SCIENCE CHINA Life Sciences, Volume 63 , Issue 7 : 986-995(2020) https://doi.org/10.1007/s11427-019-1677-8

Understanding the proteome encoded by “non-coding RNAs”: new insights into human genome

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  • ReceivedNov 29, 2019
  • AcceptedMar 12, 2020
  • PublishedApr 20, 2020


A great number of non-coding RNAs (ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Based on the development of ribosome profiling (Ribo-seq), full length translating RNA analysis (RNC-seq) and mass spectrometry technology, more and more ncRNAs are being found to be translated in different organism, and some of them can produce functional peptides. While recently, not only individual new functional proteins, but also a new proteome have been experimentally discovered to be encoded by endogenous lncRNAs and circRNAs. These new proteins are of biological significance, suggesting the connection of the translation of ncRNAs to human physiology and diseases. Therefore, an in-depth and systematic understanding of the coding capabilities of ncRNAs is necessary for basic biology and medicine. In this review, we summarize the advances in the field of discovering this new proteome, i.e. “ncRNA-coded” proteins.

Funded by

the National Key Research and Development Program(2017YFA0505100,2017YFA0505001,2018YFC0910202)

the National Natural and Science Foundation of China(81372135,to,TW;,81322028,31300649,to,GZ;,31570828,31770888,to,Q.Y.H.)


This work was supported by the National Key Research and Development Program (2017YFA0505100, 2017YFA0505001, 2018YFC0910202) and the National Natural and Science Foundation of China (81372135 to TW; 81322028 and 31300649 to GZ; 31570828 and 31770888 to Q.Y.H.).

Interest statement

The author(s) declare that they have no conflict of interest.


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  • Figure 1

    The difference between RNC-seq and Ribo-seq. A, Schematic workflow of RNC-seq and Ribo-seq. B, RNC-seq with long reads can eliminate the small RNA fragment contaminants but Ribo-seq cannot. C and D, RNC-seq’s advantages in detecting splice junctions. E, RNC-seq’s advantages in detecting translating circRNAs.

  • Figure 2

    Hypothesis of new protein origin.

  • Table 1   Table 1 Commonly used human genome annotation databases based on algorithmic modelling and classification

    Databases name








    Sequence similarity and homology







  • Table 2   Table 2 Typical features of PE1 protein-coding genes, new protein-coding genes and non-coding genes

    Typical features

    Gene class

    PE1 protein-coding genes

    New protein-coding genes

    Non-coding genes

    RNA length




    ORF length




    Exon count




    ORF exon count

    Multiple exons

    Mostly single exon


    Expression level




    Isoelectric point (protein)




    Amino acid compositions


    More positively charged, less negatively charged


    Stability (protein)

    More stable

    Less stable


    Evolutionary conservation


    Poorly conserved

    Poorly conserved

  • Table 3   Table 3 Functions of human new proteins

    Gene name

    Protein length (aa)



    linear lncRNA



    A novel biomarker for intracranial germinoma and embryonal carcinoma

    (Wanggou et al., 2012)



    Regulates mTORC1 and muscle regeneration

    (Matsumoto et al., 2017)



    Involved in mRNA processing and negatively regulates P-body association

    (D’Lima et al., 2017)



    Controls cell fusion and muscle formation

    (Zhang et al., 2017)



    Suppresses colon cancer growth

    (Huang et al., 2017)



    A mitochondrial that enhances fatty acid β-Oxidation

    (Makarewich et al., 2018)



    Controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation

    (Polycarpou-Schwarz et al., 2018)





    Promote cell proliferation and clone formation

    Suppresses oncogenic signaling in hepatocellular carcinoma cells

    (Lu et al., 2019)

    (Xu et al., 2019)





    Functions in myogenesis

    (Legnini et al., 2017)



    Suppresses glioma tumorigenesis

    (Zhang et al., 2018a)



    Suppresses oncogenic transcriptional elongation in glioblastoma

    (Zhang et al., 2018b)

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