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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.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.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

RT-PCR products corresponding to novel transcripts in Callimico goeldii. a RT-PCR products following amplification of a 525 bp contig resulted in two fragments of 403 and 279 bp. b Transcript composition (E1 = exon 1; E2 = exon 2). Arrows indicate the primer positions. The new alternative exon, homologous to part of human intron 2, is shown in black. c Schematic representation of the novel exon and the alternative splicing resulting in the two new transcripts. Start and stop codons indicate three likely open reading frames. IN1 = intron 1; IN2 = intron 2; IN3 = intron 3; E1 = exon 1; E2 = exon 2; E3 = exon 3
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Fig4: RT-PCR products corresponding to novel transcripts in Callimico goeldii. a RT-PCR products following amplification of a 525 bp contig resulted in two fragments of 403 and 279 bp. b Transcript composition (E1 = exon 1; E2 = exon 2). Arrows indicate the primer positions. The new alternative exon, homologous to part of human intron 2, is shown in black. c Schematic representation of the novel exon and the alternative splicing resulting in the two new transcripts. Start and stop codons indicate three likely open reading frames. IN1 = intron 1; IN2 = intron 2; IN3 = intron 3; E1 = exon 1; E2 = exon 2; E3 = exon 3

Mentions: RT-PCR confirmed the presence of a third novel transcript of 525 nt. From this, there were two amplified products, one fragment of the expected size (403 bp) and an additional 279 bp product that was C. goeldii–specific. The larger product matched the 525 bp contig while the smaller one matched exon 1 and the noncontiguous fragment of intron 2 (Fig. 4).Fig. 4


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)

RT-PCR products corresponding to novel transcripts in Callimico goeldii. a RT-PCR products following amplification of a 525 bp contig resulted in two fragments of 403 and 279 bp. b Transcript composition (E1 = exon 1; E2 = exon 2). Arrows indicate the primer positions. The new alternative exon, homologous to part of human intron 2, is shown in black. c Schematic representation of the novel exon and the alternative splicing resulting in the two new transcripts. Start and stop codons indicate three likely open reading frames. IN1 = intron 1; IN2 = intron 2; IN3 = intron 3; E1 = exon 1; E2 = exon 2; E3 = exon 3
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: RT-PCR products corresponding to novel transcripts in Callimico goeldii. a RT-PCR products following amplification of a 525 bp contig resulted in two fragments of 403 and 279 bp. b Transcript composition (E1 = exon 1; E2 = exon 2). Arrows indicate the primer positions. The new alternative exon, homologous to part of human intron 2, is shown in black. c Schematic representation of the novel exon and the alternative splicing resulting in the two new transcripts. Start and stop codons indicate three likely open reading frames. IN1 = intron 1; IN2 = intron 2; IN3 = intron 3; E1 = exon 1; E2 = exon 2; E3 = exon 3
Mentions: RT-PCR confirmed the presence of a third novel transcript of 525 nt. From this, there were two amplified products, one fragment of the expected size (403 bp) and an additional 279 bp product that was C. goeldii–specific. The larger product matched the 525 bp contig while the smaller one matched exon 1 and the noncontiguous fragment of intron 2 (Fig. 4).Fig. 4

Bottom Line: 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.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