ncRNA database from previous publications

Here is the database with 3,898 ncRNA that was compared to the set of lncRNA indentified by us.

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