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A cap 0-dependent mRNA capture method to analyze the yeast transcriptome

Nowacka, Martyna and Latoch, Przemysław and Izert, Matylda A and Karolak, Natalia K and Tomecki, Rafał and Koper, Michał and Tudek, Agnieszka and Starosta, Agata L and Górna, Maria W (2022) A cap 0-dependent mRNA capture method to analyze the yeast transcriptome. Nucleic Acids Research . ISSN 1362-4962


Official URL: https://doi.org/10.1093/nar/gkac903


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.

Item Type:Article
Subjects:Q Science > QH Natural history > QH301 Biology
ID Code:2183
Deposited By: Dr Agata Starosta
Deposited On:20 Oct 2022 07:13
Last Modified:24 Oct 2022 13:23

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