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Characterization of the bovine pregnancy-associated glycoprotein gene family--analysis of gene sequences, regulatory regions within the promoter and expression of selected genes.

Telugu BP, Walker AM, Green JA - BMC Genomics (2009)

Bottom Line: The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order.However, a preponderance of conserved regions, that harbor recognition sites for putative transcriptional factors (TFs), were found to be unique to the modern boPAG grouping, but not the ancient boPAGs.These experiments mark the crucial first step in discerning the complex transcriptional regulation operating within the boPAG gene family.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA. telugub@missouri.edu

ABSTRACT

Background: The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown that the PAG family segregates into 'ancient' and 'modern' groupings. Along with sequence differences between family members, there are clear distinctions in their spatio-temporal distribution and in their relative level of expression. In this report, 1) we performed an in silico analysis of the bovine genome to further characterize the PAG gene family, 2) we scrutinized proximal promoter sequences of the PAG genes to evaluate the evolution pressures operating on them and to identify putative regulatory regions, 3) we determined relative transcript abundance of selected PAGs during pregnancy and, 4) we performed preliminary characterization of the putative regulatory elements for one of the candidate PAGs, bovine (bo) PAG-2.

Results: From our analysis of the bovine genome, we identified 18 distinct PAG genes and 14 pseudogenes. We observed that the first 500 base pairs upstream of the translational start site contained multiple regions that are conserved among all boPAGs. However, a preponderance of conserved regions, that harbor recognition sites for putative transcriptional factors (TFs), were found to be unique to the modern boPAG grouping, but not the ancient boPAGs. We gathered evidence by means of Q-PCR and screening of EST databases to show that boPAG-2 is the most abundant of all boPAG transcripts. Finally, we provided preliminary evidence for the role of ETS- and DDVL-related TFs in the regulation of the boPAG-2 gene.

Conclusion: PAGs represent a relatively large gene family in the bovine genome. The proximal promoter regions of these genes display differences in putative TF binding sites, likely contributing to observed differences in spatial and temporal expression. We also discovered that boPAG-2 is the most abundant of all boPAG transcripts and provided evidence for the role of ETS and DDVL TFs in its regulation. These experiments mark the crucial first step in discerning the complex transcriptional regulation operating within the boPAG gene family.

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Relative distribution of non-LTR (SINE, LINE), LTR and transposable elements (TEs) within several bovine PAG genes. A. Each colored bar represents the relative distribution of the corresponding element in each boPAG gene. The TE elements were shown on the -X axis. The relative % of the sequence contributed by each element is shown on the Y-axis. The definition of the acronyms used in the figure is as follow: LTR: long terminal repeat; SINE: short interspersed element; LINE: long interspersed element; MIR: mammalian wild- interspersed repeat (sub-class of SINE); RTE: retrotransposable elements; MaLR: mammalian apparent long terminal repeat; MER: medium reiterated element. B. and C. show the cumulative total of the number of TEs, as well as the % contribution to the sequence of individual boPAGs. B: represents the cumulative total of the all the different kinds of the elements in individual PAG genes. C: shows the % make-up of the PAG genes by the TEs.
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Figure 2: Relative distribution of non-LTR (SINE, LINE), LTR and transposable elements (TEs) within several bovine PAG genes. A. Each colored bar represents the relative distribution of the corresponding element in each boPAG gene. The TE elements were shown on the -X axis. The relative % of the sequence contributed by each element is shown on the Y-axis. The definition of the acronyms used in the figure is as follow: LTR: long terminal repeat; SINE: short interspersed element; LINE: long interspersed element; MIR: mammalian wild- interspersed repeat (sub-class of SINE); RTE: retrotransposable elements; MaLR: mammalian apparent long terminal repeat; MER: medium reiterated element. B. and C. show the cumulative total of the number of TEs, as well as the % contribution to the sequence of individual boPAGs. B: represents the cumulative total of the all the different kinds of the elements in individual PAG genes. C: shows the % make-up of the PAG genes by the TEs.

Mentions: The incorporation of TE within genes can produce changes in the gene structure. Furthermore, the presence of TE in genes can provide insight into the evolutionary history of gene families. In order to evaluate the implications of transposition events on the boPAG genes, a preliminary evaluation was performed on the sequence of each PAG (including 3000 bp 5' and 3' of the coding regions of the gene). The distribution of TE in representative candidate boPAGs is shown in Figure 2A. The Repeat Masker software revealed that TEs were distributed only within the intronic and non-coding regions of the PAG genes. Consequently, the TEs are not directly influencing the reading frame of boPAGs.


Characterization of the bovine pregnancy-associated glycoprotein gene family--analysis of gene sequences, regulatory regions within the promoter and expression of selected genes.

Telugu BP, Walker AM, Green JA - BMC Genomics (2009)

Relative distribution of non-LTR (SINE, LINE), LTR and transposable elements (TEs) within several bovine PAG genes. A. Each colored bar represents the relative distribution of the corresponding element in each boPAG gene. The TE elements were shown on the -X axis. The relative % of the sequence contributed by each element is shown on the Y-axis. The definition of the acronyms used in the figure is as follow: LTR: long terminal repeat; SINE: short interspersed element; LINE: long interspersed element; MIR: mammalian wild- interspersed repeat (sub-class of SINE); RTE: retrotransposable elements; MaLR: mammalian apparent long terminal repeat; MER: medium reiterated element. B. and C. show the cumulative total of the number of TEs, as well as the % contribution to the sequence of individual boPAGs. B: represents the cumulative total of the all the different kinds of the elements in individual PAG genes. C: shows the % make-up of the PAG genes by the TEs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2682831&req=5

Figure 2: Relative distribution of non-LTR (SINE, LINE), LTR and transposable elements (TEs) within several bovine PAG genes. A. Each colored bar represents the relative distribution of the corresponding element in each boPAG gene. The TE elements were shown on the -X axis. The relative % of the sequence contributed by each element is shown on the Y-axis. The definition of the acronyms used in the figure is as follow: LTR: long terminal repeat; SINE: short interspersed element; LINE: long interspersed element; MIR: mammalian wild- interspersed repeat (sub-class of SINE); RTE: retrotransposable elements; MaLR: mammalian apparent long terminal repeat; MER: medium reiterated element. B. and C. show the cumulative total of the number of TEs, as well as the % contribution to the sequence of individual boPAGs. B: represents the cumulative total of the all the different kinds of the elements in individual PAG genes. C: shows the % make-up of the PAG genes by the TEs.
Mentions: The incorporation of TE within genes can produce changes in the gene structure. Furthermore, the presence of TE in genes can provide insight into the evolutionary history of gene families. In order to evaluate the implications of transposition events on the boPAG genes, a preliminary evaluation was performed on the sequence of each PAG (including 3000 bp 5' and 3' of the coding regions of the gene). The distribution of TE in representative candidate boPAGs is shown in Figure 2A. The Repeat Masker software revealed that TEs were distributed only within the intronic and non-coding regions of the PAG genes. Consequently, the TEs are not directly influencing the reading frame of boPAGs.

Bottom Line: The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order.However, a preponderance of conserved regions, that harbor recognition sites for putative transcriptional factors (TFs), were found to be unique to the modern boPAG grouping, but not the ancient boPAGs.These experiments mark the crucial first step in discerning the complex transcriptional regulation operating within the boPAG gene family.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA. telugub@missouri.edu

ABSTRACT

Background: The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown that the PAG family segregates into 'ancient' and 'modern' groupings. Along with sequence differences between family members, there are clear distinctions in their spatio-temporal distribution and in their relative level of expression. In this report, 1) we performed an in silico analysis of the bovine genome to further characterize the PAG gene family, 2) we scrutinized proximal promoter sequences of the PAG genes to evaluate the evolution pressures operating on them and to identify putative regulatory regions, 3) we determined relative transcript abundance of selected PAGs during pregnancy and, 4) we performed preliminary characterization of the putative regulatory elements for one of the candidate PAGs, bovine (bo) PAG-2.

Results: From our analysis of the bovine genome, we identified 18 distinct PAG genes and 14 pseudogenes. We observed that the first 500 base pairs upstream of the translational start site contained multiple regions that are conserved among all boPAGs. However, a preponderance of conserved regions, that harbor recognition sites for putative transcriptional factors (TFs), were found to be unique to the modern boPAG grouping, but not the ancient boPAGs. We gathered evidence by means of Q-PCR and screening of EST databases to show that boPAG-2 is the most abundant of all boPAG transcripts. Finally, we provided preliminary evidence for the role of ETS- and DDVL-related TFs in the regulation of the boPAG-2 gene.

Conclusion: PAGs represent a relatively large gene family in the bovine genome. The proximal promoter regions of these genes display differences in putative TF binding sites, likely contributing to observed differences in spatial and temporal expression. We also discovered that boPAG-2 is the most abundant of all boPAG transcripts and provided evidence for the role of ETS and DDVL TFs in its regulation. These experiments mark the crucial first step in discerning the complex transcriptional regulation operating within the boPAG gene family.

Show MeSH