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Novel primate-specific genes, RMEL 1, 2 and 3, with highly restricted expression in melanoma, assessed by new data mining tool.

Sousa JF, Torrieri R, Silva RR, Pereira CG, Valente V, Torrieri E, Peronni KC, Martins W, Muto N, Francisco G, Brohem CA, Carlotti CG, Maria-Engler SS, Chammas R, Espreafico EM - PLoS ONE (2010)

Bottom Line: We found 29 UniGene clusters of multiple ESTs with the potential to predict novel genes with melanoma-specific expression.Interestingly, we found correlations of RMEL2 and RMEL3 expression with improved patient outcome, suggesting tumor and/or metastasis suppressor functions for these genes.They are well conserved throughout primates, but not other genomes, and were predicted as having no coding potential, although primate-conserved and human-specific short ORFs could be found.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.

ABSTRACT
Melanoma is a highly aggressive and therapy resistant tumor for which the identification of specific markers and therapeutic targets is highly desirable. We describe here the development and use of a bioinformatic pipeline tool, made publicly available under the name of EST2TSE, for the in silico detection of candidate genes with tissue-specific expression. Using this tool we mined the human EST (Expressed Sequence Tag) database for sequences derived exclusively from melanoma. We found 29 UniGene clusters of multiple ESTs with the potential to predict novel genes with melanoma-specific expression. Using a diverse panel of human tissues and cell lines, we validated the expression of a subset of three previously uncharacterized genes (clusters Hs.295012, Hs.518391, and Hs.559350) to be highly restricted to melanoma/melanocytes and named them RMEL1, 2 and 3, respectively. Expression analysis in nevi, primary melanomas, and metastatic melanomas revealed RMEL1 as a novel melanocytic lineage-specific gene up-regulated during melanoma development. RMEL2 expression was restricted to melanoma tissues and glioblastoma. RMEL3 showed strong up-regulation in nevi and was lost in metastatic tumors. Interestingly, we found correlations of RMEL2 and RMEL3 expression with improved patient outcome, suggesting tumor and/or metastasis suppressor functions for these genes. The three genes are composed of multiple exons and map to 2q12.2, 1q25.3, and 5q11.2, respectively. They are well conserved throughout primates, but not other genomes, and were predicted as having no coding potential, although primate-conserved and human-specific short ORFs could be found. Hairpin RNA secondary structures were also predicted. Concluding, this work offers new melanoma-specific genes for future validation as prognostic markers or as targets for the development of therapeutic strategies to treat melanoma.

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Structural organization, phylogenetic conservation, and predicted products for RMEL2 (Hs.518391).(A) Genome context of the gene. The numbers indicate the intron and exon lengths in nucleotides. The region in blue represents the longest ORF found, spanning 294 bp and encoding 98 aa. (B) VISTA plot displaying the conservation of the gene in nine species. The upper and lower limits of the box representing each species correspond, respectively, to 100 and 50% of sequence identity. (C) Multiple alignment with ClustalW of the deduced amino acid sequences for the longest AUG-starting ORF of RMEL2 in several primate species (for all species, ORFs were deduced from putative transcribed sequences obtained by alignments of the human cDNA BC063324 against the genomic sequences). (D) Diagram showing an RNA secondary structure predicted by RNAz software. Rule indicates RNA length; pointed blue bar indicates a segment predicted to form the hairpin structure shown, and the number is the RNA-class probability (P) of the prediction, considered significant when greater than 0.5.
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pone-0013510-g005: Structural organization, phylogenetic conservation, and predicted products for RMEL2 (Hs.518391).(A) Genome context of the gene. The numbers indicate the intron and exon lengths in nucleotides. The region in blue represents the longest ORF found, spanning 294 bp and encoding 98 aa. (B) VISTA plot displaying the conservation of the gene in nine species. The upper and lower limits of the box representing each species correspond, respectively, to 100 and 50% of sequence identity. (C) Multiple alignment with ClustalW of the deduced amino acid sequences for the longest AUG-starting ORF of RMEL2 in several primate species (for all species, ORFs were deduced from putative transcribed sequences obtained by alignments of the human cDNA BC063324 against the genomic sequences). (D) Diagram showing an RNA secondary structure predicted by RNAz software. Rule indicates RNA length; pointed blue bar indicates a segment predicted to form the hairpin structure shown, and the number is the RNA-class probability (P) of the prediction, considered significant when greater than 0.5.

Mentions: The three validated genes are composed of multiple exons. RMEL1 (Figure 4A) spans over a region of 19,212 bp on chromosome 2q12.2 and includes six exons supported by EST data, four of which are constant and two alternatively spliced. Although the UniGene cluster of this gene is composed of 16 expressed sequences, 1 derived from polyadenylated mRNA (long cDNA) and 15 ESTs, the UCSC Genome Browser shows the same sequences as the UniGene cluster plus 4 ESTs, totalizing 20 expressed sequences, derived from four different melanoma libraries, mapping to this locus. RMEL2 spans 7,545 bp and is composed of three exons mapped to chromosome 1q25.3 with no evidence of alternative transcripts (Figure 5A). Also for this gene, the UCSC Genome Browser indicates the existence of additional expressed sequences (6 cDNAs and 11 ESTs) mapping to this locus in comparison to the UniGene cluster (12 ESTs). The third gene, RMEL3, maps to an extension of 138,365 bp on the chromosome region 5q11.2 and is organized in four exons separated by very large introns. There are only three ESTs representing this gene according to the UniGene and UCSC Genome Browser as well. Curiously, an intron-less gene annotated as ACTBL2 maps to the longest intron of RMEL3 (Figure 6A).


Novel primate-specific genes, RMEL 1, 2 and 3, with highly restricted expression in melanoma, assessed by new data mining tool.

Sousa JF, Torrieri R, Silva RR, Pereira CG, Valente V, Torrieri E, Peronni KC, Martins W, Muto N, Francisco G, Brohem CA, Carlotti CG, Maria-Engler SS, Chammas R, Espreafico EM - PLoS ONE (2010)

Structural organization, phylogenetic conservation, and predicted products for RMEL2 (Hs.518391).(A) Genome context of the gene. The numbers indicate the intron and exon lengths in nucleotides. The region in blue represents the longest ORF found, spanning 294 bp and encoding 98 aa. (B) VISTA plot displaying the conservation of the gene in nine species. The upper and lower limits of the box representing each species correspond, respectively, to 100 and 50% of sequence identity. (C) Multiple alignment with ClustalW of the deduced amino acid sequences for the longest AUG-starting ORF of RMEL2 in several primate species (for all species, ORFs were deduced from putative transcribed sequences obtained by alignments of the human cDNA BC063324 against the genomic sequences). (D) Diagram showing an RNA secondary structure predicted by RNAz software. Rule indicates RNA length; pointed blue bar indicates a segment predicted to form the hairpin structure shown, and the number is the RNA-class probability (P) of the prediction, considered significant when greater than 0.5.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2958148&req=5

pone-0013510-g005: Structural organization, phylogenetic conservation, and predicted products for RMEL2 (Hs.518391).(A) Genome context of the gene. The numbers indicate the intron and exon lengths in nucleotides. The region in blue represents the longest ORF found, spanning 294 bp and encoding 98 aa. (B) VISTA plot displaying the conservation of the gene in nine species. The upper and lower limits of the box representing each species correspond, respectively, to 100 and 50% of sequence identity. (C) Multiple alignment with ClustalW of the deduced amino acid sequences for the longest AUG-starting ORF of RMEL2 in several primate species (for all species, ORFs were deduced from putative transcribed sequences obtained by alignments of the human cDNA BC063324 against the genomic sequences). (D) Diagram showing an RNA secondary structure predicted by RNAz software. Rule indicates RNA length; pointed blue bar indicates a segment predicted to form the hairpin structure shown, and the number is the RNA-class probability (P) of the prediction, considered significant when greater than 0.5.
Mentions: The three validated genes are composed of multiple exons. RMEL1 (Figure 4A) spans over a region of 19,212 bp on chromosome 2q12.2 and includes six exons supported by EST data, four of which are constant and two alternatively spliced. Although the UniGene cluster of this gene is composed of 16 expressed sequences, 1 derived from polyadenylated mRNA (long cDNA) and 15 ESTs, the UCSC Genome Browser shows the same sequences as the UniGene cluster plus 4 ESTs, totalizing 20 expressed sequences, derived from four different melanoma libraries, mapping to this locus. RMEL2 spans 7,545 bp and is composed of three exons mapped to chromosome 1q25.3 with no evidence of alternative transcripts (Figure 5A). Also for this gene, the UCSC Genome Browser indicates the existence of additional expressed sequences (6 cDNAs and 11 ESTs) mapping to this locus in comparison to the UniGene cluster (12 ESTs). The third gene, RMEL3, maps to an extension of 138,365 bp on the chromosome region 5q11.2 and is organized in four exons separated by very large introns. There are only three ESTs representing this gene according to the UniGene and UCSC Genome Browser as well. Curiously, an intron-less gene annotated as ACTBL2 maps to the longest intron of RMEL3 (Figure 6A).

Bottom Line: We found 29 UniGene clusters of multiple ESTs with the potential to predict novel genes with melanoma-specific expression.Interestingly, we found correlations of RMEL2 and RMEL3 expression with improved patient outcome, suggesting tumor and/or metastasis suppressor functions for these genes.They are well conserved throughout primates, but not other genomes, and were predicted as having no coding potential, although primate-conserved and human-specific short ORFs could be found.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.

ABSTRACT
Melanoma is a highly aggressive and therapy resistant tumor for which the identification of specific markers and therapeutic targets is highly desirable. We describe here the development and use of a bioinformatic pipeline tool, made publicly available under the name of EST2TSE, for the in silico detection of candidate genes with tissue-specific expression. Using this tool we mined the human EST (Expressed Sequence Tag) database for sequences derived exclusively from melanoma. We found 29 UniGene clusters of multiple ESTs with the potential to predict novel genes with melanoma-specific expression. Using a diverse panel of human tissues and cell lines, we validated the expression of a subset of three previously uncharacterized genes (clusters Hs.295012, Hs.518391, and Hs.559350) to be highly restricted to melanoma/melanocytes and named them RMEL1, 2 and 3, respectively. Expression analysis in nevi, primary melanomas, and metastatic melanomas revealed RMEL1 as a novel melanocytic lineage-specific gene up-regulated during melanoma development. RMEL2 expression was restricted to melanoma tissues and glioblastoma. RMEL3 showed strong up-regulation in nevi and was lost in metastatic tumors. Interestingly, we found correlations of RMEL2 and RMEL3 expression with improved patient outcome, suggesting tumor and/or metastasis suppressor functions for these genes. The three genes are composed of multiple exons and map to 2q12.2, 1q25.3, and 5q11.2, respectively. They are well conserved throughout primates, but not other genomes, and were predicted as having no coding potential, although primate-conserved and human-specific short ORFs could be found. Hairpin RNA secondary structures were also predicted. Concluding, this work offers new melanoma-specific genes for future validation as prognostic markers or as targets for the development of therapeutic strategies to treat melanoma.

Show MeSH
Related in: MedlinePlus