Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms

Table 1

Landmarks in the study of yeast lncRNA.

Discovery	lncRNA class	Strain manipulation	Technique	Reference
Cryptic Pol II transcripts		RRP6 deletion	Microarray	[12]
Nonannotated transcripts		Wild type	Tiling array	[10]
CUT termination dependent on Nab3p		NAB3 mutation	Microarray	[37]
Heterogenous unstable RNAs		RRP6 deletion	Microarray	[11]
Telomeric repeat-containing RNAs (TERRAs)	TERRAs	rat1-1 mutants	RT-PCR, northerns	[35]
Cryptic unstable transcripts (CUTs)	CUTs	RRP6 & TRF4 deletion	3-long SAGE	[14]
Stable unannotated transcripts (SUTs) & CUTs	SUTs, CUTs	RRP6 deletion	Microarray	[15]
PHO84 antisense lncRNA can repress in trans		Ectopic PHO84 expression	qPCR, northerns	[59]
PWR1/ICR1 lncRNAs and FLO11 expression		ΔPFLO11, cit6, and sfl1	Northern blot	[41]
Condition-dependent antisense transcripts		Stationary phase, etc.	Stranded RNA-seq	[26]
Meiotic unannotated transcripts (MUTs), respiration/sporulation unannotated transcripts (rsCUTs)	MUTs, rsCUTs	Meiotic a/α diploids	Tiling array	[28]
Xrn1-sensitive unstable transcripts (XUTs)	XUTs	XRN1 deletion	RNA-seq	[34]
RME2 lncRNA regulates IME2 expression		RME2 promoter deletion	RT-PCR	[27]
CUT repression of metal homeostasis genes	CD-CUTs	NMD/CD-CUT mutants	Northern blot	[31]
IME1 and IME4 expression regulated by lncRNA		set2, set3, haploid/diploid	ChIP, northerns	[29]
lncRNA/gene pairs, coregulated in colonies		GFP-tagged ATO1	Microarrays	[66]
Nrd1-unterminated transcripts (NUTs)	NUTs	FRB-tagged NRD1	4tU-seq	[22]
Stress/Hog1p-regulated lncRNA transcription		HOG1 deletion	Tiling arrays	[32]

Italics: lncRNA classes discovered; bold: classes discussed here in relation to smooth and biofilm colonies.