia retrotransposons). Mol Biol Evol (2002) 1.27
Antizyme expression: a subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit. Nucleic Acids Res (2000) 1.25
RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression. Nucleic Acids Res (2001) 1.24
Post-transcriptional regulation of transposition by Ty retrotransposons of Saccharomyces cerevisiae. J Biol Chem (1995) 1.22
The retrotransposon Tf1 assembles virus-like particles that contain excess Gag relative to integrase because of a regulated degradation process. Mol Cell Biol (1996) 1.21
Analysis of natural variants of the human immunodeficiency virus type 1 gag-pol frameshift stem-loop structure. J Virol (2002) 1.21
Prokaryotic ribosomes recode the HIV-1 gag-pol-1 frameshift sequence by an E/P site post-translocation simultaneous slippage mechanism. Nucleic Acids Res (1995) 1.21
Predominance of six different hexanucleotide recoding signals 3' of read-through stop codons. Nucleic Acids Res (2002) 1.18
RIRE2, a novel gypsy-type retrotransposon from rice. Genes Genet Syst (1999) 1.15
Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA. Mol Cell Biol (1995) 1.14
The retrotransposon copia controls the relative levels of its gene products post-transcriptionally by differential expression from its two major mRNAs. Nucleic Acids Res (1990) 1.13
The context effect does not require a fourth base pair. Science (1986) 1.13
One protein from two open reading frames: mechanism of a 50 nt translational bypass. EMBO J (2000) 1.09
Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression. RNA (2002) 1.08
The nucleic acid-binding zinc finger protein of potato virus M is translated by internal initiation as well as by ribosomal frameshifting involving a shifty stop codon and a novel mechanism of P-site slippage. Nucleic Acids Res (1994) 1.04
Expression and processing of proteins encoded by the Saccharomyces retrotransposon Ty5. J Virol (2001) 0.86
Two novel Pao-like retrotransposons (Kamikaze and Yamato) from the silkworm species Bombyx mori and B. mandarina: common structural features of Pao-like elements. Mol Genet Genomics (2001) 0.84
Developmental expression analysis of the 1731 retrotransposon reveals an enhancement of Gag-Pol frameshifting in males of Drosophila melanogaster. Gene (1997) 0.83
Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res (2011) 16.53
Targeting DNA double-strand breaks with TAL effector nucleases. Genetics (2010) 14.49
Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell (2008) 11.24
TAL effectors: customizable proteins for DNA targeting. Science (2011) 9.47
Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods (2010) 8.86
High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature (2009) 7.19
In vivo genome editing using a high-efficiency TALEN system. Nature (2012) 7.11
Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods (2008) 6.51
Efficient TALEN-mediated gene knockout in livestock. Proc Natl Acad Sci U S A (2012) 4.99
High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci U S A (2010) 4.78
TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res (2012) 4.45
Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome. PLoS Genet (2012) 4.42
Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Protoc (2006) 4.16
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res (2010) 3.59
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Res (2007) 3.47
High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J (2005) 3.45
Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays. Nat Protoc (2009) 3.01
DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics (2010) 2.84
Recoding: translational bifurcations in gene expression. Gene (2002) 2.72
Common physical properties of DNA affecting target site selection of sleeping beauty and other Tc1/mariner transposable elements. J Mol Biol (2002) 2.56
An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci U S A (2008) 2.54
An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins. Nucleic Acids Res (2008) 2.42
Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol (2012) 2.36
Deletion of selenoprotein P alters distribution of selenium in the mouse. J Biol Chem (2003) 2.27
Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res (2011) 2.16
Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucleic Acids Res (2008) 1.87
Phosphorylation regulates integration of the yeast Ty5 retrotransposon into heterochromatin. Mol Cell (2007) 1.86
TALEN-based gene correction for epidermolysis bullosa. Mol Ther (2013) 1.84
TALEN-engineered AR gene rearrangements reveal endocrine uncoupling of androgen receptor in prostate cancer. Proc Natl Acad Sci U S A (2013) 1.77
Controlling integration specificity of a yeast retrotransposon. Proc Natl Acad Sci U S A (2003) 1.74
The diversity of LTR retrotransposons. Genome Biol (2004) 1.74
A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting. Virol J (2009) 1.69
Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res (2007) 1.68
Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production. J Gen Virol (2011) 1.61
Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways. Genome Res (2013) 1.57
DNA replicons for plant genome engineering. Plant Cell (2014) 1.57
Rapid and efficient gene modification in rice and Brachypodium using TALENs. Mol Plant (2013) 1.56
Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation. Nucleic Acids Res (2007) 1.55
Screening the SPO11 and EIF5A2 genes in a population of infertile men. Fertil Steril (2005) 1.51
Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli. EMBO J (2003) 1.51
Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res (2012) 1.50
NS1' of flaviviruses in the Japanese encephalitis virus serogroup is a product of ribosomal frameshifting and plays a role in viral neuroinvasiveness. J Virol (2009) 1.50
Readthrough of dystrophin stop codon mutations induced by aminoglycosides. Ann Neurol (2004) 1.47
P-site tRNA is a crucial initiator of ribosomal frameshifting. RNA (2004) 1.46
RECODE 2003. Nucleic Acids Res (2003) 1.46
Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons. EMBO J (2005) 1.45
Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element. Nucleic Acids Res (2011) 1.44
Recoding in bacteriophages and bacterial IS elements. Trends Genet (2006) 1.43
Pyrrolysine and selenocysteine use dissimilar decoding strategies. J Biol Chem (2005) 1.43
Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res (2008) 1.39
Targeting G with TAL effectors: a comparison of activities of TALENs constructed with NN and NK repeat variable di-residues. PLoS One (2012) 1.38
Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma. Virol J (2008) 1.33
Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression. Genome Biol (2005) 1.33
Programmed ribosomal frameshifting in decoding the SARS-CoV genome. Virology (2005) 1.33
uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs. Proc Natl Acad Sci U S A (2008) 1.33
Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases. Plant Physiol (2011) 1.29
Release factor 2 frameshifting sites in different bacteria. EMBO Rep (2002) 1.29
GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res (2013) 1.28
Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae. Genome Biol (2004) 1.27
Genes of the Pseudoviridae (Ty1/copia retrotransposons). Mol Biol Evol (2002) 1.27
TALEN-mediated editing of the mouse Y chromosome. Nat Biotechnol (2013) 1.26
Computational identification of putative programmed translational frameshift sites. Bioinformatics (2002) 1.25
Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1). Proc Natl Acad Sci U S A (2010) 1.24
TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol (2013) 1.24
The selenium-rich C-terminal domain of mouse selenoprotein P is necessary for the supply of selenium to brain and testis but not for the maintenance of whole body selenium. J Biol Chem (2007) 1.22
Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein. Proc Natl Acad Sci U S A (2012) 1.22
Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res (2002) 1.22
Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides. RNA (2004) 1.21
Targeted mutagenesis of Arabidopsis thaliana using engineered TAL effector nucleases. G3 (Bethesda) (2013) 1.19
Predominance of six different hexanucleotide recoding signals 3' of read-through stop codons. Nucleic Acids Res (2002) 1.18
Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5. Nucleic Acids Res (2011) 1.18
Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs. EMBO J (2003) 1.16
Recode-2: new design, new search tools, and many more genes. Nucleic Acids Res (2009) 1.15
Comparing zinc finger nucleases and transcription activator-like effector nucleases for gene targeting in Drosophila. G3 (Bethesda) (2013) 1.14
A TALE of two nucleases: gene targeting for the masses? Zebrafish (2011) 1.14
Darned in 2013: inclusion of model organisms and linking with Wikipedia. Nucleic Acids Res (2012) 1.12
A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene. J Biol Chem (2006) 1.11
TAL effector nucleases induce mutations at a pre-selected location in the genome of primary barley transformants. Plant Mol Biol (2013) 1.10
Maintenance of the correct open reading frame by the ribosome. EMBO Rep (2003) 1.09
AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana. PLoS One (2011) 1.09
Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses. Virology (2010) 1.08
Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression. RNA (2002) 1.08
A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. Mol Biol Evol (2011) 1.08
A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation. Nucleic Acids Res (2009) 1.07
Production of selenoprotein P (Sepp1) by hepatocytes is central to selenium homeostasis. J Biol Chem (2012) 1.06
Compact designer TALENs for efficient genome engineering. Nat Commun (2013) 1.06
SIRE1, an endogenous retrovirus family from Glycine max, is highly homogeneous and evolutionarily young. Mol Biol Evol (2003) 1.06
Identification of a new antizyme mRNA +1 frameshifting stimulatory pseudoknot in a subset of diverse invertebrates and its apparent absence in intermediate species. J Mol Biol (2004) 1.04
rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments. Bioinformatics (2013) 1.04
Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. Plant Biotechnol J (2014) 1.04