Ed, skipped exons exhibited substantially (P < 0.01) lower methylation level than randomly selected exons

Ed, skipped exons exhibited substantially (P < 0.01) lower methylation level than randomly selected exons (Figure 5A), and the presence of alternative splice site in 5 or 3 affected the methylation levels of upstream and downstream exons (Figure 5B ). The fact that these changes were relatively minor suggests that the link between DNA methylation and alternative splice site selection is either restricted to a subset of genes or that additional RNA-seq data is required to improve the detection of alternative isoforms. Nonetheless, these results and observations in other species [27, 28] support a connection between DNA methylation and the selection of alternative exons and splice sites. To further investigate the relationship between DNA methylation and alternative splicing, we manually analyzed the Camponotus homolog of lipophorin receptor 2 (Cflo_09743), a gene PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/21182226 involved in oogenesis [29], the Harpegnathos homolog of ciboulot (Hsal_08119), a gene involved in caste determination in termites [30], as well as the Harpegnathos endonuclease G gene (Hsal_05204). Within the initial two circumstances, inclusion of an option exon correlated with hypomethylation (Figure S6A ), as observed for the alk gene in honeybees [27] and CD45B in human cells [28], whereas exon inclusion in Hsal_05204 correlated with hypermethylation (Figure S6C). This suggests that, if DNA methylation changes have an effect on the inclusion prices of exons, they likely do so by way of recruitment of (or interference with) various variables in diverse genes. Monoallelic DNA methylation correlates with monoallelic gene expression In vertebrates, allele-specific DNA methylation (ASM) underpins vital epigenetic phenomena which include X chromosome inactivation [31] and parental imprinting [32], and ASM at gene promoters correlates inversely with allele-specific expression [33]. To our knowledge, this aspect of DNA methylation has not been investigated in invertebrates. Employing single nucleotide polymorphisms (SNPs), we assigned each BS-seq study to one of twoHHMI Author Manuscript HHMI Author Manuscript HHMI Author ManuscriptCurr Biol. Author manuscript; readily available in PMC 2013 April 09.Bonasio et al.Pagealleles in every single sample and we detected patches of ASM in all samples analyzed (Table S6), even though only regions with informative A or G SNPs might be interrogated. Some cases of ASM have been caste-specific; by way of example, in Camponotus, an ASM area was methylated on allele #1 in non-reproductives and allele #2 in reproductive folks (Figure 6A). This area mapped to Cflo_11155, a conserved gene involved in reproduction and gamete generation in C. elegans and preferentially expressed in Drosophila ovaries. Among the regions displaying ASM in Harpegnathos, we discovered 1 that was devoid of methylation in the embryos but acquired ASM within the adults (Figure 6B). In all samples, ASM related with allele-specific expression (Figure 6C ), supporting a partnership amongst DNA methylation and gene expression in these regions.HHMI Author Manuscript HHMI Author Manuscript HHMI Author ManuscriptDISCUSSIONWe generated the initial single-nucleotide resolution DNA methylomes in ants with all the goal of understanding the partnership in between this epigenetic mark plus the comprehensive Saroglitazar (Magnesium) web polyphenism observed in these social insects. Though genetic effects in ant caste determination have already been observed [34], they may be regarded maladaptive in monogynous and monandrous species (which include Camponotus and Harpegnathos) and thus unlikely to become r.