Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 1992 Nov 15;89(22):10706-10.
doi: 10.1073/pnas.89.22.10706.

On "Genomenclature": A Comprehensive (And Respectful) Taxonomy for Pseudogenes and Other "Junk DNA"

Affiliations
Free PMC article

On "Genomenclature": A Comprehensive (And Respectful) Taxonomy for Pseudogenes and Other "Junk DNA"

J Brosius et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

Genomic nomenclature has not kept pace with the levels and depth of analyzing and understanding genomic structure, function, and evolution. We wish to propose a general terminology that might aid the integrated study of evolution and molecular biology. Here we designate as a "nuon" any stretch of nucleic acid sequence that may be identifiable by any criterion. We show how such a general term will facilitate contemplation of the structural and functional contributions of such elements to the genome in its past, current, or future state. We focus in this paper on pseudogenes and dispersed repetitive elements, since their current names reflect the prevalent view that they constitute dispensable genomic noise (trash), rather than a vast repertoire of sequences with the capacity to shape an organism during evolution. This potential to contribute sequences for future use is reflected in the suggested terms "potonuons" or "potogenes." If such a potonuon has been coopted into a variant or novel function, an evolutionary process termed "exaptation," we employ the term "xaptonuon." If a potonuon remains without function (nonaptive nuon), it is a "nonaptation" and we term it "naptonuon." A number of examples for potonuons and xaptonuons are given.

Similar articles

  • Mining treasures from 'junk DNA'.
    Nowak R. Nowak R. Science. 1994 Feb 4;263(5147):608-10. doi: 10.1126/science.7508142. Science. 1994. PMID: 7508142 No abstract available.
  • Pseudogenes.
    Wilde CD. Wilde CD. CRC Crit Rev Biochem. 1986;19(4):323-52. CRC Crit Rev Biochem. 1986. PMID: 2421975 Review.
  • SINEs.
    Okada N. Okada N. Curr Opin Genet Dev. 1991 Dec;1(4):498-504. doi: 10.1016/s0959-437x(05)80198-4. Curr Opin Genet Dev. 1991. PMID: 1668310 Review.
  • An evolutionary classification of genomic function.
    Graur D, Zheng Y, Azevedo RB. Graur D, et al. Genome Biol Evol. 2015 Jan 28;7(3):642-5. doi: 10.1093/gbe/evv021. Genome Biol Evol. 2015. PMID: 25635041 Free PMC article. Review.
  • [Pseudogenes: structure conservation, expression, and functions].
    Balakirev ES, Ayala FJ. Balakirev ES, et al. Zh Obshch Biol. 2004 Jul-Aug;65(4):306-21. Zh Obshch Biol. 2004. PMID: 15490577 Review. Russian.
See all similar articles

Cited by 99 articles

See all "Cited by" articles

References

    1. Proc Natl Acad Sci U S A. 1992 May 1;89(9):4004-8 - PubMed
    1. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3280-4 - PubMed
    1. Science. 1991 Dec 20;254(5039):1805-8 - PubMed
    1. Mol Cell Biol. 1990 Jun;10(6):2513-20 - PubMed
    1. J Biol Chem. 1991 Nov 25;266(33):22319-22 - PubMed

Publication types

LinkOut - more resources

Feedback