DOI: 10.6084/m9.figshare.20747884
title: ncRNA database from previous publications

description: Here is the database with 3,898 ncRNA that was compared to the set of lncRNA indentified by us. <br> The database was built based on the papers below: Berretta J, Pinskaya M, Morillon A (2008) A cryptic unstable transcript mediates transcriptional trans -silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev 22:615–626. https://doi.org/10.1101/gad.458008 Bumgarner SL, Dowell RD, Grisafi P, et al (2009) Toggle involving cis -interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci 106:18321–18326. https://doi.org/10.1073/pnas.0909641106 Camblong J, Beyrouthy N, Guffanti E, et al (2009) Trans -acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev 23:1534–1545. https://doi.org/10.1101/gad.522509 Geisler S, Lojek L, Khalil AM, et al (2012) Decapping of Long Noncoding RNAs Regulates Inducible Genes. Mol Cell 45:279–291. https://doi.org/10.1016/J.MOLCEL.2011.11.025 Gelfand B, Mead J, Bruning A, et al (2011) Regulated Antisense Transcription Controls Expression of Cell-Type-Specific Genes in Yeast. Mol Cell Biol 31:1701–1709. https://doi.org/10.1128/MCB.01071-10 Hongay CF, Grisafi PL, Galitski T, Fink GR (2006) Antisense Transcription Controls Cell Fate in Saccharomyces cerevisiae. Cell 127:735–745. https://doi.org/10.1016/j.cell.2006.09.038 Houseley J, Rubbi L, Grunstein M, et al (2008) A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster. Mol Cell 32:685–695. https://doi.org/10.1016/J.MOLCEL.2008.09.027 Huang Y-C, Chen H-T, Teng S-C (2010) Intragenic transcription of a noncoding RNA modulates expression of ASP3 in budding yeast. RNA 16:2085–2093. https://doi.org/10.1261/rna.2177410 Huber F, Bunina D, Gupta I, et al (2016) Protein Abundance Control by Non-coding Antisense Transcription. Cell Rep 15:2625–2636. https://doi.org/10.1016/j.celrep.2016.05.043 Kyriakou D, Stavrou E, Demosthenous P, et al (2016) Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae. BMC Biol 14:106. https://doi.org/10.1186/s12915-016-0325-7 Luke B, Panza A, Redon S, et al (2008) The Rat1p 5′ to 3′ Exonuclease Degrades Telomeric Repeat-Containing RNA and Promotes Telomere Elongation in Saccharomyces cerevisiae. Mol Cell 32:465–477. https://doi.org/10.1016/j.molcel.2008.10.019 Martens JA, Wu P-YJ, Winston F (2005) Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev 19:2695–2704. https://doi.org/10.1101/gad.1367605 Nadal-Ribelles M, Solé C, Xu Z, et al (2014) Control of Cdc28 CDK1 by a Stress-Induced lncRNA. Mol Cell 53:549–561. https://doi.org/10.1016/J.MOLCEL.2014.01.006 Neil H, Malabat C, D’Aubenton-Carafa Y, et al (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457:1038–1042. https://doi.org/10.1038/nature07747 Parker S, Fraczek MG, Wu J, et al (2017) A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae. RNA 23:1166–1171. https://doi.org/10.1261/rna.061564.117 Parker S, Fraczek MG, Wu J, et al (2018) Large-scale profiling of noncoding RNA function in yeast. PLOS Genet 14:e1007253. https://doi.org/10.1371/journal.pgen.1007253 Schulz D, Schwalb B, Kiesel A, et al (2013) Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis. Cell 155:1075–1087. https://doi.org/10.1016/j.cell.2013.10.024 Till P, Mach RL, Mach-Aigner AR (2018) A current view on long noncoding RNAs in yeast and filamentous fungi. Appl Microbiol Biotechnol 102:7319–7331. https://doi.org/10.1007/s00253-018-9187-y van Dijk EL, Chen CL, D’Aubenton-Carafa Y, et al (2011) XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature 475:114–117. https://doi.org/10.1038/nature10118 van Werven FJ, Neuert G, Hendrick N, et al (2012) Transcription of Two Long Noncoding RNAs Mediates Mating-Type Control of Gametogenesis in Budding Yeast. Cell 150:1170–1181. https://doi.org/10.1016/j.cell.2012.06.049 Xu Z, Wei W, Gagneur J, et al (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457:1033–1037. https://doi.org/10.1038/nature07728 Yu Y, Yarrington RM, Chuong EB, et al (2016) Disruption of promoter memory by synthesis of a long noncoding RNA. Proc Natl Acad Sci 113:9575–9580. https://doi.org/10.1073/pnas.1601793113 Zappulla DC, Cech TR (2004) Yeast telomerase RNA: A flexible scaffold for protein subunits. Proc Natl Acad Sci 101:10024–10029. https://doi.org/10.1073/pnas.0403641101