What does CLIP-seq stand for?
CLIP-seq or HITS-CLIP, which stands for high-throughput sequencing of RNA that is isolated after ultraviolet (UV) irradiation-induced crosslinking and immunoprecipitation (Chi et al. 2009; Moore et al.
What is a clip assay?
Cross-linking immunoprecipitation (CLIP) is a method used in molecular biology that combines UV cross-linking with immunoprecipitation in order to analyse protein interactions with RNA or to precisely locate RNA modifications (e.g. m6A).
What is clip in immunology?
During the process of class II MHC assembly and cell surface expression, the class II-associated invariant chain peptide (CLIP) is removed from the peptide-binding groove of MHC, a task mediated by H-2M. This allows binding and presentation of peptide epitopes.
What is the difference between ATAC-seq and RNA Seq?
Unlike RNA sequencing, which provides information about the genes that are being expressed, ATAC-Seq (A(ssay for) T(ransposase)-A(ccessible) C(hromatin using) Seq(uencing)) provides a genome-wide view of potentially active gene switches and transcription factor-binding sites.
How does primer extension work?
Primer extension can be used to determine the start site of transcription (the end site cannot be determined by this method) by which its sequence is known. This technique requires a radiolabelled primer (usually 20 – 50 nucleotides in length) which is complementary to a region near the 3′ end of the mRNA.
What is clip in biology?
What is the function of CLIP in MHC II?
CLIP is one of the most prevalent self peptides found in the thymic cortex of most antigen-presenting cells. The purpose of CLIP is to prevent the degradation of MHC II dimers before antigenic peptides bind, and to prevent autoimmunity.
What is HITS-CLIP?
High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP, also known as CLIP-Seq) is a genome-wide means of mapping protein–RNA binding sites or RNA modification sites in vivo.
Can HITS-CLIP be used for genome-wide RNA target identification?
Since these studies, HITS-CLIP has been used by several labs to address genome-wide RNA target identification for other RNABPs. The first of these was a genome-wide study of the binding sites of Fox2 (Rbm9) by Gene Yeo, Fred Gage and colleagues67.
CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods. 2005;37:376–386. [PubMed] [Google Scholar] 36. Ule J, et al. CLIP identifies Nova-regulated RNA networks in the brain.