Limits...
Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures.

Greco D, Volpicelli F, Di Lieto A, Leo D, Perrone-Capano C, Auvinen P, di Porzio U - PLoS ONE (2009)

Bottom Line: We integrate bioinformatics and functional genomics, together with developmental neurobiology.Moreover, we propose guidelines for the computational analysis of microarray gene expression data.Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland. dario.greco@helsinki.fi

ABSTRACT
In the mammalian central nervous system (CNS) an important contingent of dopaminergic neurons are localized in the substantia nigra and in the ventral tegmental area of the ventral midbrain. They constitute an anatomically and functionally heterogeneous group of cells involved in a variety of regulatory mechanisms, from locomotion to emotional/motivational behavior. Midbrain dopaminergic neuron (mDA) primary cultures represent a useful tool to study molecular mechanisms involved in their development and maintenance. Considerable information has been gathered on the mDA neurons development and maturation in vivo, as well as on the molecular features of mDA primary cultures. Here we investigated in detail the gene expression differences between the tissue of origin and ventral midbrain primary cultures enriched in mDA neurons, using microarray technique. We integrated the results based on different re-annotations of the microarray probes. By using knowledge-based gene network techniques and promoter sequence analysis, we also uncovered mechanisms that might regulate the expression of CNS genes involved in the definition of the identity of specific cell types in the ventral midbrain. We integrate bioinformatics and functional genomics, together with developmental neurobiology. Moreover, we propose guidelines for the computational analysis of microarray gene expression data. Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

Show MeSH
Knowledge-based gene network of the MesPC-specific genes.The nodes represent the genes. In BLUE, the MesPC-upregulated genes; in WHITE, the transcription factors not included in the list of significant genes that interact with the MesPC specific genes. The BLACK edges indicate co-citation of two genes in the PubMed database; the GREEN edges indicate the presence of a significant TFBS on the promoter of the given gene for the specific interacting transcription factor. Lower-right corner: summary of the regulatory model possibly regulating the expression of MesPC genes. The matrix elements present in the model (V$EGRF and V$SP1F), the DNA strand where they are present on the promoter regions, their relative distance, and the p-value are shown.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2654915&req=5

pone-0004977-g002: Knowledge-based gene network of the MesPC-specific genes.The nodes represent the genes. In BLUE, the MesPC-upregulated genes; in WHITE, the transcription factors not included in the list of significant genes that interact with the MesPC specific genes. The BLACK edges indicate co-citation of two genes in the PubMed database; the GREEN edges indicate the presence of a significant TFBS on the promoter of the given gene for the specific interacting transcription factor. Lower-right corner: summary of the regulatory model possibly regulating the expression of MesPC genes. The matrix elements present in the model (V$EGRF and V$SP1F), the DNA strand where they are present on the promoter regions, their relative distance, and the p-value are shown.

Mentions: We investigated the interactions of the MesPC genes based on the PubMed co-citation and the presence of TFBS in their promoter sequences. From this analysis, a number of genes emerged to have a specific consensus binding sequence for EGR1 transcription factor in their promoters (PCR validation of the microarray results shown in Figure S1). By multiple alignments, we found a conserved module constituted by a binding site for EGR1 and a second site for SP1 (Figure 2). Next, we searched for this module in the whole set of known promoter sequences in Rattus norvegicus, locating it in the promoters of 659 genes. Geneontology classification showed significant over-representation of such families as neuron differentiation (34 genes), neurogenesis (37 genes), and neuron development (26 genes), suggesting a central role of EGR1-SP1 module during production and differentiation of neurons (Table S3).


Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures.

Greco D, Volpicelli F, Di Lieto A, Leo D, Perrone-Capano C, Auvinen P, di Porzio U - PLoS ONE (2009)

Knowledge-based gene network of the MesPC-specific genes.The nodes represent the genes. In BLUE, the MesPC-upregulated genes; in WHITE, the transcription factors not included in the list of significant genes that interact with the MesPC specific genes. The BLACK edges indicate co-citation of two genes in the PubMed database; the GREEN edges indicate the presence of a significant TFBS on the promoter of the given gene for the specific interacting transcription factor. Lower-right corner: summary of the regulatory model possibly regulating the expression of MesPC genes. The matrix elements present in the model (V$EGRF and V$SP1F), the DNA strand where they are present on the promoter regions, their relative distance, and the p-value are shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2654915&req=5

pone-0004977-g002: Knowledge-based gene network of the MesPC-specific genes.The nodes represent the genes. In BLUE, the MesPC-upregulated genes; in WHITE, the transcription factors not included in the list of significant genes that interact with the MesPC specific genes. The BLACK edges indicate co-citation of two genes in the PubMed database; the GREEN edges indicate the presence of a significant TFBS on the promoter of the given gene for the specific interacting transcription factor. Lower-right corner: summary of the regulatory model possibly regulating the expression of MesPC genes. The matrix elements present in the model (V$EGRF and V$SP1F), the DNA strand where they are present on the promoter regions, their relative distance, and the p-value are shown.
Mentions: We investigated the interactions of the MesPC genes based on the PubMed co-citation and the presence of TFBS in their promoter sequences. From this analysis, a number of genes emerged to have a specific consensus binding sequence for EGR1 transcription factor in their promoters (PCR validation of the microarray results shown in Figure S1). By multiple alignments, we found a conserved module constituted by a binding site for EGR1 and a second site for SP1 (Figure 2). Next, we searched for this module in the whole set of known promoter sequences in Rattus norvegicus, locating it in the promoters of 659 genes. Geneontology classification showed significant over-representation of such families as neuron differentiation (34 genes), neurogenesis (37 genes), and neuron development (26 genes), suggesting a central role of EGR1-SP1 module during production and differentiation of neurons (Table S3).

Bottom Line: We integrate bioinformatics and functional genomics, together with developmental neurobiology.Moreover, we propose guidelines for the computational analysis of microarray gene expression data.Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland. dario.greco@helsinki.fi

ABSTRACT
In the mammalian central nervous system (CNS) an important contingent of dopaminergic neurons are localized in the substantia nigra and in the ventral tegmental area of the ventral midbrain. They constitute an anatomically and functionally heterogeneous group of cells involved in a variety of regulatory mechanisms, from locomotion to emotional/motivational behavior. Midbrain dopaminergic neuron (mDA) primary cultures represent a useful tool to study molecular mechanisms involved in their development and maintenance. Considerable information has been gathered on the mDA neurons development and maturation in vivo, as well as on the molecular features of mDA primary cultures. Here we investigated in detail the gene expression differences between the tissue of origin and ventral midbrain primary cultures enriched in mDA neurons, using microarray technique. We integrated the results based on different re-annotations of the microarray probes. By using knowledge-based gene network techniques and promoter sequence analysis, we also uncovered mechanisms that might regulate the expression of CNS genes involved in the definition of the identity of specific cell types in the ventral midbrain. We integrate bioinformatics and functional genomics, together with developmental neurobiology. Moreover, we propose guidelines for the computational analysis of microarray gene expression data. Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

Show MeSH