ArticleMethods in molecular biology (Clifton, N.J.)2014
High-throughput sequencing of RNA isolated by cross-linking and immunoprecipitation (HITS-CLIP) to determine sites of binding of CstF-64 on nascent RNAs.
Article in Methods in molecular biology (Clifton, N.J.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
7 citing papers in PubMed, 12 citations in OpenAlex.
- Identification of lncRNA-Protein Interactions by CLIP and RNA Pull-Down Assays.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Comprehensive analysis of circular RNAs in pathological states: biogenesis, cellular regulation, and therapeutic relevance.Cellular and molecular life sciences : CMLS · 2019Review
- The structural basis of CstF-77 modulation of cleavage and polyadenylation through stimulation of CstF-64 activity.Nucleic acids research · 2018Article
- Cstf2t Regulates expression of histones and histone-like proteins in male germ cells.Andrology · 2018Article
- Multiple nuclear-replicating viruses require the stress-induced protein ZC3H11A for efficient growth.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- TauCstF-64 Mediates Correct mRNA Polyadenylation and Splicing of Activator and Repressor Isoforms of the Cyclic AMP-Responsive Element Modulator (CREM) in Mouse Testis.Biology of reproduction · 2016Article
- Generation of plasmid vectors expressing FLAG-tagged proteins under the regulation of human elongation factor-1α promoter using Gibson assembly.Journal of visualized experiments : JoVE · 2015Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Genome-wide analysis of gene expression has changed the RNA world. Recent techniques leading to this revolution have been the use of cross-linking and immunoprecipitation (CLIP) combined with high-throughput sequencing (HITS-CLIP) to determine sites on nascent mRNAs to which RNA-binding proteins bind. Several researchers (including us) have been examining the role of RNA-binding proteins in polyadenylation, including the role of the 64,000 Mr component of the cleavage stimulation factor, CstF-64. In this chapter, we present our optimizations of the CLIP procedure for examination of CstF-64 binding to nascent pre-mRNAs expressed in testis. For CstF-64 CLIP, we use a well-characterized monoclonal antibody (3A7) that recognizes CstF-64. Rather than optimizing tricky but essential RNA fragment cloning schemes, we illustrate the use of the proprietary Illumina TruSeq Small RNA Sample Preparation kit for this step. Other techniques such as SDS-PAGE and the transfer to the nitrocellulose membrane techniques follow the original Illumina protocol (though we point out potential pitfalls). Finally, we discuss the options for high-throughput sequencing and some general suggestions for bioinformatic analysis of the data.
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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.