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EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues.

Scheibye-Alsing K, Cirera S, Gilchrist MJ, Fredholm M, Gorodkin J - BMC Genomics (2007)

Bottom Line: Our results present novel insight into differences in mitochondrial gene expression, emphasizing differences between adult and developmental tissues.Our work indicates that there are presently unknown mechanisms which work to customize mitochondrial processes to the specific needs of the cell, illustrated by the different patterns between adult and developmental tissues.Furthermore, our results also provide novel insight into how in-depth sequencing can provide significant information about expression patterns.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark. scheibye@genome.ku.dk

ABSTRACT

Background: The mitochondria are involved in many basic functions in cells of vertebrates, and can be considered the power generator of the cell. Though the mitochondria have been extensively studied there appear to be only few expression studies of mitochondrial genes involving a large number of tissues and developmental stages. Here, we conduct an analysis using the PigEST resource 1 which contains expression information from 35 tissues distributed on one normalized and 97 non-normalized cDNA libraries of which 24 are from developmental stages. The mitochondrial PigEST resource contains 41,499 mitochondrial sequences.

Results: The mitochondrial EST (Expressed Sequence Tag) sequences were assembled into contigs which covers more than 94 percent of the porcine mitochondrial genome, with an average of 976 EST sequences per nucleotide. This data was converted into expression values for the individual genes in each cDNA library revealing differential expression between genes expressed in cDNA libraries from developmental and adult stages. For the 13 protein coding genes (and several RNA genes), we find one set of six genes, containing all cytochrome oxidases, that are upregulated in developmental tissues, whereas the remaining set of seven genes, containing all ATPases, that are upregulated in adult muscle and brain tissues. Further, the COX I (Cytochrome oxidase subunit one) expression profile differs from that of the remaining genes, which could be explained by a tissue specific cleavage event or degradation pattern, and is especially pronounced in developmental tissues. Finally, as expected cDNA libraries from muscle tissues contain by far the largest amount (up to 20%) of expressed mitochondrial genes.

Conclusion: Our results present novel insight into differences in mitochondrial gene expression, emphasizing differences between adult and developmental tissues. Our work indicates that there are presently unknown mechanisms which work to customize mitochondrial processes to the specific needs of the cell, illustrated by the different patterns between adult and developmental tissues. Furthermore, our results also provide novel insight into how in-depth sequencing can provide significant information about expression patterns.

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Related in: MedlinePlus

Coverage of the COX I gene. The coverage of the COX I gene (position 5270 to 6824). The division into groups, A, B, and C (not shown) of different libraries were performed by clustering on coverage of the different parts of the gene. (A) A subset of libraries from group A having the characteristic dip in expression level in the range approximately from position 5800 to 6000. (B) A subset of group B libraries having a general lack of expression within the region ranging from position 5270 to approximately 5900. The full plots for all groups are shown in [additional file 1], and plots for individual libraries can be found in [additional file 3].
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Figure 5: Coverage of the COX I gene. The coverage of the COX I gene (position 5270 to 6824). The division into groups, A, B, and C (not shown) of different libraries were performed by clustering on coverage of the different parts of the gene. (A) A subset of libraries from group A having the characteristic dip in expression level in the range approximately from position 5800 to 6000. (B) A subset of group B libraries having a general lack of expression within the region ranging from position 5270 to approximately 5900. The full plots for all groups are shown in [additional file 1], and plots for individual libraries can be found in [additional file 3].

Mentions: For the first group (A), we observe the drop in EST coverage (Figure 5(A)), splitting the expression profile in two, with elevated coverage of the first part of the region, whereas for the second group (B) (Figure 5(B)) we observe EST coverage mainly in the region corresponding to the second part of the region. For the final group (C) a more uniform coverage is present, (see in [additional file 2], Figure 1). Furthermore, we observe that group A has an over-representation of developmental libraries, whereas groups B and C contains an over-representation of muscle libraries (see Figure 4). Furthermore, group B contains an over-representation of brain related libraries. These observations, of developmental and brain/muscle specific patterns, are in accordance with the similar type of observations made for the mitochondrial genome expression presented above.


EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues.

Scheibye-Alsing K, Cirera S, Gilchrist MJ, Fredholm M, Gorodkin J - BMC Genomics (2007)

Coverage of the COX I gene. The coverage of the COX I gene (position 5270 to 6824). The division into groups, A, B, and C (not shown) of different libraries were performed by clustering on coverage of the different parts of the gene. (A) A subset of libraries from group A having the characteristic dip in expression level in the range approximately from position 5800 to 6000. (B) A subset of group B libraries having a general lack of expression within the region ranging from position 5270 to approximately 5900. The full plots for all groups are shown in [additional file 1], and plots for individual libraries can be found in [additional file 3].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194790&req=5

Figure 5: Coverage of the COX I gene. The coverage of the COX I gene (position 5270 to 6824). The division into groups, A, B, and C (not shown) of different libraries were performed by clustering on coverage of the different parts of the gene. (A) A subset of libraries from group A having the characteristic dip in expression level in the range approximately from position 5800 to 6000. (B) A subset of group B libraries having a general lack of expression within the region ranging from position 5270 to approximately 5900. The full plots for all groups are shown in [additional file 1], and plots for individual libraries can be found in [additional file 3].
Mentions: For the first group (A), we observe the drop in EST coverage (Figure 5(A)), splitting the expression profile in two, with elevated coverage of the first part of the region, whereas for the second group (B) (Figure 5(B)) we observe EST coverage mainly in the region corresponding to the second part of the region. For the final group (C) a more uniform coverage is present, (see in [additional file 2], Figure 1). Furthermore, we observe that group A has an over-representation of developmental libraries, whereas groups B and C contains an over-representation of muscle libraries (see Figure 4). Furthermore, group B contains an over-representation of brain related libraries. These observations, of developmental and brain/muscle specific patterns, are in accordance with the similar type of observations made for the mitochondrial genome expression presented above.

Bottom Line: Our results present novel insight into differences in mitochondrial gene expression, emphasizing differences between adult and developmental tissues.Our work indicates that there are presently unknown mechanisms which work to customize mitochondrial processes to the specific needs of the cell, illustrated by the different patterns between adult and developmental tissues.Furthermore, our results also provide novel insight into how in-depth sequencing can provide significant information about expression patterns.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark. scheibye@genome.ku.dk

ABSTRACT

Background: The mitochondria are involved in many basic functions in cells of vertebrates, and can be considered the power generator of the cell. Though the mitochondria have been extensively studied there appear to be only few expression studies of mitochondrial genes involving a large number of tissues and developmental stages. Here, we conduct an analysis using the PigEST resource 1 which contains expression information from 35 tissues distributed on one normalized and 97 non-normalized cDNA libraries of which 24 are from developmental stages. The mitochondrial PigEST resource contains 41,499 mitochondrial sequences.

Results: The mitochondrial EST (Expressed Sequence Tag) sequences were assembled into contigs which covers more than 94 percent of the porcine mitochondrial genome, with an average of 976 EST sequences per nucleotide. This data was converted into expression values for the individual genes in each cDNA library revealing differential expression between genes expressed in cDNA libraries from developmental and adult stages. For the 13 protein coding genes (and several RNA genes), we find one set of six genes, containing all cytochrome oxidases, that are upregulated in developmental tissues, whereas the remaining set of seven genes, containing all ATPases, that are upregulated in adult muscle and brain tissues. Further, the COX I (Cytochrome oxidase subunit one) expression profile differs from that of the remaining genes, which could be explained by a tissue specific cleavage event or degradation pattern, and is especially pronounced in developmental tissues. Finally, as expected cDNA libraries from muscle tissues contain by far the largest amount (up to 20%) of expressed mitochondrial genes.

Conclusion: Our results present novel insight into differences in mitochondrial gene expression, emphasizing differences between adult and developmental tissues. Our work indicates that there are presently unknown mechanisms which work to customize mitochondrial processes to the specific needs of the cell, illustrated by the different patterns between adult and developmental tissues. Furthermore, our results also provide novel insight into how in-depth sequencing can provide significant information about expression patterns.

Show MeSH
Related in: MedlinePlus