![]() *Co-corresponding authors are marked by a star. #Iclip genetics full#The algorithm utilizes the deep sequencing reads generated from PAR-CLIP experiments.For the full list of publications, click here PARalyzer: PARalyzer is an algorithm that generates a high resolution map of interaction sites between RNA-binding proteins and their targets.dCLIP: dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.miRTarCLIP: A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing.BIMSB doRiNA database: a database for exploring protein-RNA, microRNA-target interactions from PAR-CLIP, CLIP-Seq, HITS-CLIP, iCLIP data, and PICTAR microRNA target site predictions.starBase database: decoding miRNA-mRNA, miRNA- lncRNA, miRNA-sncRNA, miRNA-circRNA, miRNA- pseudogene, protein-lncRNA, protein-ncRNA interactions and ceRNA networks from PAR-CLIP( CLIP-Seq, HITS-CLIP, iCLIP) data, and TargetScan, PicTar, RNA22, miRanda and PITA microRNA target sites."A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation". ^ Ke, S Alemu, EA Mertens, C Gantman, EC Fak, JJ Mele, A Haripal, B Zucker-Scharff, I Moore, MJ Park, CY Vågbø, CB Kusnierczyk, A Klungland, A Darnell, JE Darnell, RB (24 September 2015)."HITS-CLIP yields genome-wide insights into brain alternative RNA processing". ^ Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB (November 2008)."Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines". ^ Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, Ohler U, Cullen BR (2011)."The viral and cellular microRNA targetome in lymphoblastoid cell lines". ^ Skalsky RL, Corcoran DL, Gottwein E, Frank CL, Kang D, Hafner M, Nusbaum JD, Feederle R, Delecluse HJ, Luftig MA, Tuschl T, Ohler U, Cullen BR (2012)."starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data". ^ Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH (2011)."PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins". "Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP". ^ a b c Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T (2010).CLIP-Seq, a similar method for identifying the binding sites of cellular RNA-binding proteins (RBPs) or RNA modification sites using UV light to cross-link RNA to RBPs without the incorporation of photoactivatable groups into RNA.Recently, PAR-CLIP have been applied to determine the transcriptome-wide binding sites of several known RBPs and microRNA-containing ribonucleoprotein complexes at high resolution. The isolated RNA is converted into a cDNA library and is deep sequenced using next-generation sequencing technology. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. Irradiation of the cells by ultraviolet light of 365 nm wavelength induces efficient crosslinking of photoreactive nucleoside– labeled cellular RNAs to interacting RBPs. The method relies on the incorporation of ribonucleoside analogs that are photoreactive, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG), into nascent RNA transcripts by living cells. PAR-CLIP ( photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation) is a biochemical method for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). ![]()
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