Molecular Mechanisms and Function Prediction of Long Noncoding RNA

Table 2

Function classification of lncRNAs.

Archetype	lncRNA name	Length	Target	Function	cis-/trans-	References
Signal	KCNQ1ot1, Air, Xist	91 kb, 108 kb, ~17 kb	G9a, PRC, YY1	Transcriptional silencing of multiple genes; X inactivation (XCI)	cis-	[11, 14, 22, 23]
	HOTAIR, Frigidair, HOTTIP,	2.2 kb, N.A., 3.7 kb	LSD1-CoREST	Signals of anatomic position,	trans-	[6, 11, 14]
	lincRNA-p21, PANDA	3 kb; 1.5 kb	hnRNP-K	p53 targets in response to DNA damage	trans-	[14, 24, 25]
	lincRNA-RoR	2.6 kb	Oct4, Sox2, Nanog	Pluripotency-associated	N.A.^b	[11, 26]
	COOLAIR, COLDAIR	Multiple spliced: 400 bp/750 bp; ~1.1 kb	FLC, PRC2	Combinatorial transcriptional regulation	N.A.	[27, 28]
	eRNA	Various sizes	MLL-WDR5, TFs^a	Promotes mRNA synthesis	cis-	[29, 30]
	Gas5	~7 kb	Glucocorticoid receptor	Represses the glucocorticoid receptor	N.A.	[31]
	1/2-sbsRNAs	N.A.^c	SMD	Formation of STAU1 binding sites	N.A.	[32]
Decoys	DHFR-Minor	7.3, 5.0, 1.4, and 0.8 kb	TFIIB	Inhibits assembly of the preinitiation complex	N.A.	[33]
	TERRA	Various sizes	Telomerase	Regulation and protection of chromosome ends	N.A.	[34]
	PANDA	1.5 kb	NF-YA	Inhibits expression of apoptotic genes	trans-	[35]
	PTENP1	~3.9 kb	PTEN	Sequestration of miRNAs	N.A.	[36, 37]
	MALAT1	~7 kb	SR splicing factors	Alters pattern of alternative splicing	N.A.	[38, 39]
Guides	Xist	~17 kb	PRC2, YY1	Inactives X chromosome	cis-	[14, 40–42]
	Air, COLDAIR	108 kb,	G9a, PRC2	Silences transcription, affects histone acetylation and methylation states	cis-	[28, 43, 44]
	HOTTIP	~3.8 kb	MLL-WDR5	Chromosomal looping, chromatin modifications	cis-; (looping)	[11, 45]
	HOTAIR	2.2 kb	LSD1-CoREST	Alters and regulates epigenetic states	trans-	[14, 46, 47]
	Jpx	Multiple isoforms	polycomb complex^a	Activation of Xist RNA on the inactive X	trans-	[11, 48]
	lincRNA-p21	3 kb	hnRNP-K^a	p53 targets in response to DNA damage	trans-	[11, 24]
Scaffold	TERC	Various sizes	TERT	Telomerase catalytic activity	trans-	[49, 50]
	HOTAIR	2.2 kb	PRC2, LSD1, CoREST, REST	Demethylates histone H3 on K4 to antagonize gene activation	trans-	[46, 51]
	ANRIL	Multiple spliced: 3.9 kb/34.8 kb	PRC1, PRC2	Contributes to the functions of both PRC1 and PRC2 proteins	trans-	[52, 53]
	Alpha Satellite Repeat LncRNA	N.A.	SUMO-HP1	Molecular scaffold for the targeting and local accumulation of HP1	N.A.	[11, 54]

^aNot yet understood.
^bNot clearly referred as cis-action.
^cNo length data available in all six databases listed in Table 3.