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iCLIP: protein-RNA interactions at nucleotide resolution.
Huppertz I, Attig J, D'Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, König J, Ule J. Huppertz I, et al. Methods. 2014 Feb;65(3):274-87. doi: 10.1016/j.ymeth.2013.10.011. Epub 2013 Oct 25. Methods. 2014. PMID: 24184352 Free PMC article.
Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) identifies protein-RNA crosslink sites on a genome-wide scale. The high resolution and specificity of this method are achieved by an intramolecular cDNA circularization step that enables analy …
Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) identifies protein-RNA crosslink sites on a genome-w …
Insights into the design and interpretation of iCLIP experiments.
Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J. Haberman N, et al. Genome Biol. 2017 Jan 16;18(1):7. doi: 10.1186/s13059-016-1130-x. Genome Biol. 2017. PMID: 28093074 Free PMC article.
In contrast, we show that a broad size range of cDNAs in iCLIP allows the cDNA-starts to efficiently delineate the complete RNA-binding sites. CONCLUSIONS: We demonstrate the advantage of iCLIP and related methods that can amplify cDNAs that truncate at crosslink si …
In contrast, we show that a broad size range of cDNAs in iCLIP allows the cDNA-starts to efficiently delineate the complete RNA-bindi …
A systems view of spliceosomal assembly and branchpoints with iCLIP.
Briese M, Haberman N, Sibley CR, Faraway R, Elser AS, Chakrabarti AM, Wang Z, König J, Perera D, Wickramasinghe VO, Venkitaraman AR, Luscombe NM, Saieva L, Pellizzoni L, Smith CWJ, Curk T, Ule J. Briese M, et al. Nat Struct Mol Biol. 2019 Oct;26(10):930-940. doi: 10.1038/s41594-019-0300-4. Epub 2019 Sep 30. Nat Struct Mol Biol. 2019. PMID: 31570875 Free PMC article.
Studies of spliceosomal interactions are challenging due to their dynamic nature. Here we used spliceosome iCLIP, which immunoprecipitates SmB along with small nuclear ribonucleoprotein particles and auxiliary RNA binding proteins, to map spliceosome engagement with pre-me …
Studies of spliceosomal interactions are challenging due to their dynamic nature. Here we used spliceosome iCLIP, which immunoprecipi …
Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein-RNA Interactions.
Sibley CR. Sibley CR. Methods Mol Biol. 2018;1649:427-454. doi: 10.1007/978-1-4939-7213-5_29. Methods Mol Biol. 2018. PMID: 29130215
In this chapter we detail a functional genomics approach, termed individual nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP), that can determine the interactions of RBPs with their RNA targets in high throughput and at nucleotide resolution. iCLIP …
In this chapter we detail a functional genomics approach, termed individual nucleotide resolution UV cross-linking and immunoprecipitation ( …
Publisher Correction: A systems view of spliceosomal assembly and branchpoints with iCLIP.
Briese M, Haberman N, Sibley CR, Faraway R, Elser AS, Chakrabarti AM, Wang Z, König J, Perera D, Wickramasinghe VO, Venkitaraman AR, Luscombe NM, Saieva L, Pellizzoni L, Smith CWJ, Curk T, Ule J. Briese M, et al. Nat Struct Mol Biol. 2021 May;28(5):455. doi: 10.1038/s41594-021-00595-5. Nat Struct Mol Biol. 2021. PMID: 33953383 No abstract available.
Author Correction: A systems view of spliceosomal assembly and branchpoints with iCLIP.
Briese M, Haberman N, Sibley CR, Faraway R, Elser AS, Chakrabarti AM, Wang Z, König J, Perera D, Wickramasinghe VO, Venkitaraman AR, Luscombe NM, Saieva L, Pellizzoni L, Smith CWJ, Curk T, Ule J. Briese M, et al. Nat Struct Mol Biol. 2020 Aug;27(8):768. doi: 10.1038/s41594-020-0470-0. Nat Struct Mol Biol. 2020. PMID: 32641771
Erratum to: Insights into the design and interpretation of iCLIP experiments.
Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J. Haberman N, et al. Genome Biol. 2017 Aug 15;18(1):154. doi: 10.1186/s13059-017-1294-z. Genome Biol. 2017. PMID: 28810898 Free PMC article. No abstract available.
The interaction of PRC2 with RNA or chromatin is mutually antagonistic.
Beltran M, Yates CM, Skalska L, Dawson M, Reis FP, Viiri K, Fisher CL, Sibley CR, Foster BM, Bartke T, Ule J, Jenner RG. Beltran M, et al. Genome Res. 2016 Jul;26(7):896-907. doi: 10.1101/gr.197632.115. Epub 2016 May 9. Genome Res. 2016. PMID: 27197219 Free PMC article.
However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromatin all remain unclear. By performing iCLIP for PRC2 in comparison with other RNA binding proteins, we show here that PRC2 binds nascen …
However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromati …
Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.
Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR. Wickramasinghe VO, et al. Genome Biol. 2015 Sep 21;16(1):201. doi: 10.1186/s13059-015-0749-3. Genome Biol. 2015. PMID: 26392272 Free PMC article.
RESULTS: Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns with weak 5' splice sites. iCLIP of spliceosome components reveals …
RESULTS: Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellu …