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

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dc.abstract.enAnalysis 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.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorStarosta, Agata
dc.contributor.authorTudek, Agnieszka
dc.contributor.authorTomecki, Rafał
dc.contributor.authorLatoch, Przemysław
dc.contributor.authorGórna, Maria
dc.contributor.authorKoper, Michał
dc.contributor.authorKarolak, Natalia
dc.contributor.authorIzert, Matylda
dc.contributor.authorNowacka, Martyna
dc.date.accessioned2024-01-24T17:17:35Z
dc.date.available2024-01-24T17:17:35Z
dc.date.copyright2022-10-19
dc.date.issued2022
dc.description.accesstimeAT_PUBLICATION
dc.description.financePublikacja bezkosztowa
dc.description.number22
dc.description.versionFINAL_PUBLISHED
dc.description.volume50
dc.identifier.doi10.1093/NAR/GKAC903
dc.identifier.issn0305-1048
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/101436
dc.identifier.weblinkhttps://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkac903/46565562/gkac903.pdf
dc.languageeng
dc.pbn.affiliationbiological sciences
dc.relation.ispartofNucleic Acids Research
dc.relation.pagese132 (1-14)
dc.rightsCC-BY
dc.sciencecloudnosend
dc.subject.plbrak
dc.titleA cap 0-dependent mRNA capture method to analyze the yeast transcriptome
dc.typeJournalArticle
dspace.entity.typePublication