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Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster.

Gonsalves SE, Moses AM, Razak Z, Robert F, Westwood JT - PLoS ONE (2011)

Bottom Line: There were also genes that showed changes in transcript levels that did not appear to correlate with HSF binding sites.We also found that the insulator protein, BEAF, has enriched binding prior to HS to promoters of genes that are bound by HSF upon HS but that are not transcriptionally induced during HS.These results suggest that Drosophila HSF may be regulating many genes besides the known HS genes and that some of these genes may be regulated during non-stress conditions.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Systems Biology, University of Toronto, Mississauga, Canada.

ABSTRACT
During heat shock (HS) and other stresses, HS gene transcription in eukaryotes is up-regulated by the transcription factor heat shock factor (HSF). While the identities of the major HS genes have been known for more than 30 years, it has been suspected that HSF binds to numerous other genes and potentially regulates their transcription. In this study, we have used a chromatin immunoprecipitation and microarray (ChIP-chip) approach to identify 434 regions in the Drosophila genome that are bound by HSF. We have also performed a transcript analysis of heat shocked Kc167 cells and third instar larvae and compared them to HSF binding sites. The heat-induced transcription profiles were quite different between cells and larvae and surprisingly only about 10% of the genes associated with HSF binding sites show changed transcription. There were also genes that showed changes in transcript levels that did not appear to correlate with HSF binding sites. Analysis of the locations of the HSF binding sites revealed that 57% were contained within genes with approximately 2/3rds of these sites being in introns. We also found that the insulator protein, BEAF, has enriched binding prior to HS to promoters of genes that are bound by HSF upon HS but that are not transcriptionally induced during HS. When the genes associated with HSF binding sites in promoters were analyzed for gene ontology terms, categories such as stress response and transferase activity were enriched whereas analysis of genes having HSF binding sites in introns identified those categories plus ones related to developmental processes and reproduction. These results suggest that Drosophila HSF may be regulating many genes besides the known HS genes and that some of these genes may be regulated during non-stress conditions.

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The BEAF cis regulatory motif is enriched in promoters, but not introns, bound by HSF.The occurrence of 111 PWMs from TRANSFAC and the Drosophila DNase I Footprint Database in HSF-bound promoters and introns was scored with Patser [38]. The histograms show the number of matches (Bonferroni corrected p-value<5.6×10−2) to PWMs representing HSF and BEAF binding sites in 50 bp windows centered on the peak of each HSF-bound segment (blue for promoters, red for introns). The PMW for DREF is very similar to the one for BEAF and gives the same result. P-values at the top right of each histogram indicate the probability given by a X2 test that the difference in the number of matches to the PWM found in promoters and introns is due to chance.
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pone-0015934-g009: The BEAF cis regulatory motif is enriched in promoters, but not introns, bound by HSF.The occurrence of 111 PWMs from TRANSFAC and the Drosophila DNase I Footprint Database in HSF-bound promoters and introns was scored with Patser [38]. The histograms show the number of matches (Bonferroni corrected p-value<5.6×10−2) to PWMs representing HSF and BEAF binding sites in 50 bp windows centered on the peak of each HSF-bound segment (blue for promoters, red for introns). The PMW for DREF is very similar to the one for BEAF and gives the same result. P-values at the top right of each histogram indicate the probability given by a X2 test that the difference in the number of matches to the PWM found in promoters and introns is due to chance.

Mentions: Because of the difference in functional classification of genes associated with HSF-bound promoters versus HSF-bound introns, we were interested in determining if any other transcription factor(s)/DNA binding protein(s) were associated with these sites. To identify possible candidates, we used Patser to scan HSF-bound promoters and introns for matches (Bonferroni corrected p-value<5.6×10−2) to PWMs representing 111 different DNA binding proteins from two databases, Transfac and the Drosophila DNase I Footprint Database. As expected, the PWM representing the 15 bp HSE composed of inverted repeats of nGAAn (Figure 5A) was enriched near the peak of both HSF-bound promoters and HSF-bound introns (Figure 9). Of the remaining PWMs, the PWM for BEAF was the only one enriched near the peak of HSF-bound promoters to also have a similar chi squared value (X2>40) and show the same level of significance in a chi square test (Bonferroni corrected p-value<2.3×10−8) as the PWM representing the canonical HSE (Figure 9). Unlike the HSE PWM, however, this enrichment was only seen for those HSF-bound sites found in promoters; the occurrence of the BEAF PWM in HSF-bound segments located within introns was no different than the background (Figure 9). Consistent with this finding is a recent report that BEAF (boundary element associated factor) binding sites are enriched in 5′ UTRs and in the first 200 bp upstream of gene's TSS [40], [41]. Genes having both BEAF and HSF binding sites do not appear to be strongly enriched in any categories that differ from those enriched among all promoters except for a modest enrichment for genes with cell cycle annotation (p-value  = 0.0011; data not shown) which is consistent with the function of genes BEAF has been shown to regulate [42].


Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster.

Gonsalves SE, Moses AM, Razak Z, Robert F, Westwood JT - PLoS ONE (2011)

The BEAF cis regulatory motif is enriched in promoters, but not introns, bound by HSF.The occurrence of 111 PWMs from TRANSFAC and the Drosophila DNase I Footprint Database in HSF-bound promoters and introns was scored with Patser [38]. The histograms show the number of matches (Bonferroni corrected p-value<5.6×10−2) to PWMs representing HSF and BEAF binding sites in 50 bp windows centered on the peak of each HSF-bound segment (blue for promoters, red for introns). The PMW for DREF is very similar to the one for BEAF and gives the same result. P-values at the top right of each histogram indicate the probability given by a X2 test that the difference in the number of matches to the PWM found in promoters and introns is due to chance.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3021535&req=5

pone-0015934-g009: The BEAF cis regulatory motif is enriched in promoters, but not introns, bound by HSF.The occurrence of 111 PWMs from TRANSFAC and the Drosophila DNase I Footprint Database in HSF-bound promoters and introns was scored with Patser [38]. The histograms show the number of matches (Bonferroni corrected p-value<5.6×10−2) to PWMs representing HSF and BEAF binding sites in 50 bp windows centered on the peak of each HSF-bound segment (blue for promoters, red for introns). The PMW for DREF is very similar to the one for BEAF and gives the same result. P-values at the top right of each histogram indicate the probability given by a X2 test that the difference in the number of matches to the PWM found in promoters and introns is due to chance.
Mentions: Because of the difference in functional classification of genes associated with HSF-bound promoters versus HSF-bound introns, we were interested in determining if any other transcription factor(s)/DNA binding protein(s) were associated with these sites. To identify possible candidates, we used Patser to scan HSF-bound promoters and introns for matches (Bonferroni corrected p-value<5.6×10−2) to PWMs representing 111 different DNA binding proteins from two databases, Transfac and the Drosophila DNase I Footprint Database. As expected, the PWM representing the 15 bp HSE composed of inverted repeats of nGAAn (Figure 5A) was enriched near the peak of both HSF-bound promoters and HSF-bound introns (Figure 9). Of the remaining PWMs, the PWM for BEAF was the only one enriched near the peak of HSF-bound promoters to also have a similar chi squared value (X2>40) and show the same level of significance in a chi square test (Bonferroni corrected p-value<2.3×10−8) as the PWM representing the canonical HSE (Figure 9). Unlike the HSE PWM, however, this enrichment was only seen for those HSF-bound sites found in promoters; the occurrence of the BEAF PWM in HSF-bound segments located within introns was no different than the background (Figure 9). Consistent with this finding is a recent report that BEAF (boundary element associated factor) binding sites are enriched in 5′ UTRs and in the first 200 bp upstream of gene's TSS [40], [41]. Genes having both BEAF and HSF binding sites do not appear to be strongly enriched in any categories that differ from those enriched among all promoters except for a modest enrichment for genes with cell cycle annotation (p-value  = 0.0011; data not shown) which is consistent with the function of genes BEAF has been shown to regulate [42].

Bottom Line: There were also genes that showed changes in transcript levels that did not appear to correlate with HSF binding sites.We also found that the insulator protein, BEAF, has enriched binding prior to HS to promoters of genes that are bound by HSF upon HS but that are not transcriptionally induced during HS.These results suggest that Drosophila HSF may be regulating many genes besides the known HS genes and that some of these genes may be regulated during non-stress conditions.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Systems Biology, University of Toronto, Mississauga, Canada.

ABSTRACT
During heat shock (HS) and other stresses, HS gene transcription in eukaryotes is up-regulated by the transcription factor heat shock factor (HSF). While the identities of the major HS genes have been known for more than 30 years, it has been suspected that HSF binds to numerous other genes and potentially regulates their transcription. In this study, we have used a chromatin immunoprecipitation and microarray (ChIP-chip) approach to identify 434 regions in the Drosophila genome that are bound by HSF. We have also performed a transcript analysis of heat shocked Kc167 cells and third instar larvae and compared them to HSF binding sites. The heat-induced transcription profiles were quite different between cells and larvae and surprisingly only about 10% of the genes associated with HSF binding sites show changed transcription. There were also genes that showed changes in transcript levels that did not appear to correlate with HSF binding sites. Analysis of the locations of the HSF binding sites revealed that 57% were contained within genes with approximately 2/3rds of these sites being in introns. We also found that the insulator protein, BEAF, has enriched binding prior to HS to promoters of genes that are bound by HSF upon HS but that are not transcriptionally induced during HS. When the genes associated with HSF binding sites in promoters were analyzed for gene ontology terms, categories such as stress response and transferase activity were enriched whereas analysis of genes having HSF binding sites in introns identified those categories plus ones related to developmental processes and reproduction. These results suggest that Drosophila HSF may be regulating many genes besides the known HS genes and that some of these genes may be regulated during non-stress conditions.

Show MeSH
Related in: MedlinePlus