A cap 0-dependent mRNA capture method to analyze the yeast transcriptome. Issue 22 (19th October 2022)

• Record Type: Journal Article
• Authors: Nowacka, Martyna; Latoch, Przemysław; Izert, Matylda A; Karolak, Natalia K; Tomecki, Rafal; Koper, Michał; Tudek, Agnieszka; Starosta, Agata L; Górna, Maria W
• Is Part Of: Nucleic acids research. Volume 50:Issue 22(2022)
• Page Start: e132
• Page End: e132
• Publication Date: 2022-10-19
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac903
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Analysis of the protein coding transcriptome by the RNA sequencing requires either enrichment of the desired fraction of coding transcripts or depletion of the abundant non-coding fraction consisting mainly of rRNA. We propose an alternative mRNA enrichment strategy based on the RNA-binding properties of the human IFIT1, an antiviral protein recognizing cap 0 RNA. Here, we compare for Saccharomyces cerevisiae an IFIT1-based mRNA pull-down with yeast targeted rRNA depletion by the RiboMinus method. IFIT1-based RNA capture depletes rRNA more effectively, producing high quality RNA-seq data with an excellent coverage of the protein coding transcriptome, while depleting cap-less transcripts such as mitochondrial or some non-coding RNAs. We propose IFIT1 as a cost effective and versatile tool to prepare mRNA libraries for a variety of organisms with cap 0 mRNA ends, including diverse plants, fungi and eukaryotic microbes. Graphical Abstract: