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Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus.

Tchitchek N, Jacquelin B, Wincker P, Dossat C, Silva CD, Weissenbach J, Blancher A, Müller-Trutwin M, Benecke A - BMC Genomics (2012)

Bottom Line: For 506 transcripts, sequences were quasi-complete.In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes.Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

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Affiliation: Institut des Hautes Études Scientifiques-Centre National de la Recherche Scientifique, Bures-sur-Yvette, France.

ABSTRACT

Background: African Green Monkeys (AGM) are amongst the most frequently used nonhuman primate models in clinical and biomedical research, nevertheless only few genomic resources exist for this species. Such information would be essential for the development of dedicated new generation technologies in fundamental and pre-clinical research using this model, and would deliver new insights into primate evolution.

Results: We have exhaustively sequenced an Expression Sequence Tag (EST) library made from a pool of Peripheral Blood Mononuclear Cells from sixteen Chlorocebus sabaeus monkeys. Twelve of them were infected with the Simian Immunodeficiency Virus. The mononuclear cells were or not stimulated in vitro with Concanavalin A, with lipopolysacharrides, or through mixed lymphocyte reaction in order to generate a representative and broad library of expressed sequences in immune cells. We report here 37,787 sequences, which were assembled into 14,410 contigs representing an estimated 12% of the C. sabaeus transcriptome. Using data from primate genome databases, 9,029 assembled sequences from C. sabaeus could be annotated. Sequences have been systematically aligned with ten cDNA references of primate species including Homo sapiens, Pan troglodytes, and Macaca mulatta to identify ortholog transcripts. For 506 transcripts, sequences were quasi-complete. In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes.

Conclusions: The EST library we provide here will prove useful in gene annotation efforts for future sequencing of the African Green Monkey genomes. Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

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Related in: MedlinePlus

Alignment details for the CXCL10 gene. Alignment details for the C-X-C motif chemokine 10 gene of the M. mulatta species (Ensembl ID: ENSMMUT00000029391). Assembled ESTs have been aligned at different positions of the gene: (1) Contig2229.
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Figure 3: Alignment details for the CXCL10 gene. Alignment details for the C-X-C motif chemokine 10 gene of the M. mulatta species (Ensembl ID: ENSMMUT00000029391). Assembled ESTs have been aligned at different positions of the gene: (1) Contig2229.

Mentions: The M. mulatta species is the closest primate species to the C. sabaeus for which significant genomic information is available. In order to gain additional information about the transcript fragments that we provide, we annotated them with the particular section positions of the messenger RNAs available for the M. mulatta species. We specified for each EST of the assembled library the positions of the 5’-untranslated region (5’UTR), coding DNA sequence (CDS), and 3’-untranslated region (3’UTR) based on the M. mulatta cDNA reference annotations. Among the 14,410 assembled ESTs, 11,211 could be annotated: 6,244 ESTs with the 5’UTR, 9,657 ESTs with the CDS, and 5,313 ESTs with the 3’UTR. We report 506 M. mulatta transcripts that have been mapped to more than 90% by an EST (Additional file 2: Table S1). CXCL10 (Figure 3) and S100A4 (Additional file 3: Figure S2) are part of these transcripts and given as examples.


Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus.

Tchitchek N, Jacquelin B, Wincker P, Dossat C, Silva CD, Weissenbach J, Blancher A, Müller-Trutwin M, Benecke A - BMC Genomics (2012)

Alignment details for the CXCL10 gene. Alignment details for the C-X-C motif chemokine 10 gene of the M. mulatta species (Ensembl ID: ENSMMUT00000029391). Assembled ESTs have been aligned at different positions of the gene: (1) Contig2229.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3539953&req=5

Figure 3: Alignment details for the CXCL10 gene. Alignment details for the C-X-C motif chemokine 10 gene of the M. mulatta species (Ensembl ID: ENSMMUT00000029391). Assembled ESTs have been aligned at different positions of the gene: (1) Contig2229.
Mentions: The M. mulatta species is the closest primate species to the C. sabaeus for which significant genomic information is available. In order to gain additional information about the transcript fragments that we provide, we annotated them with the particular section positions of the messenger RNAs available for the M. mulatta species. We specified for each EST of the assembled library the positions of the 5’-untranslated region (5’UTR), coding DNA sequence (CDS), and 3’-untranslated region (3’UTR) based on the M. mulatta cDNA reference annotations. Among the 14,410 assembled ESTs, 11,211 could be annotated: 6,244 ESTs with the 5’UTR, 9,657 ESTs with the CDS, and 5,313 ESTs with the 3’UTR. We report 506 M. mulatta transcripts that have been mapped to more than 90% by an EST (Additional file 2: Table S1). CXCL10 (Figure 3) and S100A4 (Additional file 3: Figure S2) are part of these transcripts and given as examples.

Bottom Line: For 506 transcripts, sequences were quasi-complete.In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes.Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut des Hautes Études Scientifiques-Centre National de la Recherche Scientifique, Bures-sur-Yvette, France.

ABSTRACT

Background: African Green Monkeys (AGM) are amongst the most frequently used nonhuman primate models in clinical and biomedical research, nevertheless only few genomic resources exist for this species. Such information would be essential for the development of dedicated new generation technologies in fundamental and pre-clinical research using this model, and would deliver new insights into primate evolution.

Results: We have exhaustively sequenced an Expression Sequence Tag (EST) library made from a pool of Peripheral Blood Mononuclear Cells from sixteen Chlorocebus sabaeus monkeys. Twelve of them were infected with the Simian Immunodeficiency Virus. The mononuclear cells were or not stimulated in vitro with Concanavalin A, with lipopolysacharrides, or through mixed lymphocyte reaction in order to generate a representative and broad library of expressed sequences in immune cells. We report here 37,787 sequences, which were assembled into 14,410 contigs representing an estimated 12% of the C. sabaeus transcriptome. Using data from primate genome databases, 9,029 assembled sequences from C. sabaeus could be annotated. Sequences have been systematically aligned with ten cDNA references of primate species including Homo sapiens, Pan troglodytes, and Macaca mulatta to identify ortholog transcripts. For 506 transcripts, sequences were quasi-complete. In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes.

Conclusions: The EST library we provide here will prove useful in gene annotation efforts for future sequencing of the African Green Monkey genomes. Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

Show MeSH
Related in: MedlinePlus