Research Progress on Invertebrates DNA Methylation

doi:10.13560/j.cnki.biotech.bull.1985.2015.08.003

Abstract

Abstract: DNA methylation is an important epigentic mechanism which can change organism’s transcriptome and phenotype without altering DNA sequence. In different evolutionary braches, the states of DNA methylation are fundamentally different. In invertebrates, DNA methylation usually occurs in transcription region and is closely related to genetic expression. Research shows that DNA methylation plays an important role in caste formation of social insects. It can improve the phenotypic plasticity of organism by increasing the amount of transcription variants via promoter recognition and exon skipping in highly fluctuating environments. This article reviewed the mechanism and function of DNA methylation in invertebrates to provide reference to related research and make prospects for future research.

Key words: DNA methylation, gene body methylation（GBM）, transcriptome

Liu Ying, Tang Yongzheng, Gao Li. Research Progress on Invertebrates DNA Methylation[J]. Biotechnology Bulletin, 2015, 31(8): 17-23.

References

[1] Zemach A, McDaniel IE, Silva P, et al. Genome-wide evolutionary analysis of eukaryotic DNA methylation[J]. Science, 2010, 328：916-919.
[2] Gadau J, Helmkampf M, Nygaard S, et al. The genomic impact of 100 million years of social evolution in seven ant species[J]. Trends in Genetics, 2012, 28：14-21.
[3] Bestor TH. DNA methylation-evolution of a bacterial immune function into a regulator of gene-expression and genome structure in higher eukaryotes[J]. Biological Sciences Philosophical Transactions of the Royal Society of London Series B, 1990, 326： 179-187.
[4] Klose RJ, Bird AP. Genomic DNA methylation：the mark and its mediators[J]. Trends in Biochemical Sciences, 2006, 31： 89-97.
[5] Jurkowski TP, Meusburger M, Phalke S, et al. Human DNMT2 methylates tRNA（Asp）molecules using a DNA methyltransferase-like catalytic mechanism[J]. RNA, 2008, 14： 1663-1670.
[6] Bogdanovic O, Veenstra GJC. DNA methylation and methyl-CpG binding proteins：developmental requirements and function[J]. Chromosoma, 2009, 118：549-565.
[7] Collier J. Epigenetic regulation of the bacterial cell cycle[J]. Current Opinion in Microbiology, 2009, 12：722-729.
[8] Cokus SJ, Feng S, Zhang X, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning[J]. Nature, 2008, 452：215-219.
[9] Zhang X, Yazaki J, Sundaresan A, et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis[J]. Cell, 2006, 126：1189-1201.
[10] Schaefer M, Lyko F. Lack of evidence for DNA methylation of Invader4 retroelements in Drosophila and implications for Dnmt2-mediated epigenetic regulation[J]. Nature Genetics, 2010, 42： 920-921.
[11] Gavery MR, Roberts SB. Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusk[J]. PeerJ, 2013, 1：e215.
[12] Wang X, Wheeler D, Avery A, et al. Function and evolution of DNA methylation in Nasonia vitripennis[J]. PLoS Genetics, 2013, 9：e1003872.
[13] Field LM. Methylation and expression of amplified esterase genes in the aphid Myzus persicae （Sulzer）[J]. Biochemical Journal, 2000, 349： 863-868.
[14] Ono M, Swanson JJ, Field LM, et al. Amplification and methylation of an esterase gene associated with insecticide-resistance in greenbugs, Schizaphis graminum （Rondani）（Homoptera ： Aphididae）[J]. Insect Biochemistry and Molecular Biology, 1999, 29： 1065-1073.
[15] Walsh TK, Brisson JA, Robertson HM, et al. A functional DNA methylation system in the pea aphid, Acyrthosiphon pisum[J]. Insect Molecular Biology, 2010, 19： 215-228.
[16] Xiang H, Zhu J, Chen Q, et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map[J]. Nature Biotechnology, 2010, 28：516-520.
[17] Feng S, Cokus SJ, Zhang X, et al. Conservation and divergence of methylation patterning in plants and animals[J]. Proceedings of the National Academy of Science, USA, 2010, 107：8689-8694.
[18] Elango N, Yi SV. DNA methylation and structural and functional bimodality of vertebrate promoters[J]. Molecular Biology Evolution, 2008, 25：1602-1608.
[19] Shimizu TS, Takahashi K, Tomita M. CpG distribution patterns in methylated and non-methylated species[J]. Gene, 1997, 205：103-107.
[20] Glastad KM, Hunt BG, Yi SV, et al. DNA methylation in insects：on the brink of the epigenomic era[J]. Insect Molecular Biology, 2011, 20（5）：553-565.
[21] Elango N, Hunt BG, Goodisman MAD, et al. DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera[J], Proceedings of the National Academy of Sciences, USA, 2009, 106：11206-11211.
[22] Lyko F, Foret S, Kucharski R, et al. The honey bee epigenomes：differential methylation of brain DNA in queens and workers[J]. PLoS Biology, 2010, 8：e1000506.
[23] Sarda S, Zeng J, Hunt BG, et al. The evolution of invertebrate gene body methylation[J]. Molecular Biology and Evolution, 2012, 29：1907-1916.
[24] Hunt BG, Brisson JA, Yi SV, et al. Functional conservation of DNA methylation in the pea aphid and the honeybee[J]. Genome Biology and Evolution, 2010, 2：719-728.
[25] Kucharski R, Maleszka J, Foret S, et al. Nutritional control of reproductive status in honeybees via DNA methylation[J]. Science, 2008, 319：1827-1830.
[26] Herb BR, Wolschin F, Hansen KD, et al. Reversible switching between epigenetic states in honeybee behavioral subcastes[J]. Nature Neuroscience, 2012, 15： 1371-1373.
[27] Weiner SA, Galbraith DA, Adams DC, et al. A survey of DNA methylation across social insect species, life stages, and castes reveals abundant and caste-associated methylation in a primitively social wasp[J]. Naturwissenschaften, 2013, 100：795-799.
[28] Bonasio R, Li Q, Lian J, et al. Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator[J]. Current Biology, 2012, 22：1755-1764.
[29] Terrapon N, Li C, Robertson HM, et al, Molecular traces of alternative social organization in a termite genome[J]. Nature Communications, 2014, 5：3636.
[30] Schübeler D. Epigenetic islands in a genetic ocean[J]. Science, 2012, 338：756-757.
[31] Rajasethupathy P, Antonov I, Sheridan R, et al. A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity[J]. Cell, 2012, 149：693-707.
[32] Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters[J]. Nature, 2010, 466：253-257.
[33] Roberts SB, Gavery MR. Is there a relationship between DNA methylation and phenotypic plasticity in invertebrates?[J]. Fronties in Physiology, 2012, 2：116.
[34] Riviere G. Epigenetic features in the oyster Crassostrea gigas suggestive of functionally relevant promoter DNA methylation in invertebrates[J]. Fronties in Physiology, 2014, 5：129.
[35] Flores K, Wolschin F, Corneveaux JJ, et al. Genome-wide association between DNA methylation and alternative splicing in an invertebrate[J]. BMC Genomics, 2012, 13：480.
[36] Maunakea AK, Chepelev I, Cui K, et al. Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition[J]. Cell Research, 2013, 11：1-14.
[37] Zwier MV, Verhulst EC, Zwahlen RD, et al. DNA methylation plays a crucial role during early Nasonia development[J]. Insect Molecular Biology, 2012, 21：129-138.
[38] Jouaux A, Heude-Berthelin C, Sourdaine P, et al. Gametogenic stages in triploid oysters Crassostrea gigas：irregular locking of gonial proliferation and subsequent reproductive effort[J]. Journal of Experimental Marine Biology and Ecology, 2010, 395：162-170.
[39] Riviere G, Wu G, Fellous A, et al. DNA methylation is crucial for the early development in the Oyster Crassostrea gigas[J]. Marine Biotechnology, 2013, 15：739-753.
[40] Park J, Peng Z, Zeng J, et al. Comparative analyses of DNA methylation and sequence evolution using Nasonia genomes[J]. Molecular Biology and Evolution, 2011, 28：3345-3354.
[41] Marais G. Biased gene conversion：implications for genome and sex evolution[J]. Trends in Genetics, 2003, 19： 330-338.
[42] Riggs AD. X inactivation, differentiation, and DNA methylation[J]. Cytogenetics and Cell Genetics, 1975, 14：9-25.
[43] Holliday R, Pugh JE. DNA modification mechanisms and gene activity during development[J]. Science, 1975, 187：226-232.
[44] Lister R, Pelizzola M, Dowen RH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences[J]. Nature, 2009, 462：315-322.
[45] Margueron R, Reinberg D. Chromatin structure and the inheritance of epigenetic information[J]. Nature Reviews Genetics, 2010, 11： 285-296.
[46] Hata K, Okano M, Lei H, et al. Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice[J]. Development, 2002, 129： 1983-1993.