Patterning and regulatory associations of DNA methylation are mirrored by histone modifications in insects

Genome Biology and Evolution

Volumn 5, Issue 3, 2013, Pages 591-598

  Hunt, Brendan G ^a   Glastad, Karl M ^a   Yi, Soojin V ^a   Goodisman, Michael A D ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

DNA methylome; Epigenetics; Eusocial; Gene regulation; Solenopsis invicta

Indexed keywords

APIS MELLIFERA; DROSOPHILA MELANOGASTER; EUKARYOTA; HEXAPODA; SOLENOPSIS GEMINATA; SOLENOPSIS INVICTA;

EID: 84876520219     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt030     Document Type: Article

References (57)

1. Bell O, et al. 2010. Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing. Nat Struct Mol Biol. 17:894-900.
2. Bernstein BE, et al. 2005. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120:169-181.
3. Bintu L, et al. 2012. Nucleosomal elements that control the topography of the barrier to transcription. Cell 151:738-749.
4. Bird A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev. 16:6-21.
5. Bird AP, Wolffe AP. 1999. Methylation-induced repression-belts, braces, and chromatin. Cell 99:451-454.
6. Bonasio R, et al. 2012. Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol. 22:1755-1764.
7. Cedar H, Bergman Y. 2009. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 10:295-304.
8. Celniker SE, et al. 2009. Unlocking the secrets of the genome. Nature 459: 927-930.
9. Chintapalli VR, Wang J, Dow JAT. 2007. Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet. 39: 715-720.
10. Chodavarapu RK, et al. 2010. Relationship between nucleosome positioning and DNA methylation. Nature 466:388-392.
11. Choy JS, et al. 2010. DNA methylation increases nucleosome compaction and rigidity. J Am Chem Soc. 132:1782-1783.
12. Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symp Quant Biol. Advance access published December 18, 2012, doi:10.1101/ sqb.2012.77.014944.
13. Conesa A, et al. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
14. Dickman MJ, Kucharski R, Maleszka R, Hurd PJ. 2013. Extensive histone post-translationalmodification in honey bees. Insect BiochemMol Biol. 43:125-137.
15. Engström PG, Ho Sui SJ, Drivenes 1, Becker TS, Lenhard B. 2007. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res. 17:1898-1908.
16. Feng S, Jacobsen SE. 2011. Epigenetic modifications in plants: an evolutionary perspective. Curr Opin Plant Biol. 14:179-186.
17. Filion GJ, et al. 2010. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143:212-224.
18. Foret S, Kucharski R, Pittelkow Y, Lockett G, Maleszka R. 2009. Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes. BMC Genomics 10:472.
19. Glastad KM, Hunt BG, Yi SV, Goodisman MAD. 2011. DNA methylation in insects: on the brink of the epigenomic era. Insect Mol Biol. 20: 553-565.
20. Honeybee Genome Sequencing Consortium. 2006. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443:931-949.
21. Hoskins RA, et al. 2011. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 21:182-192.
22. Hunt BG, Brisson JA, Yi SV, Goodisman MAD. 2010. Functional conservation of DNA methylation in the pea aphid and the honeybee. Genome Biol Evol. 2:719-728.
23. Hunt BG, Ometto L, Keller L, Goodisman MAD. 2013. Evolution at two levels in fire ants: the relationship between patterns of gene expression and protein sequence evolution. Mol Biol Evol. 30:263-271.
24. Hunt BG, Glastad KM, Yi SV, GoodismanMAD. Forthcoming. The function of intragenic DNA methylation: insights from insect epigenomes. Integr Comp Biol.
25. Jjingo D, Conley AB, Yi SV, Lunyak VV, Jordan IK. 2012. On the presence and role of human gene-body DNA methylation. Oncotarget 3: 462-474.
26. Kharchenko PV, et al. 2011. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471:480-485.
27. Kolasinska-Zwierz P, et al. 2009. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet. 41:376-381.
28. Krueger F, Andrews SR. 2011. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571-1572.
29. Lafos M, et al. 2011. Dynamic regulation of H3K27 trimethylation during Arabidopsis differentiation. PLoS Genet. 7:e1002040.
30. Lee JY, Lee T-H. 2011. Effects of DNA methylation on the structure of nucleosomes. J Am Chem Soc. 134:173-175.
31. Lenhard B, Sandelin A, Carninci P. 2012. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet. 13:233-245.
32. Li G, Widom J. 2004. Nucleosomes facilitate their own invasion. Nat Struct Mol Biol. 11:763-769.
33. LorinczMC, Dickerson DR, SchmittM, GroudineM. 2004. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol. 11:1068-1075.
34. Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T. 2011. Epigenetics in alternative pre-mRNA splicing. Cell 144:16-26.
35. Luco RF, et al. 2010. Regulation of alternative splicing by histone modifications. Science 327:996-1000.
36. Lyko F, et al. 2010. The honey bee epigenomes: differentialmethylation of brain DNA in queens and workers. PLoS Biol. 8:e1000506.
37. Maunakea AK, et al. 2010. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466:253-257.
38. Meissner A, et al. 2008. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766-770.
39. Nanty L, et al. 2011. Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates. Genome Res. 21:1841-1850.
40. Negre N, et al. 2011. A cis-regulatory map of the Drosophila genome. Nature 471:527-531.
41. Ometto L, Shoemaker D, Ross KG, Keller L. 2011. Evolution of gene expression in fire ants: the effects of developmental stage, caste, and species. Mol Biol Evol. 28:1381-1392.
42. Ooi SKT, et al. 2007. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448:714-717.
43. Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y. 2011. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genet. 7:e1001316.
44. Sarda S, Zeng J, Hunt BG, Yi SV. 2012. The evolution of invertebrate gene body methylation. Mol Biol Evol. 29:1907-1916.
45. Schwartz S, Meshorer E, Ast G. 2009. Chromatin organization marks exon-intron structure. Nat Struct Mol Biol. 16:990-995.
46. Sexton T, et al. 2012. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148:458-472.
47. Shukla S, et al. 2011. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479:74-79.
48. Suganuma T, Workman JL. 2011. Signals and combinatorial functions of histone modifications. Annu Rev Biochem. 80:473-499.
49. Wang H, et al. 2012. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res. 22:1680-1688.
50. Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, Kriventseva EV. 2011. OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. Nucleic Acids Res. 39:D283-D288.
51. Wiegmann B, et al. 2009. Single-copy nuclear genes resolve the phylogeny of the holometabolous insects. BMC Biol. 7:34.
52. Woo YH, Li W-H. 2012. Evolutionary conservation of histone modifications in mammals. Mol Biol Evol. 29:1757-1767.
53. Wurm Y, et al. 2011. The genome of the fire ant Solenopsis invicta. Proc Natl Acad Sci U S A. 108:5679-5684.
54. Yin H, Sweeney S, Raha D, Snyder M, Lin H. 2011. A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster. PLoS Genet. 7:e1002380.
55. Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328: 916-919.
56. Zeng J, et al. 2012. Divergent whole-genomemethylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. Am J Hum Genet. 91:455-465.
57. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2007. Genomewide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet. 39:61-69.