What Is a Genome?
The genome is often described as the information repository of an organism. Whether millions or billions of letters of DNA, its transmission across generations confers the principal medium for inheritance of organismal traits. Several emerging areas of research demonstrate that this definition is an oversimplification. Here, we explore ways in which a deeper understanding of genomic diversity and cell physiology is challenging the concepts of physical permanence attached to the genome as well as its role as the sole information source for an organism.
Vyšlo v časopise:
What Is a Genome?. PLoS Genet 12(7): e32767. doi:10.1371/journal.pgen.1006181
Kategorie:
Review
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1006181
Souhrn
The genome is often described as the information repository of an organism. Whether millions or billions of letters of DNA, its transmission across generations confers the principal medium for inheritance of organismal traits. Several emerging areas of research demonstrate that this definition is an oversimplification. Here, we explore ways in which a deeper understanding of genomic diversity and cell physiology is challenging the concepts of physical permanence attached to the genome as well as its role as the sole information source for an organism.
Zdroje
1. Lederberg J, McCray AT. 'Ome Sweet 'Omics: A Genealogical Treasury of Words. The Scientist. 2001;15:8.
2. Sutton WS. On the morphology of the chromosome group in Brachystola magna. Biol. Bull. 1902;4:24–39
3. Avery OT, MacLeod CM, McCarty M. Studies on the chemical nature of the substance inducing transformation of Pneumococcal types. J Exp Med, 1944;79:137–159. 19871359
4. Watson JD, Crick FHC. Genetical Implications of the structure of Deoxyribonucleic Acid. Nature. 1953;171:964–967. 13063483
5. Crick FHC. On protein synthesis. Symp Soc Exp Biol. 1958;12:138–163. 13580867
6. Michel JB, Shen YK, Aiden AP, Veres A, Gray MK, et al. Quantitative analysis of culture using millions of digitized books. Science. 2011;331:176–182. doi: 10.1126/science.1199644 21163965
7. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res. 2005;33:D34–D38. 15608212
8. Nassal M, Schaller H. Hepatitis B virus replication. Trends Microbiol. 1993;1:221–228. 8137119
9. Nowacki M, Shetty K, Landweber LF. RNA-Mediated Epigenetic Programming of Genome Rearrangements. Annu Rev Genomics Hum Genet. 2011;12:367–389. doi: 10.1146/annurev-genom-082410-101420 21801022
10. Goldman AD, Landweber LF. Oxytricha as a modern analog of ancient genome evolution. Trends Genet. 2012;28:382–388. doi: 10.1016/j.tig.2012.03.010 22622227
11. Bracht JR, Fang W, Goldman AD, Dolzhenko E, Stein EM, Landweber LF. Genomes on the edge: programmed genome instability in ciliates. Cell. 2013;152:406–416. doi: 10.1016/j.cell.2013.01.005 23374338
12. Zoller SD, Hammersmith RL, Swart EC, Higgins BP, Doak TG, et al. Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology. Protist. 2012;163:643–657
13. Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, et al. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell. 2014;158:1187–98. doi: 10.1016/j.cell.2014.07.034 25171416
14. Swart EC, Bracht JR, Magrini V, Minx P, Chen X, et al. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol. 2013;11:e1001473. doi: 10.1371/journal.pbio.1001473 23382650
15. Prescott DM. The DNA of ciliated protozoa. Microbiol Mol Biol Rev. 1994;58:233–267.
16. Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature. 2008;451:153–158. 18046331
17. Nowacki M, Haye JE, Fang W, Vijayan V, Landweber LF. RNA-mediated epigenetic regulation of DNA copy number. Proc Natl Acad Sci U S A, 2010;107:22140–22144. doi: 10.1073/pnas.1012236107 21078984
18. Vogt A, Goldman AD, Mochizuki K, Landweber LF. Transposon domestication versus mutualism in ciliate genome rearrangements. PLoS Genet. 2013;9:e1003659. doi: 10.1371/journal.pgen.1003659 23935529
19. Fang W, Wang X, Bracht JR, Nowacki M, Landweber LF. Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. Cell. 2012;151:1243–1255. doi: 10.1016/j.cell.2012.10.045 23217708
20. Zahler AM, Neeb ZT, Lin A, Katzman S. Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27 nt small RNAs derived from the parental macronucleus. PLoS ONE, 2012;7:e42371. doi: 10.1371/journal.pone.0042371 22900016
21. Cello J, Paul AV, Wimmer E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 2002;297:1016–1018. 12114528
22. Smith HO, Hutchison CA 3rd, Pfannkoch C, Venter JC. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A. 2003;100:15440–5. 14657399
23. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 2010;329:52–56. doi: 10.1126/science.1190719 20488990
24. Nanney DL. Corticotype transmission in Tetrahymena. Genetics. 1966;54:955–968. 5972435
25. Walker SI. Top-down causation and the rise of information in the Emergence of Life. Information. 2014;5:424–439.
26. Riggs AD. X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet. 1975;14:9–25. 1093816
27. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet. 2003;33:245–254. 12610534
28. D’Urso A, Brickner JH. Mechanisms of epigenetic memory. Trends Genet. 2014;30:230–236. doi: 10.1016/j.tig.2014.04.004 24780085
29. Siklenka K, Erkek S, Godmann M, Lambrot R, McGraw S, et al. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science. 2015;350:aab2006 doi: 10.1126/science.aab2006 26449473
30. Zordan R, Miller M, Galgoczy D, Tuch B, Johnson A. Interlocking transcriptional feedback loops control white-opaque switching in Candida albicans. PLoS Biol. 2007;5:1–11.
31. Zacharioudakis I, Gligoris T, Tzamarias D. A yeast catabolic enzyme controls transcriptional memory. Curr Biol. 2007;17:2041–2046. 17997309
32. Rassoulzadegan M, Grandjean V, Gounon P, Vincent S, Gillot I, Cuzin F. RNA-mediated non-Mendelian inheritance of an epigenetic change in the mouse. Nature. 2006;441:469–474. 16724059
33. Rodgers AB, Morgan CP, Leu NA, Bale TL. Transgenerational epigenetic programming via sperm microRNA recapitulates effects of paternal stress. Proc Natl Acad Sci U S A. 2015;112:13699–13704. doi: 10.1073/pnas.1508347112 26483456
34. Bush WS, Moore JH. Chapter 11: Genome-Wide Association Studies. PLoS Comput Biol. 2012;8:e1002822. doi: 10.1371/journal.pcbi.1002822 23300413
35. Gibson G. Rare and common variants: twenty arguments. Nat Rev Genet. 2012;13:135–145. doi: 10.1038/nrg3118 22251874
36. Smith EN, Kruglyak L. Gene-environment interaction in yeast gene expression. PLoS Biol. 2008;6:e83. doi: 10.1371/journal.pbio.0060083 18416601
37. Manuck SB, McCaffery JM. Gene-environment interaction. Annu Rev Psychol. 2014;65:41–70. doi: 10.1146/annurev-psych-010213-115100 24405358
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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