An evolutionary classification of genomic function

Genome Biology and Evolution

Volumn 7, Issue 3, 2015, Pages 642-645

  Graur, Dan ^a   Zheng, Yichen ^a   Azevedo, Ricardo B R ^a  

^a University of Houston   (United States)

Author keywords

Functional DNA; Garbage DNA; Indifferent DNA; Jekyll to Hyde DNA; Junk DNA; Lazarus DNA; Literal DNA; Pseudogene; Rubbish DNA; Zombie DNA

Indexed keywords

DNA; SPACER DNA;

CLASSIFICATION; GENOME; GENOMICS; MOLECULAR EVOLUTION; NOMENCLATURE;

DNA; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENOME; GENOMICS; TERMINOLOGY AS TOPIC;

EID: 84940107361     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv021     Document Type: Article

References (31)

1. Brenner S. 1998. Refuge of spandrels. Curr. Biol. 8:R669.
2. Brosius J, Gould SJ. 1992. On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". Proc Natl Acad Sci U S A. 89:10706-10710.
3. Brunet TDP, Doolittle WF. 2014. Getting "function" right. Proc Natl Acad Sci U S A. 111:E3365.
4. Cavalier-Smith T. 1978. Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox. J Cell Sci. 34:247-278.
5. Chen YH, et al. 2003. KCNQ1 gain-of-function mutation in familial atrial fibrillation. Science 299:251-254.
6. Cho JH, Brant SR. 2011. Recent insights into the genetics of inflammatory bowel disease. Gastroenterology 140:1704-1712.
7. Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci U S A. 110:5294-5300.
8. Eddy SR. 2012. The C-value paradox, junk DNA and ENCODE. Curr Biol. 22:R898-R899.
9. Ehret CF, De Haller G. 1963. Origin, development, and maturation of organelles and organelle systems of the cell surface in Paramecium. J Ultrastruct Res. 23(Supplement 6):1-42.
10. ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
11. Graur D, et al. 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol. 5:578-590.
12. Huneman P, editor. 2013. Functions: selection and mechanisms. Dordrecht (The Netherlands): Springer.
13. Hurst LD. 2013. Open questions: A logic (or lack thereof) of genome organization. BMC Biol. 11:58.
14. Kellis M, et al. 2014. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 111:6131-6138.
15. Kolata G, 2010. Reanimated "junk" DNA is found to cause disease. New York Times. Available from: http://www.nytimes.com/2010/08/20/sci ence/20gene.html?-r=0.
16. Krams SM, Bromberg JS. 2013. ENCODE: life, the universe and everything. Am J Transplant. 13:245.
17. Makalowski W. 2003. Not junk after all. Science 300:1246-1247.
18. Mehta G, Jalan R, Mookerjee RP. 2013. Cracking the ENCODE: from transcription to therapeutics. Hepatology 57:2532-2535.
19. Millikan RG. 1989. In defense of proper functions. Philos Sci. 56:288-302.
20. Neander K. 1991. Functions as selected effects: the conceptual analysts defense. Philos Sci. 58:168-184.
21. Neander K. 2002. Types of traits: the importance of functional homologues. In: Ariew A, Cummins R, Perlman M, editors. Functions: new essays in the philosophy of psychology and biology. Oxford: Oxford University Press. p. 390-415.
22. Nielsen R. 2005. Molecular signatures of natural selection. Annu Rev Genet. 39:197-218.
23. Niu DK, Jiang L. 2013. Can ENCODE tell us how much junk DNA we carry in our genome? Biochem Biophys Res Commun. 430:1340-1343.
24. Nóbrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM. 2004. Megabase deletions of gene deserts result in viable mice. Nature 431:988-993.
25. Ohno S. 1972. So much "junk" DNA in our genome. Brookhaven Symp Biol. 23:366-370.
26. Ohta T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246:96-98.
27. Palazzo AF, Gregory TR. 2014. The case for junk DNA. PLoS Genet. 10:e1004351.
28. Stevenson RL 1886., Strange case of Dr. Jekyll and Mr. Hyde. New York: Charles Scribner's Sons.
29. Sundaram V, et al. Forthcoming 2014. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res. 24:1963-1976.
30. Vitti JJ, Grossman SR, Sabeti PC. 2013. Detecting natural selection in genomic data. Annu. Rev. Genet. 47:97-120.
31. Wen Y-Z, Zheng L-L, Qu L-H, Ayala FJ, Lun Z-R. 2012. Pseudogenes are not pseudo any more. RNA Biol. 9:27-32.