Journal
NUCLEIC ACIDS RESEARCH
Volume 50, Issue 22, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkac903
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Funding
- National Centre for Research and Development, Poland [LIDER/039/L-6/14/NCBR/2015]
- EMBO Installation Grant [3315, 3914]
- Foundation for Polish Science FIRST TEAM [POIR.04.04.00-00-3E9C/17-00]
- European Social Fund [POWR.03.02.00-00-I007/16-00]
- National Science Centre Poland, SONATA [2020/39/D/NZ2/02174]
- L'Or'eal Poland
- Polish Ministry of Science and Higher Education [6817/IA/SP/2018]
- European Regional Development Fund [POIG.02.02.00-14-024/08-00]
- University of Warsaw
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This study proposes an mRNA enrichment strategy based on the RNA-binding properties of human IFIT1, which effectively depletes rRNA while maintaining high quality RNA-seq data with coverage of the protein coding transcriptome. It is a cost-effective and versatile tool for preparing mRNA libraries for various organisms.
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.
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