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Evidence for large domains of similarly expressed genes in the Drosophila genome.

Spellman PT, Rubin GM - J. Biol. (2002)

Bottom Line: We found about 200 groups of adjacent and similarly expressed genes, each having between 10 and 30 members; together these groups account for over 20% of assayed genes.Groups do not appear to show any correlation with polytene banding patterns or other known chromosomal structures, nor were genes within groups functionally related to one another.The mechanism underlying this phenomenon is not yet known.

View Article: PubMed Central - HTML - PubMed

Affiliation: Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3400, USA. spellman@bdgp.lbl.gov

ABSTRACT

Background: Transcriptional regulation in eukaryotes generally operates at the level of individual genes. Regulation of sets of adjacent genes by mechanisms operating at the level of chromosomal domains has been demonstrated in a number of cases, but the fraction of genes in the genome subject to regulation at this level is unknown.

Results: Drosophila gene-expression profiles that were determined from over 80 experimental conditions using high-density oligonucleotide microarrays were searched for groups of adjacent genes that show similar expression profiles. We found about 200 groups of adjacent and similarly expressed genes, each having between 10 and 30 members; together these groups account for over 20% of assayed genes. Each group covers between 20 and 200 kilobase pairs of genomic sequence, with a mean group size of about 100 kilobase pairs. Groups do not appear to show any correlation with polytene banding patterns or other known chromosomal structures, nor were genes within groups functionally related to one another.

Conclusions: Groups of adjacent and co-regulated genes that are not otherwise functionally related in any obvious way can be identified by expression profiling in Drosophila. The mechanism underlying this phenomenon is not yet known.

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Similarly expressed adjacent genes on the left arm of Drosophila chromosome 2 (2L). (a) Ratiograms show the relative expression of all gene groups on 2L that are significant at p < 10-2. In each ratiogram, columns represent individual experimental conditions and rows represent individual genes. For each square on the resulting grid, red denotes relative expression higher than the average for a gene in an experiment, green denotes lower relative expression and black indicates that the expression is equal to the average. The black bar represents the chromosome, and the ticks along its left side mark 1 megabase (Mb) distances. The black shapes link the positions of groups on 2L to the expanded views of certain groups that are shown in (b,c). (b) An expanded view of about 5 Mb. (c) The genes in two groups are shown in detail. The CT (computed transcript identifier), CG (computed gene identifier), and gene name are shown for each of the genes in these two groups. Each of the two expanded sections represents one group.
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Figure 2: Similarly expressed adjacent genes on the left arm of Drosophila chromosome 2 (2L). (a) Ratiograms show the relative expression of all gene groups on 2L that are significant at p < 10-2. In each ratiogram, columns represent individual experimental conditions and rows represent individual genes. For each square on the resulting grid, red denotes relative expression higher than the average for a gene in an experiment, green denotes lower relative expression and black indicates that the expression is equal to the average. The black bar represents the chromosome, and the ticks along its left side mark 1 megabase (Mb) distances. The black shapes link the positions of groups on 2L to the expanded views of certain groups that are shown in (b,c). (b) An expanded view of about 5 Mb. (c) The genes in two groups are shown in detail. The CT (computed transcript identifier), CG (computed gene identifier), and gene name are shown for each of the genes in these two groups. Each of the two expanded sections represents one group.

Mentions: The 44 groups (681 genes in total) that map to the left arm of chromosome two and have a p value of less than 10-2 are shown, using a ratiogram [8] aligned to the chromosome arm, in Figure 2. The distribution of groups along the chromosomes appears random and there is little bias for genes in a group to be on the same strand. The length of genomic sequence occupied by similarly expressed gene groups is highly variable. The average group size is nearly 125 kilo-base pairs (kbp) in length, with a standard deviation of about 90 kbp, while the smallest group is 22 kbp and the largest is over 450 kbp. As might be expected, there is a relationship between the number of genes in a group and the length of genomic DNA covered by each group (Pearson correlation 0.59).


Evidence for large domains of similarly expressed genes in the Drosophila genome.

Spellman PT, Rubin GM - J. Biol. (2002)

Similarly expressed adjacent genes on the left arm of Drosophila chromosome 2 (2L). (a) Ratiograms show the relative expression of all gene groups on 2L that are significant at p < 10-2. In each ratiogram, columns represent individual experimental conditions and rows represent individual genes. For each square on the resulting grid, red denotes relative expression higher than the average for a gene in an experiment, green denotes lower relative expression and black indicates that the expression is equal to the average. The black bar represents the chromosome, and the ticks along its left side mark 1 megabase (Mb) distances. The black shapes link the positions of groups on 2L to the expanded views of certain groups that are shown in (b,c). (b) An expanded view of about 5 Mb. (c) The genes in two groups are shown in detail. The CT (computed transcript identifier), CG (computed gene identifier), and gene name are shown for each of the genes in these two groups. Each of the two expanded sections represents one group.
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Related In: Results  -  Collection

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Figure 2: Similarly expressed adjacent genes on the left arm of Drosophila chromosome 2 (2L). (a) Ratiograms show the relative expression of all gene groups on 2L that are significant at p < 10-2. In each ratiogram, columns represent individual experimental conditions and rows represent individual genes. For each square on the resulting grid, red denotes relative expression higher than the average for a gene in an experiment, green denotes lower relative expression and black indicates that the expression is equal to the average. The black bar represents the chromosome, and the ticks along its left side mark 1 megabase (Mb) distances. The black shapes link the positions of groups on 2L to the expanded views of certain groups that are shown in (b,c). (b) An expanded view of about 5 Mb. (c) The genes in two groups are shown in detail. The CT (computed transcript identifier), CG (computed gene identifier), and gene name are shown for each of the genes in these two groups. Each of the two expanded sections represents one group.
Mentions: The 44 groups (681 genes in total) that map to the left arm of chromosome two and have a p value of less than 10-2 are shown, using a ratiogram [8] aligned to the chromosome arm, in Figure 2. The distribution of groups along the chromosomes appears random and there is little bias for genes in a group to be on the same strand. The length of genomic sequence occupied by similarly expressed gene groups is highly variable. The average group size is nearly 125 kilo-base pairs (kbp) in length, with a standard deviation of about 90 kbp, while the smallest group is 22 kbp and the largest is over 450 kbp. As might be expected, there is a relationship between the number of genes in a group and the length of genomic DNA covered by each group (Pearson correlation 0.59).

Bottom Line: We found about 200 groups of adjacent and similarly expressed genes, each having between 10 and 30 members; together these groups account for over 20% of assayed genes.Groups do not appear to show any correlation with polytene banding patterns or other known chromosomal structures, nor were genes within groups functionally related to one another.The mechanism underlying this phenomenon is not yet known.

View Article: PubMed Central - HTML - PubMed

Affiliation: Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3400, USA. spellman@bdgp.lbl.gov

ABSTRACT

Background: Transcriptional regulation in eukaryotes generally operates at the level of individual genes. Regulation of sets of adjacent genes by mechanisms operating at the level of chromosomal domains has been demonstrated in a number of cases, but the fraction of genes in the genome subject to regulation at this level is unknown.

Results: Drosophila gene-expression profiles that were determined from over 80 experimental conditions using high-density oligonucleotide microarrays were searched for groups of adjacent genes that show similar expression profiles. We found about 200 groups of adjacent and similarly expressed genes, each having between 10 and 30 members; together these groups account for over 20% of assayed genes. Each group covers between 20 and 200 kilobase pairs of genomic sequence, with a mean group size of about 100 kilobase pairs. Groups do not appear to show any correlation with polytene banding patterns or other known chromosomal structures, nor were genes within groups functionally related to one another.

Conclusions: Groups of adjacent and co-regulated genes that are not otherwise functionally related in any obvious way can be identified by expression profiling in Drosophila. The mechanism underlying this phenomenon is not yet known.

Show MeSH
Related in: MedlinePlus