Using Cross-Linking and ImmunoPrecipitation (CLIP) to Identify Targets and Specificity Determinants of the YTHDC2 Helicase.

Yuhki Saito, Devanshi Jain, Robert B Darnell

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Article in Methods in molecular biology (Clifton, N.J.), 2027. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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3 authors.

Yuhki SaitoLaboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA. yuki.saito.01@daiichisankyo.com.

Devanshi JainDepartment of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA. devanshi.jain@rutgers.edu.

Robert B DarnellLaboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA.ORCID http://orcid.org/0000-0002-5134-8088

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The 3'→5' RNA helicase YTHDC2 is a posttranscriptional regulator of gene expression in reproductive cells, where it is essential for the progression of meiosis. But a detailed understanding of its molecular mechanism is currently lacking. Cross-linking and immunoprecipitation (CLIP) followed by high-throughput sequencing is a well-established method for transcriptome-wide identification of the positions of protein-RNA interactions and has played a critical role in studies of RNA-binding proteins. In this chapter, we present an optimized protocol for performing YTHDC2 CLIP in mouse testes to identify YTHDC2-RNA interactions, from harvesting testis tissue, through isolation of cross-linked YTHDC2-RNA complexes, to the preparation of sequencing libraries.

Indexed as

ImmunoprecipitationNerve Tissue ProteinsRNARNA-Binding ProteinsRNA HelicasesRNA Splicing FactorsAnimalsCross-Linking ReagentsHigh-Throughput Nucleotide SequencingMaleMiceSpermatogenesisTestisCross-Linking ReagentsNerve Tissue ProteinsRNARNA-Binding ProteinsRNA HelicasesRNA Splicing FactorsYthdc2 protein, mouseCLIPm6AMeiosisRNA helicaseSpermatogenesisTestisYTHDC2

Identifiers

PMID42862227

DOI10.1016/j.celrep.2014.02.005

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.