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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-015-0240-x) contains supplementary material, which is available to authorized users.

bmc genomic data

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