Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs

@article{Palazzo2018SequenceDF,
  title={Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs},
  author={Alexander F Palazzo and Eliza S. Lee},
  journal={Frontiers in Genetics},
  year={2018},
  volume={9}
}
Eukaryotes are divided into two major compartments: the nucleus where RNA is synthesized and processed, and the cytoplasm, where mRNA is translated into proteins. Although many different RNAs are made, only a subset is allowed access to the cytoplasm, primarily RNAs involved in protein synthesis (mRNA, tRNA, and rRNA). In contrast, nuclear retained transcripts are mostly long non-coding RNAs (lncRNAs) whose role in cell physiology has been a source of much investigation in the past few years… Expand
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References

SHOWING 1-10 OF 239 REFERENCES
The Signal Sequence Coding Region Promotes Nuclear Export of mRNA
TLDR
The surprising observation that the signal sequence coding region (SSCR) can serve as a nuclear export signal of an mRNA that lacks an intron or functional cap is made and suggests a link between nuclear export and membrane targeting of mRNAs. Expand
Nuclear Retention of mRNA in Mammalian Tissues
TLDR
This study challenges the view that transcripts predominantly reside in the cytoplasm and reveals a role of the nucleus in dampening gene expression noise and demonstrates that nuclear retention of mRNA can efficiently buffer cy toplasmic transcript levels from noise that emanates from transcriptional bursts. Expand
RNA length defines RNA export pathway.
TLDR
It is shown that U1 snRNAs behaved like an mRNA in nuclear export if various approximately 300-nucleotide fragments were inserted in a central position, indicating unequivocally that this switch is indeed the result of RNA length. Expand
Splicing promotes the nuclear export of β-globin mRNA by overcoming nuclear retention elements.
TLDR
Evidence that β-globin mRNA contains an element that actively retains it in the nucleus and degrades it is provided, suggesting that contrary to many current models, the default pathway for most intronless RNAs is to be exported from the nucleus, unless the RNA contains elements that actively promote its nuclear retention. Expand
An intron with a constitutive transport element is retained in a Tap messenger RNA
TLDR
The results indicate that Tap regulates expression of its own intron-containing RNA through a CTE-mediated mechanism, indicating that CTEs are likely to be important elements that facilitate efficient expression of mammalian mRNAs with retained introns. Expand
The Consensus 5' Splice Site Motif Inhibits mRNA Nuclear Export
TLDR
The data suggests that the presence of the 5’splice site motif in mature RNAs promotes their nuclear retention and may help to distinguish mRNAs from misprocessed transcripts and transcriptional noise. Expand
Export and stability of naturally intronless mRNAs require specific coding region sequences and the TREX mRNA export complex
TLDR
It is concluded that naturally intronless mRNAs contain specific sequences that result in efficient packaging into the TREX mRNA export complex, thereby supplanting the splicing requirement for efficient mRNA export. Expand
Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells
TLDR
A pathway for regulation of RNA accumulation and subcellular localization that has been co-opted to regulate the fate of transcripts with integrated Alu elements is identified. Expand
hnRNP C Tetramer Measures RNA Length to Classify RNA Polymerase II Transcripts for Export
TLDR
A mechanism by which RNA polymerase II (Pol II) transcripts are classified according to their length is shown, which highlights the biological importance of RNA recognition by the length and reveals a new function of the C tetramer. Expand
Nuclear export as a key arbiter of "mRNA identity" in eukaryotes.
TLDR
How mRNA identity is assessed by the nuclear export machinery in order to extract meaningful information from the eukaryotic genome is discussed and an explanation of why certain sequences that are enriched in protein-coding genes, such as the signal sequence coding region, promote mRNA nuclear export in vertebrates is provided. Expand
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1
2
3
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5
...