Table 1.

Examples of noncoding RNAs and their described surveillance pathways

Budding Yeast
Noncoding RNAs	Defects	Nuclease(s)	Cofactors	Other components	References
pre-rRNAs	Aberrant processing; failure to bind proteins	Nuclear exosome	TRAMP, TRAMP5, MPP6, Rrp47		38,68,69,110,125,127–129
		Rat1	Rai1		31,209
Mature 18S rRNAs	Nonfunctional in protein synthesis	Xrn1	Ski7	Dom34, Hbs1	267,268
Mature 28S rRNAs	Nonfunctional in protein synthesis			Rtt101, Mms1	267,271,272
pre-tRNAs	Hypomodified; unspliced; misfolded; unprocessed	Nuclear exosome	Nrd1/Nab3, TRAMP		8,30,33,46,65,67
Pre-and mature tRNAs exported to cytoplasm	Nonfunctional in protein synthesis	Unknown	Unknown	Retrograde nuclear transport	263
Mature tRNAs	Weak acceptor stems	Unknown	CCA adding enzyme	CCACCA addition	203,204
	Structurally unstable tRNAs	Rat1, Xrn1	Unknown		210,219–221
pre-snoRNAs		Nuclear exosome	Nrd1-Nab3, TRAMP		8,33,45,47,65,143
pre-snRNAs	Failure to assemble with proteins	Nuclear exosome	Nrd1-Nab3, TRAMP		8,33,58,66
		XRN1	Dcp1, Dcp2		58
U6 snRNA		Nuclear exosome	TRAMP		8,33,67
5S rRNAs	Truncated	Nuclear exosome	Nrd1-Nab3, TRAMP		33,65,67,143
lncRNAs	Many without known binding proteins	Rat1	Dcp1		19
SRP RNA	Truncated	Nuclear exosome	TRAMP		33,46,57
CUTs	No known binding proteins	Nuclear exosome	Nrd1-Nab3, TRAMP, Rrp47, MPP6		8,10,11,33,105,110,122,124,140,141
XUTs	No known binding proteins	Xrn1	Dcp1, Dcp2	NMD often important	15,225–227,229–231
telomeric repeat transcripts	No known binding proteins	Rat1	Rai1		22
Mammals
pre-rRNAs	Premature termination; aberrant processing	Nuclear exosome	PAPD5/ZCCHC7/MTR4		71,72
	Aberrant precursors, excised spacers	XRN2	NKRF		126,249,250
PROMPTs	No known binding proteins	Nuclear exosome	NEXT complex		70,72,73,85,150,151,160
Enhancer RNAs	No known binding proteins	Nuclear exosome	NEXT complex		73,151,331
Pre-tRNAs	Unprocessed and nonfunctional in cytoplasm	DIS3L2	TUT4, TUT7		64,189
	Misfolded	DICER1			266,278
	Weak acceptor stems		CCA-adding enzyme	CCACCA addition	203
U6 snRNA		Nuclear exosome	TRAMP		64
		DIS3L2	TUT4, TUT7		64
Some lncRNAs, including TUG1 and NEAT1	Unknown	Nuclear exosome	PAXT, polysome protector complex		73,153,163,165,154
other lncRNAs		Unknown		NMD often important	231,235,238,239
Telomerase RNA precursor	Reduced levels of dyskerin protein	Nuclear exosome	PAPD5/hTRF4–2, DCP2		59,155,156
Mature hTR RNA	Unknown	Nucleolar exosome	DGCR8		168
Pre-snRNAs	Failure to assemble with proteins	Nuclear exosome	NEXT		151
		DIS3L2	TUT4, TUT7		189,191
Mature snoRNAs	NAD+ caps	XRN1	DCP2		58
		DXO			218,254
Pre-snoRNAs		Nuclear exosome	NEXT		151
		DIS3L2	TUT4/TUT7		189
Pre-let-7 miRNA	miRNA harmful to stem cells	DIS3L2	TUT4/TUT7		183,185–188
Transcripts from Alu elements	Unknown	DICER1	Unknown		32,278