Epigenetics in insects

Epigenetics in insects is the role that epigenetics (hertiable characteristics that do not involve changes in DNA sequence) plays in insects.

Epigenetic mechanisms are regulatory mechanisms, which change expression levels of genes. Several mechanisms are considered epigenetic, including DNA methylation, histone modifications and non-coding RNAs. Epigenetic mechanisms play a role in processes like development, learning and memory formation, aging, diseases, cell differentiation and genome defence.

DNA methylation

DNA methylation is an epigenetic mechanism. It is a chemical modification of the DNA where a methyl group is attached to cytosine. This modification is set by DNA methyltransferases (Dnmts). There are three known types of DNA methyltransferases in mammals. Those DNA methyltransferases are present in insects as well, although it varies between different species which specific Dnmt types are present. It still is a matter of discussion what the specific role of DNA methylation in insects is, as some insects such as Drosophila melanogaster just have traces of DNA methylation in their genome and in general insect genomes are much less methylated compared to mammalian genomes (0.034% vs. 7.6% in Mus musculus).^[1] In a comparison of different insect species and their respective methylation levels, there was a clear relationship between cell turn over and DNA methylation, but not between genome size or the number of repetitive sequences and DNA methylation.

In honeybees

 

Honeybees (Apis mellifera) marked after hatching with colour

Honeybees (Apis mellifera) possess homologs for all three DNA methyltransferases known in mammals.^[2][3] But unlike mammals they possess two DNA methyltransferases 1 and just one DNA methyltransferase 3. DNA methylation predominantly occurs in coding regions in honeybees.^[4] The function of the DNA methylation in honey bees is to regulate gene alternative splicing ^[5]

Development

DNA methylation plays a major role in honeybee caste and subcaste development. In honeybees there are two different castes which are workers and queens. They are genetically the same, but show morphological, physiological and behavioral differences. Among the worker caste there are two subcastes, which are nurses and foragers. Which subcaste a worker bee belongs to depends on its age. The DNA methylation pattern in queens and workers,^[4][6][7] and between nurses and foragers is different.^[8][9] DNA methylation also increases in worker larvae with age, especially in coding regions and CpG islands. If DNA methyltransferase 3 is silenced in honeybee larvae they develop into queens, whereas they otherwise would develop into workers.^[10]

Associative learning

Using the DNA methyltransferase inhibitor zebularine, the role of DNA methyltransferases during learning and memory formation has been studied. If DNA methyltransferases are inhibited during an associative learning paradigm, in which the bee is trained to associate an odour with a food reward, the odour specific associative long-term memory of bees is impaired,^[11] as well as their extinction memory.^[12] Short-term memory formation and acquisition are not affected by DNA methyltransferase inhibition.

In fruitflies

The fruitfly D. melanogaster possess just one DNA methyltransferase, which is Dnmt 2-like. Dnmt 2 is not known to methylate DNA in mammals. In Drosophila however a knock down of Dnmt 2-like protein is sufficient to deplete DNA methylation completely and an overexpression of Dnmt 2 causes hypermethylation of the DNA.^[13] However, lines deficient for Dnmt 2 retain genomic methylation, implying the presence of a novel methyltransferase.^[14]

References

1. Capuano F, Mülleder M, Kok R, Blom HJ, Ralser M (April 2014). "Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species". Analytical Chemistry. 86 (8): 3697–3702. doi:10.1021/ac500447w. PMC 4006885. PMID 24640988.
2. Wang Y, Jorda M, Jones PL, Maleszka R, Ling X, Robertson HM, Mizzen CA, Peinado MA, Robinson GE (October 2006). "Functional CpG methylation system in a social insect". Science. 314 (5799): 645–7. Bibcode:2006Sci...314..645W. doi:10.1126/science.1135213. PMID 17068262. S2CID 31709665.
3. Matsui T, Yamamoto T, Wyder S, Zdobnov EM, Kadowaki T (January 2009). "Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates". BMC Genomics. 10: 17. doi:10.1186/1471-2164-10-17. PMC 2656531. PMID 19138430.
4. Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, Maleszka R (November 2010). "The honey bee epigenomes: differential methylation of brain DNA in queens and workers". PLOS Biology. 8 (11): e1000506. doi:10.1371/journal.pbio.1000506. PMC 2970541. PMID 21072239.
5. Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, et al. (July 2013). "RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee". Proceedings of the National Academy of Sciences of the United States of America. 110 (31): 12750–12755. Bibcode:2013PNAS..11012750L. doi:10.1073/pnas.1310735110. PMC 3732956. PMID 23852726.
6. Shi YY, Yan WY, Huang ZY, Wang ZL, Wu XB, Zeng ZJ (February 2013). "Genomewide analysis indicates that queen larvae have lower methylation levels in the honey bee (Apis mellifera)". Die Naturwissenschaften. 100 (2): 193–7. Bibcode:2013NW....100..193S. doi:10.1007/s00114-012-1004-3. PMID 23238637. S2CID 15874241.
7. Shi YY, Huang ZY, Zeng ZJ, Wang ZL, Wu XB, Yan WY (April 2011). "Diet and cell size both affect queen-worker differentiation through DNA methylation in honey bees (Apis mellifera, Apidae)". PLOS ONE. 6 (4): e18808. Bibcode:2011PLoSO...618808S. doi:10.1371/journal.pone.0018808. PMC 3082534. PMID 21541319.
8. Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP (October 2012). "Reversible switching between epigenetic states in honeybee behavioral subcastes". Nature Neuroscience. 15 (10): 1371–3. doi:10.1038/nn.3218. PMC 3518384. PMID 22983211.
9. Lockett GA, Kucharski R, Maleszka R (March 2012). "DNA methylation changes elicited by social stimuli in the brains of worker honey bees". Genes, Brain and Behavior. 11 (2): 235–42. doi:10.1111/j.1601-183X.2011.00751.x. PMID 22098706. S2CID 20046768.
10. Kucharski R, Maleszka J, Foret S, Maleszka R (March 2008). "Nutritional control of reproductive status in honeybees via DNA methylation". Science. 319 (5871). New York, N.Y.: 1827–30. Bibcode:2008Sci...319.1827K. doi:10.1126/science.1153069. PMID 18339900. S2CID 955740.
11. Biergans SD, Jones JC, Treiber N, Galizia CG, Szyszka P (2012). "DNA methylation mediates the discriminatory power of associative long-term memory in honeybees". PLOS ONE. 7 (6): e39349. Bibcode:2012PLoSO...739349B. doi:10.1371/journal.pone.0039349. PMC 3377632. PMID 22724000.
12. Lockett GA, Helliwell P, Maleszka R (August 2010). "Involvement of DNA methylation in memory processing in the honey bee". NeuroReport. 21 (12): 812–6. doi:10.1097/WNR.0b013e32833ce5be. PMID 20571459. S2CID 13281473.
13. Kunert N, Marhold J, Stanke J, Stach D, Lyko F (November 2003). "A Dnmt2-like protein mediates DNA methylation in Drosophila". Development. 130 (21): 5083–90. doi:10.1242/dev.00716. PMID 12944428. S2CID 32950308.
14. Takayama S, Dhahbi J, Roberts A, Mao G, Heo SJ, Pachter L, et al. (May 2014). "Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity". Genome Research. 24 (5). Cold Spring Harbor Laboratory: 821–830. doi:10.1101/gr.162412.113. PMC 4009611. PMID 24558263.