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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.

Show MeSH
Mitochondrial fraction of Expression. The libraries are ordered according their fraction of EST originating from mitochondria. Selected tissues and their developmental stage are marked by colored bullets.
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Figure 1: Mitochondrial fraction of Expression. The libraries are ordered according their fraction of EST originating from mitochondria. Selected tissues and their developmental stage are marked by colored bullets.

Mentions: An investigation of the proportion of mitochondrial gene expression in the different cDNA libraries was performed. We found that cDNA libraries from tissues associated with high metabolism (eg. muscles) have a larger fraction of mitochondrial ESTs compared to the total number of reads from that library as shown in Figure 1. We observed that the fraction of total reads that originates from the mitochondrion ranges from roughly 0% up to 22%, with the majority falling between 2% to 10%. However, the libraries (8 in total) with the smallest fraction seem to have unusual low mitochondrial-EST counts, and were excluded in the following clustering. Furthermore, we attempted to see if there were any correlations between the number of counts from a given tissue and diversity of expression, however we did not find any such patterns.


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)

Mitochondrial fraction of Expression. The libraries are ordered according their fraction of EST originating from mitochondria. Selected tissues and their developmental stage are marked by colored bullets.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Mitochondrial fraction of Expression. The libraries are ordered according their fraction of EST originating from mitochondria. Selected tissues and their developmental stage are marked by colored bullets.
Mentions: An investigation of the proportion of mitochondrial gene expression in the different cDNA libraries was performed. We found that cDNA libraries from tissues associated with high metabolism (eg. muscles) have a larger fraction of mitochondrial ESTs compared to the total number of reads from that library as shown in Figure 1. We observed that the fraction of total reads that originates from the mitochondrion ranges from roughly 0% up to 22%, with the majority falling between 2% to 10%. However, the libraries (8 in total) with the smallest fraction seem to have unusual low mitochondrial-EST counts, and were excluded in the following clustering. Furthermore, we attempted to see if there were any correlations between the number of counts from a given tissue and diversity of expression, however we did not find any such patterns.

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