Table 1.

List of 3′SS RNA elements and protein factors that regulate 3′SS usage, grouped according to their target constitutive factors

Target constitutive factor	Location	Regulatory element	Trans-acting factor	Regulated exon	Gene	Mechanism of regulation	References
Silencers/repressors
U2AF	Py	UCUU and UCUCU	PTB	6B	β-tropomyosin	i	[25]
		UCUU	PTB	3	α-tropomyosin	i	[26–28]
		CUCUCU	PTB	N1	c-Src	i	[16, 29, 30]
		UCUU	PTB	SM	α-actinin	i	[31, 32]
		CUCU like	PTB	24 nt exon, EN and 5	GABA receptor, Clathrin light chain B and NMDAR1	i	[33]
		C/U-rich motifs	PTB	Groupb	Groupb	ia	[34]
		UUUUUGUUGUUUUUUUU	Sxl	2	Tra	i	[35, 36]
		8/10 U	ELAV	Terminal	Neuroglian	ia	[37]
		UG repeats	SUP-12	2A	ADF/Cofilin	ia	[38]
		UG	TDP43	9	CFTR	ia	[39, 40]
		YGCU(U/G)Y	MBNL1	5	cTNT	i	[41, 42]
		UCCCU	hnRNP K	5a, 6	Snap25, Runx1	i	[43]
		UUUs	hnRNP C	10	CD55	i	[44]
	Between Py and 3′ AG	CA repeats	hnRNP L	V10	CD44	ii	[45]
		CaRRE	hnRNP L	STREX	Slo gene	ii	[46–48]
		CA repeats	hnRNPL	20	TJPI	ii	[49]
		GGGUGGGGG	hnRNP F/H	3	PRMT5 (group)b	ii	[50, 51]
U2	Near BP	UAGGG(A/U)	hnRNP A1	3	Tat (HIV)	ii	[52]
		UGUGU and GU	CUGBP2	N1	NMDA R1	ii	[53]
		UGU motifs	CUGBP2		CUGBP2	ii	[53]
		AUUAAC	QKI	12	NUMB	i	[54]
		ULM of SF1	SPF45	6	Fas	iia	[55]
		G rich	LS2	Minigene	Ftc and PEP	iia	[56]
U2AF of weaker 3′SSa	Upstream of 3′SS	UUUCUU, UUUUUC, UUUUCU	U2AF	Groupb	Groupb	iii	[22]
		ISS in IVS9	SF2/ASF, SRp40	9	CFTR	iii	[57]
Constitutive factors e.g. U1, U2AF	Py	Stem loop	MBNL1	5	cTNT	iv	[41, 42]
		U runs	Sxl	3	Sxl	iv	[58–60]
		CUCUCU	PTB	N1	c-Src	iv	[16, 29, 30]
		UUUs	hnRNP C	10	CD55 (groupb)	iva	[61]
Enhancers/activators
U2AF, U2 snRNA	Py	CUG and UG motifs	CELF	SM, NM	Actinin	I	[62]
		U/G motifs	ETR-3	5	cTNT	I	[63]
		U2AF interaction (Py)	DEK	Minigene	IgM-AdML	II	[64]
		Py	CAPER	6	VEGF	IIa	[65, 66]
		Py with 3′ CG or AG	hnRNP A1	Groupb	Groupb	II	[67]
		CAUC	YB-1	V5	CD44	II	[68]
	3′AG	3′AG	Urp	Minigene	AdML	II	[69]
	BP	AUUAAA	Sam68	V5	CD44	II	[70]
		Purine-rich ESE and BP	ASF/RS domain	Minigene	Actin, IgM	II	[71, 72]
	Between Py and 3′AG	UGC	nSR100	Groupb	Groupb	II	[34]
U2AF of competing 3′SSa	Py	CU rich	PTB	Groupb	Groupb	III	[73]
Constitutive factors e.g. U1, U2AF	Near 3′SS	Docking/selector	hrp36a	Minigene	Dscam	IV	[74–76]
		SR binding	U1, U2AF35	Minigene	dsx	IV	[77–80]
		Artificial binding sites	hnRNP A/B or hnRNP F/H	Minigene	hnRNPA1	IV	[81–84]

For mechanisms of silencing/repression, i: competition, ii: steric hindrance, iii: competing 3′SS, or iv: local RNA secondary structure/looping out. For enhancement/activation, I: competition with a repressor for the same or overlapping RNA element, II: interaction with U2AF or U2 snRNA, III: competing 3′SS, or IV: local RNA secondary structure or longer range RNA loops

^aPredicted

^bGroup of regulated exons as detailed in the text