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Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes.

Kelly S, Kramer S, Schwede A, Maini PK, Gull K, Carrington M - Open Biol (2012)

Bottom Line: We show that genes encoding mRNAs that are differentially regulated during the heat-shock response are selectively positioned in polycistronic transcription units; downregulated genes are close to transcription initiation sites and upregulated genes are distant.We demonstrate that the position of a reporter gene within a transcription unit is sufficient to reproduce this effect.Furthermore, we show that the relative abundance of mRNAs at different time points in the cell division cycle is dependent on the location of the corresponding genes to transcription initiation sites.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK. steven.kelly@plants.ox.ac.uk

ABSTRACT
The trypanosome genome is characterized by RNA polymerase II-driven polycistronic transcription of protein-coding genes. Ten to hundreds of genes are co-transcribed from a single promoter; thus, selective regulation of individual genes via initiation is impossible. However, selective responses to external stimuli occur and post-transcriptional mechanisms are thought to account for all temporal gene expression patterns. We show that genes encoding mRNAs that are differentially regulated during the heat-shock response are selectively positioned in polycistronic transcription units; downregulated genes are close to transcription initiation sites and upregulated genes are distant. We demonstrate that the position of a reporter gene within a transcription unit is sufficient to reproduce this effect. Analysis of gene ontology annotations reveals that positional bias is not restricted to stress-response genes and that there is a genome-wide organization based on proximity to transcription initiation sites. Furthermore, we show that the relative abundance of mRNAs at different time points in the cell division cycle is dependent on the location of the corresponding genes to transcription initiation sites. This work provides evidence that the genome in trypanosomes is organized to facilitate co-coordinated temporal control of gene expression in the absence of selective promoters.

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(a) Schematic cartoon describing the GO term group genome positioning analysis method. (b) Analysis of the distribution of gene ontology (GO) term groups with respect to transcription initiation sites. Grey bars indicate the number of GO term categories observed at each score level. Red line indicates the expected number of GO term categories at each score level if genes were randomly distributed in the genome. The red box encompasses the mean ± one standard error of the mean. (c) Plot of mean mRNA relative abundance within a 20 kb sliding window versus distance from transcription initiation site for four different cell cycle stages.
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RSOB120033F4: (a) Schematic cartoon describing the GO term group genome positioning analysis method. (b) Analysis of the distribution of gene ontology (GO) term groups with respect to transcription initiation sites. Grey bars indicate the number of GO term categories observed at each score level. Red line indicates the expected number of GO term categories at each score level if genes were randomly distributed in the genome. The red box encompasses the mean ± one standard error of the mean. (c) Plot of mean mRNA relative abundance within a 20 kb sliding window versus distance from transcription initiation site for four different cell cycle stages.

Mentions: The above analyses showed that the position of a gene relative to a transcription initiation site is important for controlling the differential abundance of its mRNA in response to heat-shock-induced stress. To test whether other factors influence the location of genes within polycistronic units, two approaches were taken. First, other functional categories of genes were investigated to determine whether they showed positioning biases. GO annotations were used to group genes into categories. For each GO term category containing 10 or more genes, the mean and median distance of the genes to the nearest transcription initiation site was calculated (electronic supplementary material, file S2). The mean distance of this group was then compared with the mean distance of 10 000 randomly composed groups containing the same number of genes. The proportion of randomly selected groups that achieved a mean distance to transcription initiation sites of more than the GO term group was recorded (figure 4a; electronic supplementary material, file S2). For example, if 71 per cent of the randomly generated groups were further away from transcription start sites than the GO term group, then the GO term group would obtain a score of 0.71. This analysis showed that there are some GO term categories whose constituent genes are on average closer to transcription initiation sites than expected if genes were distributed randomly in the genome (figure 4b and table 1). Similarly, there are some GO term categories whose constituent genes are on average more distant from transcription start sites than expected if genes were distributed randomly in the genome (figure 4b and table 1). To control for discrepancies in gene density within transcription units and for differential transcription unit length, a further analysis was performed where a set of false GO term categories was reconstituted from randomly selected genes, each containing the same number of genes as the real GO term categories (see §3). The same distance-based analysis was completed as before and the procedure was repeated 100 times (figure 4b, red-shaded box). This shows that if genes were randomly distributed in the genome, an even distribution of GO term groups across transcription units would be observed.Table 1.


Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes.

Kelly S, Kramer S, Schwede A, Maini PK, Gull K, Carrington M - Open Biol (2012)

(a) Schematic cartoon describing the GO term group genome positioning analysis method. (b) Analysis of the distribution of gene ontology (GO) term groups with respect to transcription initiation sites. Grey bars indicate the number of GO term categories observed at each score level. Red line indicates the expected number of GO term categories at each score level if genes were randomly distributed in the genome. The red box encompasses the mean ± one standard error of the mean. (c) Plot of mean mRNA relative abundance within a 20 kb sliding window versus distance from transcription initiation site for four different cell cycle stages.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376733&req=5

RSOB120033F4: (a) Schematic cartoon describing the GO term group genome positioning analysis method. (b) Analysis of the distribution of gene ontology (GO) term groups with respect to transcription initiation sites. Grey bars indicate the number of GO term categories observed at each score level. Red line indicates the expected number of GO term categories at each score level if genes were randomly distributed in the genome. The red box encompasses the mean ± one standard error of the mean. (c) Plot of mean mRNA relative abundance within a 20 kb sliding window versus distance from transcription initiation site for four different cell cycle stages.
Mentions: The above analyses showed that the position of a gene relative to a transcription initiation site is important for controlling the differential abundance of its mRNA in response to heat-shock-induced stress. To test whether other factors influence the location of genes within polycistronic units, two approaches were taken. First, other functional categories of genes were investigated to determine whether they showed positioning biases. GO annotations were used to group genes into categories. For each GO term category containing 10 or more genes, the mean and median distance of the genes to the nearest transcription initiation site was calculated (electronic supplementary material, file S2). The mean distance of this group was then compared with the mean distance of 10 000 randomly composed groups containing the same number of genes. The proportion of randomly selected groups that achieved a mean distance to transcription initiation sites of more than the GO term group was recorded (figure 4a; electronic supplementary material, file S2). For example, if 71 per cent of the randomly generated groups were further away from transcription start sites than the GO term group, then the GO term group would obtain a score of 0.71. This analysis showed that there are some GO term categories whose constituent genes are on average closer to transcription initiation sites than expected if genes were distributed randomly in the genome (figure 4b and table 1). Similarly, there are some GO term categories whose constituent genes are on average more distant from transcription start sites than expected if genes were distributed randomly in the genome (figure 4b and table 1). To control for discrepancies in gene density within transcription units and for differential transcription unit length, a further analysis was performed where a set of false GO term categories was reconstituted from randomly selected genes, each containing the same number of genes as the real GO term categories (see §3). The same distance-based analysis was completed as before and the procedure was repeated 100 times (figure 4b, red-shaded box). This shows that if genes were randomly distributed in the genome, an even distribution of GO term groups across transcription units would be observed.Table 1.

Bottom Line: We show that genes encoding mRNAs that are differentially regulated during the heat-shock response are selectively positioned in polycistronic transcription units; downregulated genes are close to transcription initiation sites and upregulated genes are distant.We demonstrate that the position of a reporter gene within a transcription unit is sufficient to reproduce this effect.Furthermore, we show that the relative abundance of mRNAs at different time points in the cell division cycle is dependent on the location of the corresponding genes to transcription initiation sites.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK. steven.kelly@plants.ox.ac.uk

ABSTRACT
The trypanosome genome is characterized by RNA polymerase II-driven polycistronic transcription of protein-coding genes. Ten to hundreds of genes are co-transcribed from a single promoter; thus, selective regulation of individual genes via initiation is impossible. However, selective responses to external stimuli occur and post-transcriptional mechanisms are thought to account for all temporal gene expression patterns. We show that genes encoding mRNAs that are differentially regulated during the heat-shock response are selectively positioned in polycistronic transcription units; downregulated genes are close to transcription initiation sites and upregulated genes are distant. We demonstrate that the position of a reporter gene within a transcription unit is sufficient to reproduce this effect. Analysis of gene ontology annotations reveals that positional bias is not restricted to stress-response genes and that there is a genome-wide organization based on proximity to transcription initiation sites. Furthermore, we show that the relative abundance of mRNAs at different time points in the cell division cycle is dependent on the location of the corresponding genes to transcription initiation sites. This work provides evidence that the genome in trypanosomes is organized to facilitate co-coordinated temporal control of gene expression in the absence of selective promoters.

Show MeSH
Related in: MedlinePlus