A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae
- Steven Parker1,
- Marcin G. Fraczek1,
- Jian Wu2,
- Sara Shamsah2,
- Alkisti Manousaki1,
- Kobchai Dungrattanalert1,
- Rogerio Alves de Almeida2,
- Diego Estrada-Rivadeneyra2,
- Walid Omara2,3,
- Daniela Delneri1 and
- Raymond T. O'Keefe2
- 1Division of Evolution & Genomic Sciences,
- 2Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, United Kingdom
- 3Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minya 11432, Egypt
- Corresponding authors: d.delneri{at}manchester.ac.uk, rokeefe{at}manchester.ac.uk
Abstract
Eukaryotic genomes are extensively transcribed, generating many different RNAs with no known function. We have constructed 1502 molecular barcoded ncRNA gene deletion strains encompassing 443 ncRNAs in the yeast Saccharomyces cerevisiae as tools for ncRNA functional analysis. This resource includes deletions of small nuclear RNAs (snRNAs), transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and other annotated ncRNAs as well as the more recently identified stable unannotated transcripts (SUTs) and cryptic unstable transcripts (CUTs) whose functions are largely unknown. Specifically, deletions have been constructed for ncRNAs found in the intergenic regions, not overlapping genes or their promoters (i.e., at least 200 bp minimum distance from the closest gene start codon). The deletion strains carry molecular barcodes designed to be complementary with the protein gene deletion collection enabling parallel analysis experiments. These strains will be useful for the numerous genomic and molecular techniques that utilize deletion strains, including genome-wide phenotypic screens under different growth conditions, pooled chemogenomic screens with drugs or chemicals, synthetic genetic array analysis to uncover novel genetic interactions, and synthetic dosage lethality screens to analyze gene dosage. Overall, we created a valuable resource for the RNA community and for future ncRNA research.
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Footnotes
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.061564.117.
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Freely available online through the RNA Open Access option.
- Received March 31, 2017.
- Accepted May 1, 2017.
This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
