HITS-CLIP
Encyclopedia
High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) is a genome-wide means of mapping protein–RNA binding sites in vivo. HITS-CLIP was originally used to generate genome-wide protein-RNA interaction maps for the neuron-specific RNA binding protein and splicing factor
Nova; since then a number of other splicing factor maps have been generated, including those for PTB, RbFox2, SFRS1, and hnRNP C.
HITS-CLIP of the RNA binding protein Argonaute
has been performed for the identification of microRNA targets by decoding microRNA-mRNA and protein-RNA interaction maps in mouse brain, and subsequently in Caenorhabditis elegans
, embryonic stem cells and tissue culture cells. Recently, improved bioinformatics
applied to Argonaute HITS-CLIP enables identification of binding sites with single nucleotide resolution.
Splicing factor
A splicing factor is a protein involved in the removal of introns and exons from strings of messenger RNA; the process takes place in particles known as spliceosomes....
Nova; since then a number of other splicing factor maps have been generated, including those for PTB, RbFox2, SFRS1, and hnRNP C.
HITS-CLIP of the RNA binding protein Argonaute
Argonaute
Argonaute proteins are the catalytic components of the RNA-induced silencing complex , the protein complex responsible for the gene silencing phenomenon known as RNA interference . Argonaute proteins bind different classes of small non-coding RNAs, including microRNAs , small interfering RNAs and...
has been performed for the identification of microRNA targets by decoding microRNA-mRNA and protein-RNA interaction maps in mouse brain, and subsequently in Caenorhabditis elegans
Caenorhabditis elegans
Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
, embryonic stem cells and tissue culture cells. Recently, improved bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
applied to Argonaute HITS-CLIP enables identification of binding sites with single nucleotide resolution.
Similar methods
- PAR-CLIPPAR-CLIPPAR-CLIP is a novel method, used for identifying the binding sites of cellular RNA-binding proteins and microRNA-containing ribonucleoprotein complexes...
, for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) in tissue culture cells. - CLIP-SeqCLIP-SeqCLIP-Seq, also called HITS-CLIP, is a method in molecular biology, used for finding which RNA species interact with a particular RNA-binding protein...
, a synonym for HITS-CLIP.
External links
- starBase database: a database for exploring protein-RNA and miRNA-target interactions from HITS-CLIP (CLIP-SeqCLIP-SeqCLIP-Seq, also called HITS-CLIP, is a method in molecular biology, used for finding which RNA species interact with a particular RNA-binding protein...
, PAR-CLIPPAR-CLIPPAR-CLIP is a novel method, used for identifying the binding sites of cellular RNA-binding proteins and microRNA-containing ribonucleoprotein complexes...
) data.