#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

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 medicína
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#