Regulating Gene Expression through RNA Nuclear Retention

Abstract

Multiple mechanisms have evolved to regulate the eukaryotic genome. We have identified CTN-RNA, a mouse tissue-specific approximately 8 kb nuclear-retained poly(A)+ RNA that regulates the level of its protein-coding partner. CTN-RNA is transcribed from the protein-coding mouse cationic amino acid transporter 2 (mCAT2) gene through alternative promoter and poly(A) site usage. CTN-RNA is diffusely distributed in nuclei and is also localized to paraspeckles. The 3'UTR of CTN-RNA contains elements for adenosine-to-inosine editing, involved in its nuclear retention. Interestingly, knockdown of CTN-RNA also downregulates mCAT2 mRNA. Under stress, CTN-RNA is posttranscriptionally cleaved to produce protein-coding mCAT2 mRNA. Our findings reveal a role of the cell nucleus in harboring RNA molecules that are not immediately needed to produce proteins but whose cytoplasmic presence is rapidly required upon physiologic stress. This mechanism of action highlights an important paradigm for the role of a nuclear-retained stable RNA transcript in regulating gene expression.

A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas

“…The predominant localization of HCN in tumor cell nuclei with frequent nucleolar concentration supports this hypothesis. One mechanism of nuclear retention of RNA is through A-to-I editing, post-transcriptional modification of adenosine (A) residues to inosine (I) (Bass, 2002), as in a described 8-kb poly(A) þ RNA CTN-RNA (Prasanth et al, 2005). However, we find no evidence of A-to-I editing in the HCN transcript (data not shown), suggesting other mechanisms for nuclear retention.…”

Mechanisms controlling titer and expression of bidirectional lentiviral and gammaretroviral vectors

“…This hypothesis was supported by the report that long dsRNA is subjected to A-I editing, which not only can lead to nuclear retention but also to hypermutations within the dsRNA stretch. 24,47 In this case, nucleocytoplasmic export can be induced by incorporation of the RRE but not the CTE into the message. 24 As bidirectional vectors ultimately produce two complementary RNAs (the genomic RNA and the message initiated from the mCMV) within the packaging cell this would be a perfect target for nuclear retention.…”

Editor meets silencer: crosstalk between RNA editing and RNA interference

“…Therefore, splice sites might be created or deleted due to A→I editing of intronic Alu fold-back double-stranded (ds)RNAs, leading to the inclusion or exclusion of Alu exons 6 . c | A→I editing of a SINE fold-back dsRNA present in the 3′ UTR of CTN-RNA and its binding to p54 nrb might be involved in the regulatory mechanism that retains this RNA in nuclear speckles 81 . When cells are placed under stress, CTN-RNA is cleaved and de novo polyadenylated at an alternative site to release the proteincoding Cat2 mRNA, which is then translated into cationic amino-acid transporter-2 protein 81 .…”

“…c | A→I editing of a SINE fold-back dsRNA present in the 3′ UTR of CTN-RNA and its binding to p54 nrb might be involved in the regulatory mechanism that retains this RNA in nuclear speckles 81 . When cells are placed under stress, CTN-RNA is cleaved and de novo polyadenylated at an alternative site to release the proteincoding Cat2 mRNA, which is then translated into cationic amino-acid transporter-2 protein 81 . The factors involved in the cleavage and de novo polyadenylation mechanisms are unknown.…”