Table 1.

Cis-elements and features that regulate mRNA quality control.

Cis-element or feature	Associated RNAs	Trans-factors	Effect on nuclear export	Other effects
Exon-exon junctions	Spliced protein-coding mRNAs	TREX Complex, EJC [42–45]	Promotes nuclear export [21,22]	Promotes stability, translation and nonsense-mediated decay [46–48]
GC-rich 5’ ends (ALREX elements)	Protein-coding mRNAs	RBM33, SARN/THO1/CIP29 (TREX), TPR, SR proteins?, TREX2? [26, 49–51]	Promotes nuclear export [3,23–27]	Promotes stability and translation [25,52,53]
Intact 5’SS motifs	Misprocessed mRNAs (RNAs with retained introns, IPA transcripts) and lncRNAs	ZFC3H1, U1 snRNP [31,54]	Promotes nuclear retention (in conjunction with m6A) [30,54]	Promotes nuclear RNA decay, inhibits 3’ cleavage and polyadenylation [30,55–63]
m6A	Poorly spliced mRNAs, long exons, transposable element-derived RNAs	YTH domain-containing proteins [54]	Promotes nuclear retention (in conjunction with 5’SS motifs) [54]	Promotes nuclear and cytoplasmic RNA decay and heterochromatin silencing [64–67]
A-rich sequences	Exons, transposable element-derived RNAs	HUSH Complex	Unknown	Promotes nuclear RNA decay and heterochromatin silencing [68–70]
U-rich sequences	Introns	Unknown	Unknown	Relieves silencing by the HUSH Complex? [68]
dsRNA (A to I editing by ADAR)	Transposable element-derived RNAs, viral RNAs	Major I-binding RBP is unclear, Staufen (dsRNA)	Promotes nuclear retention (A to I editing) [71,72]	Promotes RNA decay (Staufen) [73,74]