Table 1.

Elements and machinery of lncRNAs

RNA species	RNA elements	Element functions	RNA-binding proteins	RNP Machinery functions	Reference
Xist	Repeat A (tetraloop)	Recruitment of histone methylase	EZH2 (PRC2)	X-chromosome inactivation	222
	Repeat A (tetraloop)	lncRNA processing	ASF/SF2		223
	Repeat F	Bridge between lncRNA and DNA	YY1		224
HOTAIR	5′ domain (100- to 300-nt stem-loops)	Recruitment of histone methylase	PRC2	Epigenetic silencing	212
	3′ domain (1500- to 2146-nt stem-loops)	Recruitment of histone demethylase	LSD1/CoREST/REST		212
HOTTIP	Exons 1–2	Recruitment of histone methylase	WDR5	Epigenetic activation	217
Mistral	ABM (stem-loop)	Recruitment of histone methylase	MLL1	Epigenetic activation	216
ecCEBPA	R2, R5, R6 (stem-loop (with CpG))	Binding of DNA methylase	DNMT1	Epigenetic activation	219
SRA	STR7, 10, 11 (stem-loop)	Transcriptional coactivation	?	Transcriptional activation	228
	U206 in STR5 (pseudouridine)	Transcriptional coactivation	Pus1 p, Pus3p (isomerize U206)		229
GAS5	GRE-1, GRE-2 (stem-loop)	Binding of nuclear receptor	Glucocorticoid receptor	Transcriptional suppression	226
ncRNAccnd1	-454S, -341a (GGUG)	Inhibition of histone acetyltransferase	TLS/FUS	Transcriptional suppression	227
NEAT1 (NEAT1_2)	ENE-like (triple helix)	lncRNA stabilization	?	Nuclear body architecture	232, 243, 244
	tRNA-like structure	lncRNA 3′ end processing	RNase P (RNA processing)
PAN	ENE (triple helix)	lncRNA stabilization	?	Viral gene expression	245, 246
MALAT1	ENE-like (triple helix)	lncRNA stabilization	?	Epigenetic activation, splicing regulation	243, 244
	tRNA-like structure	lncRNA 3′ end processing	RNase P (RNA processing)		242
1/2-sbsRNA	Alu	mRNA binding	STAU1 (with target mRNA)	Control of mRNA decay or translation	250
TINCR	TINCR box (complementary sequence)	mRNA binding	STAU1	Control of mRNA decay or translation	252