Limits...
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.

Show MeSH

Related in: MedlinePlus

Genomic location of genes differentially regulated in response to heat shock. Each chromosome is depicted by a horizontal black line. Transcription initiation sites are indicated by vertical black lines. Genes encoding mRNAs that increase in abundance in response to heat shock by twofold or more are highlighted in blue and those encoding mRNAs that decrease by twofold or more are highlighted in red. Other genes are shown in grey. Genes above the chromosome line are transcribed left to right. Genes below the chromosome line are transcribed right to left. The green box highlights the polycistronic transcription on chromosome 4 unit selected for experimental testing.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3376733&req=5

RSOB120033F1: Genomic location of genes differentially regulated in response to heat shock. Each chromosome is depicted by a horizontal black line. Transcription initiation sites are indicated by vertical black lines. Genes encoding mRNAs that increase in abundance in response to heat shock by twofold or more are highlighted in blue and those encoding mRNAs that decrease by twofold or more are highlighted in red. Other genes are shown in grey. Genes above the chromosome line are transcribed left to right. Genes below the chromosome line are transcribed right to left. The green box highlights the polycistronic transcription on chromosome 4 unit selected for experimental testing.

Mentions: A previous analysis of the heat-shock response in procyclic form Trypanosoma brucei identified 1058 mRNAs whose abundance changed in response to heat shock [27]. In the analysis presented here, the location of the heat-shock-responsive genes on each chromosome was determined. All 1058 mRNAs showing differential abundance in response to heat shock in the microarray experiment were selected. Three criteria were applied to the filter list. First, all mRNAs with a less than twofold response were removed to reduce the number of false positives arising from inaccuracies in the microarray data. Second, all mRNAs likely to be transcribed by RNA polymerase I (i.e. variant surface glycoprotein and expression site-associated genes) were removed. Third, mRNAs arising from dispersed multi-copy genes (i.e. GRESAG4 and ‘retrotransposon hotspot protein’) for which the microarray data cannot unambiguously distinguish the originating genes were also removed. The final list contained 211 mRNAs whose relative abundance decreased and 566 mRNAs whose relative abundance increased after heat shock (electronic supplementary material, file S1). Visual inspection of the distribution of the genes in this list relative to defined RNAPII transcription initiation sites [8] suggested that the genes corresponding to mRNAs whose relative abundance increased in response to heat shock were located further away from transcription initiation sites than those that decreased (figure 1; electronic supplementary material, file S1).Figure 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)

Genomic location of genes differentially regulated in response to heat shock. Each chromosome is depicted by a horizontal black line. Transcription initiation sites are indicated by vertical black lines. Genes encoding mRNAs that increase in abundance in response to heat shock by twofold or more are highlighted in blue and those encoding mRNAs that decrease by twofold or more are highlighted in red. Other genes are shown in grey. Genes above the chromosome line are transcribed left to right. Genes below the chromosome line are transcribed right to left. The green box highlights the polycistronic transcription on chromosome 4 unit selected for experimental testing.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120033F1: Genomic location of genes differentially regulated in response to heat shock. Each chromosome is depicted by a horizontal black line. Transcription initiation sites are indicated by vertical black lines. Genes encoding mRNAs that increase in abundance in response to heat shock by twofold or more are highlighted in blue and those encoding mRNAs that decrease by twofold or more are highlighted in red. Other genes are shown in grey. Genes above the chromosome line are transcribed left to right. Genes below the chromosome line are transcribed right to left. The green box highlights the polycistronic transcription on chromosome 4 unit selected for experimental testing.
Mentions: A previous analysis of the heat-shock response in procyclic form Trypanosoma brucei identified 1058 mRNAs whose abundance changed in response to heat shock [27]. In the analysis presented here, the location of the heat-shock-responsive genes on each chromosome was determined. All 1058 mRNAs showing differential abundance in response to heat shock in the microarray experiment were selected. Three criteria were applied to the filter list. First, all mRNAs with a less than twofold response were removed to reduce the number of false positives arising from inaccuracies in the microarray data. Second, all mRNAs likely to be transcribed by RNA polymerase I (i.e. variant surface glycoprotein and expression site-associated genes) were removed. Third, mRNAs arising from dispersed multi-copy genes (i.e. GRESAG4 and ‘retrotransposon hotspot protein’) for which the microarray data cannot unambiguously distinguish the originating genes were also removed. The final list contained 211 mRNAs whose relative abundance decreased and 566 mRNAs whose relative abundance increased after heat shock (electronic supplementary material, file S1). Visual inspection of the distribution of the genes in this list relative to defined RNAPII transcription initiation sites [8] suggested that the genes corresponding to mRNAs whose relative abundance increased in response to heat shock were located further away from transcription initiation sites than those that decreased (figure 1; electronic supplementary material, file S1).Figure 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