RNA molecules play a number of important roles in cells. The processing and regulation of RNA molecules is strictly controlled by RNA-binding proteins (RBPs), which bind to RNA by recognizing sequences and structural motifs and regulate RNA processing by cell type, conditioning specificity, or time. Crosslinking and immunoprecipitation (CLIP) can now be used to capture endogenous direct RNA targets and define the actual interaction sites. CLIP technologies include Photoactivatable Ribonucleoside-Enhanced CLIP-seq (PAR-CLIP-seq), individual-nucleotide resolution CLIP-seq (iCLIP-seq), and enhanced CLIP-seq (eCLIP-seq), and the relationship between these technologies is shown in the figure:
Fig 1 Schematic of CLIP-seq technologies.
Compared with other clip-seq, eCLIP-seq is an effective and powerful technology for studying the direct binding of proteins to RNA, which completely improves the ability to identify the binding sites of RBP and greatly improves the efficiency of the linkage between the connectors and RNA. eCLIP-Seq can also identify the binding sites of the entire RNA, including introns, exons, most RNA and non-coding RNAs at 3'-UTR,5'-UTR, etc., which can be used for RNA target identification in the range of transcriptome.
Fig 2 Diagram illustrating the principle of eCLIP-seq.
The overall process of eLIP-Seq provided by Profacgen:
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 Zhu Danling, Mao Fei, Tian Yuanchun, et al. The Features and Regulation of Co-transcriptional Splicing in <em>Arabidopsis</em> [J]. Molecular Plant, 2020, 13(2):278-294.