On "genomenclature": a Comprehensive (and Respectful) Taxonomy for Pseudogenes and Other "junk DNA"

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1992 Nov 15

PMID 1279691

Citations 114

Authors

J Brosius

S J Gould

Affiliations

Soon will be listed here.

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.

Citing Articles

, a Retrovirus-Derived Gene Implicated in Autism Spectrum Disorder, Is a Microglial Gene That Responds to Noradrenaline in the Postnatal Brain.

Ishino F, Itoh J, Matsuzawa A, Irie M, Suzuki T, Hiraoka Y Int J Mol Sci. 2025; 25(24.

PMID: 39769499 PMC: 11678650. DOI: 10.3390/ijms252413738.

Retrovirus-Derived Plays an Important Role in Innate Antifungal Immunity in the Eutherian Brain.

Ishino F, Itoh J, Irie M, Matsuzawa A, Naruse M, Suzuki T Int J Mol Sci. 2023; 24(19).

PMID: 37834332 PMC: 10573853. DOI: 10.3390/ijms241914884.

Transposable elements as essential elements in the control of gene expression.

Gebrie A Mob DNA. 2023; 14(1):9.

PMID: 37596675 PMC: 10439571. DOI: 10.1186/s13100-023-00297-3.

Transposable Elements Co-Option in Genome Evolution and Gene Regulation.

Gasparotto E, Burattin F, Di Gioia V, Panepuccia M, Ranzani V, Marasca F Int J Mol Sci. 2023; 24(3).

PMID: 36768929 PMC: 9917352. DOI: 10.3390/ijms24032610.

De novo emergence, existence, and demise of a protein-coding gene in murids.

Petrzilek J, Pasulka J, Malik R, Horvat F, Kataruka S, Fulka H BMC Biol. 2022; 20(1):272.

PMID: 36482406 PMC: 9733328. DOI: 10.1186/s12915-022-01470-5.

References

Cuthbertson R, Tomarev S, Piatigorsky J . Taxon-specific recruitment of enzymes as major soluble proteins in the corneal epithelium of three mammals, chicken, and squid. Proc Natl Acad Sci U S A. 1992; 89(9):4004-8. PMC: 525620. DOI: 10.1073/pnas.89.9.4004. View

Hara Y, Rovescalli A, Kim Y, Nirenberg M . Structure and evolution of four POU domain genes expressed in mouse brain. Proc Natl Acad Sci U S A. 1992; 89(8):3280-4. PMC: 48850. DOI: 10.1073/pnas.89.8.3280. View

Dombroski B, Mathias S, Nanthakumar E, Scott A, Kazazian Jr H . Isolation of an active human transposable element. Science. 1991; 254(5039):1805-8. DOI: 10.1126/science.1662412. View

Samuelson L, Wiebauer K, Snow C, Meisler M . Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution. Mol Cell Biol. 1990; 10(6):2513-20. PMC: 360608. DOI: 10.1128/mcb.10.6.2513-2520.1990. View

Barbosa P, Wistow G, Cialkowski M, Piatigorsky J, OBrien W . Expression of duck lens delta-crystallin cDNAs in yeast and bacterial hosts. Delta 2-crystallin is an active argininosuccinate lyase. J Biol Chem. 1991; 266(33):22319-22. View

Mathias S, Scott A, Kazazian Jr H, Boeke J, Gabriel A . Reverse transcriptase encoded by a human transposable element. Science. 1991; 254(5039):1808-10. DOI: 10.1126/science.1722352. View

Matsumine H, Herbst M, Ou S, Wilson J, McPhaul M . Aromatase mRNA in the extragonadal tissues of chickens with the henny-feathering trait is derived from a distinctive promoter structure that contains a segment of a retroviral long terminal repeat. Functional organization of the Sebright, Leghorn,.... J Biol Chem. 1991; 266(30):19900-7. View

Cooper D, Baptist E, Enghild J, Isola N, Klintworth G . Bovine corneal protein 54K (BCP54) is a homologue of the tumor-associated (class 3) rat aldehyde dehydrogenase (RATALD). Gene. 1991; 98(2):201-7. DOI: 10.1016/0378-1119(91)90174-a. View

Harendza C, Johnson L . Polyadenylylation signal of the mouse thymidylate synthase gene was created by insertion of an L1 repetitive element downstream of the open reading frame. Proc Natl Acad Sci U S A. 1990; 87(7):2531-5. PMC: 53723. DOI: 10.1073/pnas.87.7.2531. View

10.

Geyer P, Green M, Corces V . Tissue-specific transcriptional enhancers may act in trans on the gene located in the homologous chromosome: the molecular basis of transvection in Drosophila. EMBO J. 1990; 9(7):2247-56. PMC: 551949. DOI: 10.1002/j.1460-2075.1990.tb07395.x. View

11.

Wistow G, Piatigorsky J . Gene conversion and splice-site slippage in the argininosuccinate lyases/delta-crystallins of the duck lens: members of an enzyme superfamily. Gene. 1990; 96(2):263-70. DOI: 10.1016/0378-1119(90)90262-p. View

12.

Manrow R, Leone A, Krug M, Eschenfeldt W, Berger S . The human prothymosin alpha gene family contains several processed pseudogenes lacking deleterious lesions. Genomics. 1992; 13(2):319-31. DOI: 10.1016/0888-7543(92)90248-q. View

13.

Post T, Arce M, Liszewski M, Thompson E, Atkinson J, Lublin D . Structure of the gene for human complement protein decay accelerating factor. J Immunol. 1990; 144(2):740-4. View

14.

Nugent J, Palmer J . RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell. 1991; 66(3):473-81. DOI: 10.1016/0092-8674(81)90011-8. View

15.

Gantt J, Baldauf S, Calie P, Weeden N, Palmer J . Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J. 1991; 10(10):3073-8. PMC: 453023. DOI: 10.1002/j.1460-2075.1991.tb07859.x. View

16.

Brosius J . Retroposons--seeds of evolution. Science. 1991; 251(4995):753. DOI: 10.1126/science.1990437. View

17.

Piatigorsky J, Wistow G . The recruitment of crystallins: new functions precede gene duplication. Science. 1991; 252(5009):1078-9. DOI: 10.1126/science.252.5009.1078. View

18.

Abedinia M, Pain T, Algar E, Holmes R . Bovine corneal aldehyde dehydrogenase: the major soluble corneal protein with a possible dual protective role for the eye. Exp Eye Res. 1990; 51(4):419-26. DOI: 10.1016/0014-4835(90)90154-m. View

19.

Krane D, Hardison R . Short interspersed repeats in rabbit DNA can provide functional polyadenylation signals. Mol Biol Evol. 1990; 7(1):1-8. DOI: 10.1093/oxfordjournals.molbev.a040583. View

20.

DeChiara T, Brosius J . Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc Natl Acad Sci U S A. 1987; 84(9):2624-8. PMC: 304710. DOI: 10.1073/pnas.84.9.2624. View