ArticleBMC genomics2016
Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 49 citations in OpenAlex.
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- Single-base resolution mapping of 2'-O-methylation sites by an exoribonuclease-enriched chemical method.Science China. Life sciences · 2023Article
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- Circr, a Computational Tool to Identify miRNA:circRNA Associations.Frontiers in bioinformatics · 2022Article
- Article
- Transcriptome-Wide Identification of 2'-O-Methylation Sites with RibOxi-Seq.Methods in molecular biology (Clifton, N.J.) · 2022Article
- capCLIP: a new tool to probe translational control in human cells through capture and identification of the eIF4E-mRNA interactome.Nucleic acids research · 2021Article
- Conserved DNA sequence features underlie pervasive RNA polymerase pausing.Nucleic acids research · 2021Article
- AGO-accessible anticancer siRNAs designed with synergistic miRNA-like activity.Molecular therapy. Nucleic acids · 2021Article
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- NAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2020Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundHigh-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) allows for high resolution, genome-wide mapping of RNA-binding proteins. This methodology is frequently used to validate predicted targets of microRNA binding, as well as direct targets of other RNA-binding proteins. Hence, the accuracy and sensitivity of binding site identification is critical.
resultsWe found that substantial mispriming during reverse transcription results in the overrepresentation of sequences complementary to the primer used for reverse transcription. Up to 45 % of peaks in publicly available HITS-CLIP libraries are attributable to this mispriming artifact, and the majority of libraries have detectable levels of mispriming. We also found that standard techniques for validating microRNA-target interactions fail to differentiate between artifactual peaks and physiologically relevant peaks.
conclusionsHere, we present a modification to the HITS-CLIP protocol that effectively eliminates this artifact and improves the sensitivity and complexity of resulting libraries.
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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.