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MECP2, a gene associated with Rett syndrome in humans, shows conserved coding regions, independent Alu insertions, and a novel transcript across primate evolution.

Viana MC, Menezes AN, Moreira MA, Pissinatti A, Seuánez HN - BMC Genet. (2015)

Bottom Line: Conversely, we found 48 sites under negative selection in different regions, 23 of which were consistently found by three different algorithms.RNAseq data in the neotropical primate Callimico goeldii revealed a novel transcript consisting of a noncontinuous region of the human-homologous intron 2 in this species; this transcript accounted for two putative polypeptides.Moreover, identification of novel MECP2 transcripts in Callimico suggests that part of a homologous human intronic region might be expressed, and that the potential open reading frame in this region might be a subject of interest in RTT patients who carry an apparently normal MECP2 sequence.

View Article: PubMed Central - PubMed

Affiliation: Genetics Division, Instituto Nacional de Câncer, Rua André Cavalcanti 37, 4th floor, 20231-050, Rio de Janeiro, RJ, Brazil. mcarolviana@gmail.com.

ABSTRACT

Background: The methyl-CpG Binding Protein two gene (MECP2) encodes a multifunctional protein comprising two isoforms involved in nuclear organization and regulation of splicing and mRNA template activity. This gene is normally expressed in all tissues, with a higher expression level in the brain during neuronal maturation. Loss of MECP2 function is the primary cause of Rett syndrome (RTT) in humans, a dominant, X-linked disorder dramatically affecting neural and motor development.

Results: We investigated the molecular evolution of MECP2 in several primate taxa including 36 species in 16 genera of neotropical (platyrrhine) primates. The coding region of the MECP2_e2 isoform showed a high level of evolutionary conservation among humans and other primates, with amino acid substitutions in 14 codons and one in-frame insertion of a single serine codon, between codons 357 and 358, in Ateles paniscus. Most substitutions occurred in noncritical regions of MECP2 and the majority of the algorithms used for analyzing selection did not provide evidence of positive selection. Conversely, we found 48 sites under negative selection in different regions, 23 of which were consistently found by three different algorithms. Similar to an inverted Alu insert found previously in a lesser ape at a parallel location, one Alu insertion of approximately 300 bp in Cebus and Sapajus was found in intron 3. Phylogenetic reconstruction of the intron 3 data provided a topology that was coincident with the consensus arrangement of the primate taxa. RNAseq data in the neotropical primate Callimico goeldii revealed a novel transcript consisting of a noncontinuous region of the human-homologous intron 2 in this species; this transcript accounted for two putative polypeptides.

Conclusions: Despite the remarkable evolutionary conservation of MECP2, one in-frame codon insertion was observed in A. paniscus, and one region of intron 3 was affected by a trans-specific Alu retrotransposition in two neotropical primate genera. Moreover, identification of novel MECP2 transcripts in Callimico suggests that part of a homologous human intronic region might be expressed, and that the potential open reading frame in this region might be a subject of interest in RTT patients who carry an apparently normal MECP2 sequence.

No MeSH data available.


Related in: MedlinePlus

Maximum likelihood topology based on MECP2 intron 3. Values above the nodes indicate the aLRT support estimates. Values below nodes indicate the posterior probabilities of the Bayesian tree and bootstrap estimates. Red circles indicate Alu insertions
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Fig3: Maximum likelihood topology based on MECP2 intron 3. Values above the nodes indicate the aLRT support estimates. Values below nodes indicate the posterior probabilities of the Bayesian tree and bootstrap estimates. Red circles indicate Alu insertions

Mentions: ML and Bayesian analyses of intron 3 generated very similar topologies to the proposed primate phylogeny [33], with three evolutionary lineages corresponding to the main families of the neotropical primates (Cebidae, Atelidae and Pitheciidae). The ML topology (Fig. 3), however, showed a different arrangement within the Cebidae, viz. (((Sapajus,Cebus)Callitrichini)(Aotus,Saimiri)), and within the Pitheciidae ((Pithecia,Chiropotes)Cacajao), although these discordant arrangements were supported by low bootstrap and aLRT estimates. The lack of a consensus arrangement for the Cebidae primates probably results from the short time span between their origin and the radiation of their derived lineages [33, 40, 41].Fig. 3


MECP2, a gene associated with Rett syndrome in humans, shows conserved coding regions, independent Alu insertions, and a novel transcript across primate evolution.

Viana MC, Menezes AN, Moreira MA, Pissinatti A, Seuánez HN - BMC Genet. (2015)

Maximum likelihood topology based on MECP2 intron 3. Values above the nodes indicate the aLRT support estimates. Values below nodes indicate the posterior probabilities of the Bayesian tree and bootstrap estimates. Red circles indicate Alu insertions
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4493987&req=5

Fig3: Maximum likelihood topology based on MECP2 intron 3. Values above the nodes indicate the aLRT support estimates. Values below nodes indicate the posterior probabilities of the Bayesian tree and bootstrap estimates. Red circles indicate Alu insertions
Mentions: ML and Bayesian analyses of intron 3 generated very similar topologies to the proposed primate phylogeny [33], with three evolutionary lineages corresponding to the main families of the neotropical primates (Cebidae, Atelidae and Pitheciidae). The ML topology (Fig. 3), however, showed a different arrangement within the Cebidae, viz. (((Sapajus,Cebus)Callitrichini)(Aotus,Saimiri)), and within the Pitheciidae ((Pithecia,Chiropotes)Cacajao), although these discordant arrangements were supported by low bootstrap and aLRT estimates. The lack of a consensus arrangement for the Cebidae primates probably results from the short time span between their origin and the radiation of their derived lineages [33, 40, 41].Fig. 3

Bottom Line: Conversely, we found 48 sites under negative selection in different regions, 23 of which were consistently found by three different algorithms.RNAseq data in the neotropical primate Callimico goeldii revealed a novel transcript consisting of a noncontinuous region of the human-homologous intron 2 in this species; this transcript accounted for two putative polypeptides.Moreover, identification of novel MECP2 transcripts in Callimico suggests that part of a homologous human intronic region might be expressed, and that the potential open reading frame in this region might be a subject of interest in RTT patients who carry an apparently normal MECP2 sequence.

View Article: PubMed Central - PubMed

Affiliation: Genetics Division, Instituto Nacional de Câncer, Rua André Cavalcanti 37, 4th floor, 20231-050, Rio de Janeiro, RJ, Brazil. mcarolviana@gmail.com.

ABSTRACT

Background: The methyl-CpG Binding Protein two gene (MECP2) encodes a multifunctional protein comprising two isoforms involved in nuclear organization and regulation of splicing and mRNA template activity. This gene is normally expressed in all tissues, with a higher expression level in the brain during neuronal maturation. Loss of MECP2 function is the primary cause of Rett syndrome (RTT) in humans, a dominant, X-linked disorder dramatically affecting neural and motor development.

Results: We investigated the molecular evolution of MECP2 in several primate taxa including 36 species in 16 genera of neotropical (platyrrhine) primates. The coding region of the MECP2_e2 isoform showed a high level of evolutionary conservation among humans and other primates, with amino acid substitutions in 14 codons and one in-frame insertion of a single serine codon, between codons 357 and 358, in Ateles paniscus. Most substitutions occurred in noncritical regions of MECP2 and the majority of the algorithms used for analyzing selection did not provide evidence of positive selection. Conversely, we found 48 sites under negative selection in different regions, 23 of which were consistently found by three different algorithms. Similar to an inverted Alu insert found previously in a lesser ape at a parallel location, one Alu insertion of approximately 300 bp in Cebus and Sapajus was found in intron 3. Phylogenetic reconstruction of the intron 3 data provided a topology that was coincident with the consensus arrangement of the primate taxa. RNAseq data in the neotropical primate Callimico goeldii revealed a novel transcript consisting of a noncontinuous region of the human-homologous intron 2 in this species; this transcript accounted for two putative polypeptides.

Conclusions: Despite the remarkable evolutionary conservation of MECP2, one in-frame codon insertion was observed in A. paniscus, and one region of intron 3 was affected by a trans-specific Alu retrotransposition in two neotropical primate genera. Moreover, identification of novel MECP2 transcripts in Callimico suggests that part of a homologous human intronic region might be expressed, and that the potential open reading frame in this region might be a subject of interest in RTT patients who carry an apparently normal MECP2 sequence.

No MeSH data available.


Related in: MedlinePlus