Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Apr 18:9:140.
doi: 10.3389/fgene.2018.00140. eCollection 2018.

Coding and Non-coding RNAs, the Frontier Has Never Been So Blurred

Florent Hubé  1   2 , Claire Francastel  1   2
Affiliations

Coding and Non-coding RNAs, the Frontier Has Never Been So Blurred

Florent Hubé et al. Front Genet. .
No abstract available

Keywords: Affymetrix U133 Plus2 array; NCI-60 panel; UCSC genes; bifunctional RNA; messenger RNA; non-coding RNA; transcript isoform.

PubMed Disclaimer

Figures

Figure 1
Figure 1
(A) Representation of the three ways to achieve bifunctionality. Genomic/intronic regions are in blue, exonic regions are in orange (coding sequences) or yellow (non-coding sequences). (B) Overlap between genes that present NM_ and NR_ isoforms. “UCSC genes” track from UCSC Genome browser was retrieved and NM_ and NR_ transcripts were sorted using Galaxy tools. Venn diagram was performed using the gene names. 16,879 (60.2%) and 8,583 (30.6%) were related to only NM_ (coding) or NR_ (non-coding) transcripts, respectively, whereas 2,586 (9.2%) hold both coding and non-coding isoforms. (C) Putative bifunctional RNAs are recognized by probes from Affymetrix U133 Plus2 array. The 2,586 genes were recognized by 5,635 probes, of which 66.7% were not able to distinguish between coding and non-coding isoforms (NM_ and NR_, respectively). The 66.7% correspond to 1,767 genes. (D) Expression values attributed to each probe corresponding to the 770 and 114 exclusively coding and non-coding genes, was retrieved from the NCI-60 panel that referred to a panel of 60 Human Tumor Cell Lines Screen related to nine different cancer types [Geo DataSet Record GDS4296, (Barrett et al., 2005)] and plotted as boxplots. Significance was assessed using Wilcoxon-Mann-Whitney test. (E) The expression of the 1,767 genes which coding and non-coding properties are not distinguishable was assessed in the Jensen Tissues (https://tissues.jensenlab.org/) using Enrichr website (http://amp.pharm.mssm.edu/Enrichr/). ATG, start codon; *, stop codon; n.s., not significant; snoRNA, small nucleolar RNA, miRNA, microRNA; p53, protein 53 (Candeias et al., 2008); CPSF1, Cleavage and polyadenylation specificity factor 1 (Hube et al., 2017); cRNA, coding RNA; ncRNA, non-coding RNA. NM_ and NR_ are the prefixes used by RefSeq to describe protein-coding and non-protein-coding transcripts, respectively.
See this image and copyright information in PMC

References

    1. Barrett T., Suzek T. O., Troup D. B., Wilhite S. E., Ngau W. C., Ledoux P., et al. (2005). NCBI GEO: mining millions of expression profiles–database and tools. Nucleic Acids Res. 33, D562–D566. 10.1093/nar/gki022 - DOI - PMC - PubMed
    1. Bashirullah A., Cooperstock R. L., Lipshitz H. D. (2001). Spatial and temporal control of RNA stability. Proc. Natl. Acad. Sci. U.S.A. 98, 7025–7028. 10.1073/pnas.111145698 - DOI - PMC - PubMed
    1. Candeias M. M., Malbert-Colas L., Powell D. J., Daskalogianni C., Maslon M. M., Naski N., et al. (2008). P53 mRNA controls p53 activity by managing Mdm2 functions. Nat. Cell Biol. 10, 1098–1105. 10.1038/ncb1770 - DOI - PubMed
    1. Ching T., Huang S., Garmire L. X. (2014). Power analysis and sample size estimation for RNA-Seq differential expression. RNA 20, 1684–1696. 10.1261/rna.046011.114 - DOI - PMC - PubMed
    1. Chooniedass-Kothari S., Emberley E., Hamedani M. K., Troup S., Wang X., Czosnek A., et al. (2004). The steroid receptor RNA activator is the first functional RNA encoding a protein. FEBS Lett. 566, 43–47. 10.1016/j.febslet.2004.03.104 - DOI - PubMed