[PDF] Top 20 The challenge of target sequence specificity in C→U RNA editing
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The challenge of target sequence specificity in C→U RNA editing
... nonidentical RNA recognition motifs as well as a carboxyl-terminus arginine- glycine–rich region and a double-stranded RNA-bind- ing domain (14, ...various RNA- binding motifs led to predictions, ... See full document
5
Evaluation of the effects of sequence length and microsatellite instability on single-guide RNA activity and specificity
... genome editing has a low incidence or undetectable genome-wide off-target mutations ...determine editing efficiency and off-target cleavage activity for single-guide RNA (sgRNA) must be ... See full document
13
Dissection of the target specificity of the RNA binding protein HOW reveals dpp mRNA as a novel HOW target
... of target mRNA species required for tissue differentiation in a spatial and temporal fashion (Kuersten and Goodwin, 2003; Lasko, 2003; Larocque and Richard, 2005; Vernet and Artzt, ...primary sequence and ... See full document
8
An alternative novel tool for DNA editing without target sequence limitation: the structure guided nuclease
... To explore whether the SGN system could edit en- dogenous genes in zebrafish embryos with a certain length spacer like ZFN and TALEN, we microinjected 1 nL of a solution containing 200 pg of SGN mRNA, plus 50 pg of each ... See full document
12
Artificial small RNA for sequence specific cleavage of target RNA through RNase III endonuclease Dicer
... guide RNA which functions in conjunction with Cas9 proteins to target a DNA and cleaves double-strand ...small RNA (asRNA), composed of a Dicer–binding RNA element and an antisense RNA, ... See full document
6
Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila
... guide RNA (gRNA). The gRNA recognizes a 20-nt target se- quence next to a trinucleotide NGG protospacer adjacent mo- tif (PAM) in the genome to direct Cas9-mediated cleavage of both DNA strands within the ... See full document
19
Directed integration of viral DNA mediated by fusion proteins consisting of human immunodeficiency virus type 1 integrase and Escherichia coli LexA protein.
... in target site selection is sequence- or struc- ture-specific DNA-binding ...and RNA polymerase III transcription factors ...may target the viral DNA to active genes ...preferred target ... See full document
10
Transcriptomic approaches to understanding ageing and metabolism in rodents
... the target site. There is a strong preference against a G and for a U in the immediate 5’ position to the target site, and a strong preference for a G in the immediate 3’ ...the sequence of ... See full document
191
RNA editing of human microRNAs
... miRNA structures were obtained from the miRBase database [6]. Stem-loop structures of antisense miRNAs were gener- ated by folding the antisense of the miRNA stem-loop sequence obtained from miRBase using MFOLD ... See full document
8
Resources for the design of CRISPR gene editing experiments
... One major goal is to achieve more efficient, predictable editing. If it were possible to convert every cell in a popu- lation to the desired genotype, the painstaking work of selecting and characterizing ... See full document
21
Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA guided Cas9 nuclease
... when specificity is ...simultaneously target multiple gene copies facilitating gene functional analysis by overcom- ing possible redundancy between the closely related se- quences ...the target ... See full document
13
Genome wide identification and functional analysis of Apobec 1 mediated C to U RNA editing in mouse small intestine and liver
... for sequence quality, strand bias, distance to end of reads, paired-end reads and genomic single nucleotide ...shared RNA editing targets between intestine and ...in RNA editing targets ... See full document
17
RCARE: RNA Sequence Comparison and Annotation for RNA Editing
... post-transcriptional sequence modification of transcripts through RNA editing is an important mechanism for regulating protein function and is associated with human disease ...of RNA ... See full document
8
Comparison of cytosine base editors and development of the BEable GPS database for targeting pathogenic SNVs
... pathogenic C-to-T SNVs. Among re- ported pathogenic C-to-T SNVs [18], we selected three sites, at which all five BEs have overlapping editing win- dows (Additional file 1: Figure ...the ... See full document
7
The Hepatitis C Virus RNA-Dependent RNA Polymerase Membrane Insertion Sequence Is a Transmembrane Segment
... into U-2 OS human osteosarcoma ...experiments. U-2 OS cells were transiently transfected with pCMVNS5Bcon (NS5B) or pCMVNS5Bcon- myc ...nontransfected U-2 OS cells were stained with a polyclonal ... See full document
6
Specificity of retroviral RNA packaging.
... Thus, we have examined RNA encapsidation into virions produced by other avian and murine retroviral packaging cell lines in the presence and absence of RNAs containing defined retroviral[r] ... See full document
10
Little Elongation Complex (lec) And Super Elongation Complex (sec) As Regulators Of Tdp-43-Associated Neurodegeneration
... supplemented with PMSF and proteinase inhibitor protease inhibitor cocktail (Roche; #1183670001). Extracts were sonicated for total 6 min using using QSonica (Newtown, CT) water bath sonicator (amplitude = 100, 30 s on, ... See full document
122
The emerging role of RNA editing in plasticity
... of editing is catalyzed by the adenosine deaminase that acts on RNA (ADAR) family of enzymes (Bass and Weintraub, 1988; Kim et ...stranded RNA binding motifs (dsRBMs) followed by a single ... See full document
10
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples
... highlight sequence variability in primer sites and the consequent lack of truly universal primers, and a likely need for a cocktail of several more specific primers when attempting to identify all of the animals ... See full document
51
A Trigram HMM Model For Solving Parts-of-Speech (PoS) Tagging Problems
... Define C (u, v, s) to be the number of times the sequence of three states (u, v, s) is seen in training data: for example, C (V,D,N) would be the number of times the sequence of ... See full document
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