Lawi cichlid was located to possess copies of DNA methyltransferases (DNMTs
Lawi cichlid was located to have copies of DNA methyltransferases (DNMTs) and ten-eleven translocation methylcytosine dioxygenases (TETs), the `readers’ and `erasers’ of DNA methylation respectively (Supplementary Fig. 4a-c). Like that of mammals and also other teleost fish, the genomes of Lake Malawi cichlids have higher levels of DNA methylation genome-wide NTR1 Agonist Species within the CG dinucleotide sequence context, consistently across all samples in each tissues analysed (Fig. 1d and Supplementary Fig. 2a-c). Gene bodies generallyshow higher methylation levels than the genome-wide average, when the majority of promoter regions are unmethylated (Fig. 1d). CpG islands (CGIs; i.e., CpG-rich regions–abundant in Lake Malawi cichlid genomes; Supplementary Fig. 5a-i, Supplementary Notes and Strategies) are just about completely devoid of methylation in promoters, even though `orphan’ CGIs, μ Opioid Receptor/MOR Inhibitor custom synthesis residing outside promoters, are largely very methylated (Fig. 1d and Supplementary Fig. 5f, g). Even though 70 of mammalian promoters include CGIs41, only 15-20 of promoters in Lake Malawi cichlids harbour CGIs (Supplementary Fig. 5d), related to frog and zebrafish genomes41. Notably, orphan CGIs, which may have significant cis-regulatory functions42, compose up to 80 of all predicted CGIs in Lake Malawi cichlids (Supplementary Fig. 5e). Moreover, repetitive regions, also as transposable components, are especially enriched for cytosine methylation, suggesting aNATURE COMMUNICATIONS | (2021)12:5870 | doi/10.1038/s41467-021-26166-2 | www.nature.com/naturecommunicationsARTICLENATURE COMMUNICATIONS | doi/10.1038/s41467-021-26166-methylation-mediated silencing of their transcription (Fig. 1d, Supplementary Fig. 6a-d), related to that observed in zebrafish as well as other animals8,18. Interestingly, certain transposon families, for instance LINE I and Tc2-Mariner, a part of the DNA transposon family–the most abundant TE family predicted in Lake Malawi cichlid genome (Supplementary Fig. 6a, b, Supplementary Notes, and ref. 38)–have lately expanded significantly in the Mbuna genome (Supplementary Fig. 6c and refs. 38,43). Even though Tc2-Mar DNA transposons show the highest median methylation levels, LINE I elements have some of the lowest, but most variable, methylation levels of all transposon families, which correlates with their evolutionary recent expansion in the genome (Fig. 1d, e and Supplementary Fig. 6d, e). Finally, transcriptional activity in liver and muscle tissues of Lake Malawi cichlids was negatively correlated with methylation in promoter regions (Spearman’s correlation test, = -0.40, p 0.002), when getting weakly positively correlated with methylation in gene bodies ( = 0.1, p 0.002; Fig. 1e and Supplementary Fig. 7a-d and Supplementary Table two). This really is constant with earlier research highlighting high methylation levels in bodies of active genes in plants and animals, and high levels of methylation at promoters of weakly expressed genes in vertebrates8,24. We conclude that the methylomes of Lake Malawi cichlids share lots of regulatory functions, and possibly connected functions, with these of other vertebrates, which renders Lake Malawi cichlids a promising model system within this context. Methylome divergence in Lake Malawi cichlids. To assess the probable role of DNA methylation in phenotypic diversification, we then sought to quantify and characterise the variations in liver and muscle methylomes across the genomes of Lake Malawi haplochromine cichlids. In spite of overall really low sequence diverge.