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. Author manuscript; available in PMC: 2021 Jul 18.
Published in final edited form as: Nat Ecol Evol. 2021 Jan 18;5(3):369–378. doi: 10.1038/s41559-020-01371-2

Fig. 4. Vertebrate origins of MECP2 and DNMT3A.

Fig. 4

a, Maximum likelihood phylogenetic tree of DNMT3 genes in animals. Nodal supports represent 100 bootstrap nonparametric replications. Schematic protein domain configurations shown for each clade. PWWP, Pro-Trp-Trp-Pro motif domain (PF00855). AAD ATRX, DNMT3, DNMT3L domain. MT, cytosine Methyltransferase domain (PF00145). CH, Calponin Homology domain (PF00307). Asterisk highlights arctic lamprey sequences. Broken domains indicate that the domain has large deletions in the given clade. b, Maximum likelihood phylogenetic tree of the Methyl-CpG Binding Domain family in animals. Nodal supports represent 100 bootstrap nonparametric replications. On the right, protein domain structure of each clade, as defined by Pfam domains. MBD, Methyl Binding Domain (PF01429). HhH-GPD, Thymine glycosylase (PF00730). MBDa, p55-binding region of MBD2/3 (PF16564). MBD_C, MBD2/3 C-terminal domain (PF14048). zf-CXXC, zinc finger (PF02008). CTD, MECP2 C-Terminal Domain. TRD, MECP2 Transcriptional Repression Domain. Asterisks highlight vertebrate sequences, percentages are shown for amino acid MBD identity between lamprey and human orthologues. c, Distribution of MECP2/MBD4 and DNMT3 genes across animal lineages. Absence of a dot indicates gene absence. Numbers indicate those species/lineages that have multiple copies of a given gene. Dnmt3c in rodents and dnmt3ba/bb.1/bb.2 are lineage-specific duplications of DNMT3B that have diverged in their function or domain architecture. “x3” indicates lineage-specific duplications. On the right, the phylogenetic relationships among animal lineages. d, Stepwise evolution of the MeCP2 and MBD4 protein domains in vertebrates, amphioxus, and non-chordates. NID stands for the N-CoR/SMRT interacting amino acids. e, Genome browser snapshot of amphioxus MBD4 locus. The longer isoform with the capacity to repair DNA has higher expression in embryonic samples, see further detail in Extended Data 10.