Getting clear about the F-word in genomics

English version

Autoři: Stefan Linquist ^aff001; W. Ford Doolittle ^aff002; Alexander F. Palazzo ^aff003
Působiště autorů: Department of Philosophy, University of Guelph, Guelph, Ontario, Canada ^aff001; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada ^aff002; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada ^aff003
Vyšlo v časopise: Getting clear about the F-word in genomics. PLoS Genet 16(4): e32767. doi:10.1371/journal.pgen.1008702
Kategorie: Opinion Piece
doi: https://doi.org/10.1371/journal.pgen.1008702

Zdroje

1. Sarkar S. The genomic challenge to adaptationism. Brit J for the Philos Sci 66: 505–536.

2. Lynch M. The origins of genome architecture. Sunderland MA: Sinauer Associates; 2007.

3. Doolittle WF. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA 2013; 110:5294–5300. doi: 10.1073/pnas.1221376110 23479647

4. Elliott TA, Linquist S, Gregory TR. Conceptual and empirical challenges of ascribing functions to transposable elements. The American Naturalist 2014; 184: 14–2. doi: 10.1086/676588 24921597

5. Brunet TDP, Doolittle WF. Getting “function” right. Proc Natl Acad Sci USA 2014; 111: E3365. doi: 10.1073/pnas.1409762111 25107292

6. Graur D, Zheng Y, Price N, Azvedo RBR, Zufall RA, Elhaik E. On the immortality of television sets: “Function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 2013; 5: 578–590. doi: 10.1093/gbe/evt028 23431001

7. Rosenberg A, Neander K. Are homologies (selected effect or causal role) function free? Phil Sci 2009; 76: 307–334.

8. Eddy S. The ENCODE project: Missteps overshadowing a success. Current Biology 2013; 23: R259–R261. doi: 10.1016/j.cub.2013.03.023 23578867

9. Mattick J.S. Dinger M.E. The extent of functionality in the human genome. HUGO J 2013; 7, 2 doi: 10.1186/1877-6566-7-2

10. Lee H., Zhang Z., and Krause H. M. (2019). Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners? TRENDS in Genetics. 2019; doi.org/10.1016/j.tig.2019.09.006

11. Ponting C. P. Biological function in the twilight zone of sequence conservation. BMC Biology. 2017; 15: 71. doi: 10.1186/s12915-017-0411-5 28814299

12. Palazzo A.F. Lee E.S. Non-coding RNA: what is functional and what is junk? Frontiers in Genetics. 2015; 6: 1–11. doi: 10.3389/fgene.2015.00001 25674101

13. Garson J. A critical overview of biological functions. New York: Springer Briefs in Philosophy; 2016.

14. Godfrey-Smith P. A modern history theory of functions. In: Linquist S, editor. Philosophy of Evolutionary Biology, volume 1. New York: Routledge; 2016.

15. Maynard Smith J. Overview—unsolved evolutionary problems. In: Dover GA, Flavell RB, editors. Genome evolution. London: Academic Press; 1982.

16. Gould SJ, Vrba ES. Exaptation—a missing term in the science of form. Paleobiology 1982; 8: 4–15.

17. Stoltzfus A. On the possibility of constructive neutral evolution. J Mol Evol. 1999;49: 169–181. doi: 10.1007/pl00006540 10441669

18. Akins R. A. Lambowitz A. M. A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative therof. Cell 1987; 50: 331–345. doi: 10.1016/0092-8674(87)90488-0 3607872

19. Lukes J. Archibald J.M. Keeling P.J. Doolittle W.F. Gray M.W. How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 2011; 63: 528–537. doi: 10.1002/iub.489 21698757

20. Doolittle WF. A ratchet for protein complexity. Nature 2010; 481:270–271.

21. Lane N, Martin W. The energetics of genome complexity. Nature 2010; 467:929–934. doi: 10.1038/nature09486 20962839

22. Naito T, Kusano K, Kobayashi I. Selfish behavior of restriction-modification systems. Science 1995;267: 897–899. doi: 10.1126/science.7846533 7846533

23. Palazzo AF, Gregory TR. The case for junk DNA. PLOS Genetics 2014;10: e1004351. doi: 10.1371/journal.pgen.1004351 24809441

24. Palazzo AF, Lee ES. Sequence determinants for nuclear retention and cytoplasmic export of mRNAs and lncRNAs. Front Genet. 2018; 9:440. doi: 10.3389/fgene.2018.00440 30386371

25. Brunet TDP, Doolittle WF. The generality of constructive neutral evolution. Biol Philos. 2018;33:2.

26. Gould SJ, Lewontin RC. The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist paradigm. Proc R Soc Lond B. 1979; 205:581–598. doi: 10.1098/rspb.1979.0086 42062

27. Craver C.F. Functions and mechanisms: A perspectivalist view. Huneman P. (ed) Function: Selection and Mechanisms, Springer, pp 1331–58.

Článek High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements

Článek The nanophthalmos protein TMEM98 inhibits MYRF self-cleavage and is required for eye size specification

Článek The MAPK substrate MASS proteins regulate stomatal development in Arabidopsis

Článek Dynamic localization of SPO11-1 and conformational changes of meiotic axial elements during recombination initiation of maize meiosis

Článek The plant mobile domain proteins MAIN and MAIL1 interact with the phosphatase PP7L to regulate gene expression and silence transposable elements in Arabidopsis thaliana

Článek Targeting mitochondrial and cytosolic substrates of TRIT1 isopentenyltransferase: Specificity determinants and tRNA-i6A37 profiles

Článek XPF-ERCC1 protects liver, kidney and blood homeostasis outside the canonical excision repair pathways

Článek Technical and social issues influencing the adoption of preprints in the life sciences

Článek DNA methylation-mediated repression of exosomal miR-652-5p expression promotes oesophageal squamous cell carcinoma aggressiveness by targeting PARG and VEGF pathways

Článek Is imprinting the result of “friendly fire” by the host defense system?

Článek The coordinate actions of calcineurin and Hog1 mediate the stress response through multiple nodes of the cell cycle network