Table 1.

A list of cis-elements and their interacting trans-factors that participate in regulating RNA nuclear retention

Categories	Cis-elements	Trans-factors	Function	Representative RNAs	References
U1 recognition and splicing	U1-recognition motif (potential 5’ss)	U1 snRNP	nuclear retention, chromatin association, RNA decay	MALAT1, MEG3, Tsix, uaRNAs, eRNA, etc.	[11]
	5’ss	U1 snRNP	nuclear retention	ftz, mvp2, sd4, gag-pol	[67–70]
	NRE	U1 snRNP	nuclear retention	MEG3	[66]
	MALAT1 regions E and M	SON, RNPS1, U1 snRNP	nuclear retention, chromatin association, localization in nuclear speckles	MALAT1	[11,38,57]
SINE-derived elements and C-rich motifs	SIRLON	HNRNPK	nuclear retention	JPX, PVT, etc.	[9]
	HNRNPK binding site (C-rich)	HNRNPK	nuclear retention	MLXIPL, etc.	[9]
	AGCCC	HNRNPK?	nuclear retention	BORG	[54]
	15nt C-rich motif	HNRNPK?	nuclear retention	MALAT1, lincSFPQ, etc.	[10]
IRAlu and paraspeckles	IRAlu	paraspeckles (NONO)	nuclear retention, localization in paraspeckles	CTN-RNA, Linc-p21, etc.	[88,98,99]
Other genomic repeat elements	L1PA16, L2b, MIRb, and MIRc	unknown	nuclear retention	RP11-5407, LINC00173, RP4-806M20.4, etc.	[12]
	CTG expansion	CELF1, MBNL1	nuclear retention, localization in nuclear speckles	DMPK, MBNL1	[113,116,120]
	CAG expansion	MBNL1, U2AF65	nuclear retention, localization in nuclear speckles	HTT	[119,122]
	GGGGCC expansion	TDP43, HNRNPH, MBNL1	nuclear retention, localization in nuclear speckles	noncoding region of C9orf72	[117,118,122]
Tandem repetitive sequences	XIST A-repeat	SPEN	nuclear retention, chromatin association	XIST	[11,126,127]
	XIST LBR binding site	LBR	Lamin localization	XIST	[124]
	XIST B-repeat	HNRNPK, polycomb proteins	nuclear retention, chromatin association, X-chromosome painting	XIST	[90,91,134]
	XIST E-repeat	CIZ1, PTBP1, MATR3, TDP43, CELF	nuclear retention, chromatin association	XIST	[36,37]
	Multiple broad regions in XIST	HNRNPU	nuclear retention, chromatin association	XIST	[37,140]
	RRD	HNRNPU	nuclear retention, chromatin association	FIRRE	[141,142]
R-loop and RNA-DNA Triplex	R-loop	RAD51, Cas9	nuclear retention, chromatin association, telomere targeting	TERRA	[151,152,155]
	RNA/DNA triplex	unknown	nuclear retention, chromatin association	MEG3, Khps1, etc.	[156–160]
SnoRNA-end	snoRNA-end	snoRNA-binding proteins?	nuclear retention, localization in nucleoli and Cajal bodies	sno-lncRNAs	[163,165,166]