Limits...
Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages.

Pehkonen P, Welter-Stahl L, Diwo J, Ryynänen J, Wienecke-Baldacchino A, Heikkinen S, Treuter E, Steffensen KR, Carlberg C - BMC Genomics (2012)

Bottom Line: The liver X receptors (LXRs) are oxysterol sensing nuclear receptors with multiple effects on metabolism and immune cells.Our results show that LXR actions are focused on 112 genomic regions that contain up to 11 T09 target genes per region under the control of highly stringent LXR binding sites with individual constellations for each region.We could confirm that LXR controls lipid metabolism and transport and observed a strong association with apoptosis-related functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Medicine, Institute of Biomedicine, University of Eastern Finland, FIN-70210 Kuopio, Finland.

ABSTRACT

Background: The liver X receptors (LXRs) are oxysterol sensing nuclear receptors with multiple effects on metabolism and immune cells. However, the complete genome-wide cistrome of LXR in cells of human origin has not yet been provided.

Results: We performed ChIP-seq in phorbol myristate acetate-differentiated THP-1 cells (macrophage-type) after stimulation with the potent synthetic LXR ligand T0901317 (T09). Microarray gene expression analysis was performed in the same cellular model. We identified 1357 genome-wide LXR locations (FDR < 1%), of which 526 were observed after T09 treatment. De novo analysis of LXR binding sequences identified a DR4-type element as the major motif. On mRNA level T09 up-regulated 1258 genes and repressed 455 genes. Our results show that LXR actions are focused on 112 genomic regions that contain up to 11 T09 target genes per region under the control of highly stringent LXR binding sites with individual constellations for each region. We could confirm that LXR controls lipid metabolism and transport and observed a strong association with apoptosis-related functions.

Conclusions: This first report on genome-wide binding of LXR in a human cell line provides new insights into the transcriptional network of LXR and its target genes with their link to physiological processes, such as apoptosis.The gene expression microarray and sequence data have been submitted collectively to the NCBI Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo under accession number GSE28319.

Show MeSH

Related in: MedlinePlus

Co-functional modules of direct LXR target genes. Associations of LXR target genes with the annotations from Reactome, CGAP tissue EST expression, KEGG and GO databases clustered and visualized using heatmap.2 function from R-package gplots [38]. The y-axis columns indicate the annotations and x-axis rows the associated genes. Each association, depicted as a cell of the heat map, has been weighted using the multiplication of log2 FC of a gene (row) and -log10 P-value of annotation (column) enrichment highlighting the most important associations. Red and green color scales are used for up- and down-regulated genes, respectively. Both columns and rows have been clustered using agglomerative hierarchical clustering with asymmetric binary distance measure. The eight gene and annotation clusters cover the majority of the gene set. Indicated is also the LXR peak strength density graph, which summarizes the peak heights over the genes on the x-axis. For each gene the peak strength has been calculated as a sum of the log2 FEs for the highest peak from the close (± 100 kb) and distant region (± 0.1 to ± 1 Mb).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3295715&req=5

Figure 6: Co-functional modules of direct LXR target genes. Associations of LXR target genes with the annotations from Reactome, CGAP tissue EST expression, KEGG and GO databases clustered and visualized using heatmap.2 function from R-package gplots [38]. The y-axis columns indicate the annotations and x-axis rows the associated genes. Each association, depicted as a cell of the heat map, has been weighted using the multiplication of log2 FC of a gene (row) and -log10 P-value of annotation (column) enrichment highlighting the most important associations. Red and green color scales are used for up- and down-regulated genes, respectively. Both columns and rows have been clustered using agglomerative hierarchical clustering with asymmetric binary distance measure. The eight gene and annotation clusters cover the majority of the gene set. Indicated is also the LXR peak strength density graph, which summarizes the peak heights over the genes on the x-axis. For each gene the peak strength has been calculated as a sum of the log2 FEs for the highest peak from the close (± 100 kb) and distant region (± 0.1 to ± 1 Mb).

Mentions: In order to detect the non-redundant sets of genes and associated biological themes, we performed a clustering analysis using enriched gene categories from the databases GO, Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome and CGAP tissue EST expression for the 1063 true LXR target genes. In order to ease the later inspection of results, we limited the number of genes used in the clustering analysis to the 150 most up-regulated and the 76 most down-regulated, preserving the same ratio as between all 706 and 357 up- and down-regulated LXR target genes. For the annotations, we used all that were enriched with FDR < 50%, corresponding to the raw P ≤ 0.036 in the GO enrichment analysis. We were able to use this loose criterion and obtain adequate data, because the clustering is robust to false positive annotations. The genes and associated annotations were clustered and visualized in parallel using the heatmap.2 function available in the R-package gplots [38]. Agglomerative hierarchical clustering with an asymmetric binary distance measure was used by treating each association between a gene and an annotation as 1 and a lack of association as 0. This resulted in eight visually homogeneous clusters of associated genes and annotations (Figure 6): translation-related genes (cluster 1), oxidation- and diabetes-related genes expressed in liver (cluster 2), mRNA processing-related genes (cluster 3), nitrogen metabolism-related genes (cluster 4), programmed cell death regulation-related genes (cluster 5), ubiquitin system genes with relation to cell cycle and apoptosis (cluster 6), genes related to intracellular transport including cholesterol transport (cluster 7) and general ubiquitin system-related genes (cluster 8).


Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages.

Pehkonen P, Welter-Stahl L, Diwo J, Ryynänen J, Wienecke-Baldacchino A, Heikkinen S, Treuter E, Steffensen KR, Carlberg C - BMC Genomics (2012)

Co-functional modules of direct LXR target genes. Associations of LXR target genes with the annotations from Reactome, CGAP tissue EST expression, KEGG and GO databases clustered and visualized using heatmap.2 function from R-package gplots [38]. The y-axis columns indicate the annotations and x-axis rows the associated genes. Each association, depicted as a cell of the heat map, has been weighted using the multiplication of log2 FC of a gene (row) and -log10 P-value of annotation (column) enrichment highlighting the most important associations. Red and green color scales are used for up- and down-regulated genes, respectively. Both columns and rows have been clustered using agglomerative hierarchical clustering with asymmetric binary distance measure. The eight gene and annotation clusters cover the majority of the gene set. Indicated is also the LXR peak strength density graph, which summarizes the peak heights over the genes on the x-axis. For each gene the peak strength has been calculated as a sum of the log2 FEs for the highest peak from the close (± 100 kb) and distant region (± 0.1 to ± 1 Mb).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3295715&req=5

Figure 6: Co-functional modules of direct LXR target genes. Associations of LXR target genes with the annotations from Reactome, CGAP tissue EST expression, KEGG and GO databases clustered and visualized using heatmap.2 function from R-package gplots [38]. The y-axis columns indicate the annotations and x-axis rows the associated genes. Each association, depicted as a cell of the heat map, has been weighted using the multiplication of log2 FC of a gene (row) and -log10 P-value of annotation (column) enrichment highlighting the most important associations. Red and green color scales are used for up- and down-regulated genes, respectively. Both columns and rows have been clustered using agglomerative hierarchical clustering with asymmetric binary distance measure. The eight gene and annotation clusters cover the majority of the gene set. Indicated is also the LXR peak strength density graph, which summarizes the peak heights over the genes on the x-axis. For each gene the peak strength has been calculated as a sum of the log2 FEs for the highest peak from the close (± 100 kb) and distant region (± 0.1 to ± 1 Mb).
Mentions: In order to detect the non-redundant sets of genes and associated biological themes, we performed a clustering analysis using enriched gene categories from the databases GO, Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome and CGAP tissue EST expression for the 1063 true LXR target genes. In order to ease the later inspection of results, we limited the number of genes used in the clustering analysis to the 150 most up-regulated and the 76 most down-regulated, preserving the same ratio as between all 706 and 357 up- and down-regulated LXR target genes. For the annotations, we used all that were enriched with FDR < 50%, corresponding to the raw P ≤ 0.036 in the GO enrichment analysis. We were able to use this loose criterion and obtain adequate data, because the clustering is robust to false positive annotations. The genes and associated annotations were clustered and visualized in parallel using the heatmap.2 function available in the R-package gplots [38]. Agglomerative hierarchical clustering with an asymmetric binary distance measure was used by treating each association between a gene and an annotation as 1 and a lack of association as 0. This resulted in eight visually homogeneous clusters of associated genes and annotations (Figure 6): translation-related genes (cluster 1), oxidation- and diabetes-related genes expressed in liver (cluster 2), mRNA processing-related genes (cluster 3), nitrogen metabolism-related genes (cluster 4), programmed cell death regulation-related genes (cluster 5), ubiquitin system genes with relation to cell cycle and apoptosis (cluster 6), genes related to intracellular transport including cholesterol transport (cluster 7) and general ubiquitin system-related genes (cluster 8).

Bottom Line: The liver X receptors (LXRs) are oxysterol sensing nuclear receptors with multiple effects on metabolism and immune cells.Our results show that LXR actions are focused on 112 genomic regions that contain up to 11 T09 target genes per region under the control of highly stringent LXR binding sites with individual constellations for each region.We could confirm that LXR controls lipid metabolism and transport and observed a strong association with apoptosis-related functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Medicine, Institute of Biomedicine, University of Eastern Finland, FIN-70210 Kuopio, Finland.

ABSTRACT

Background: The liver X receptors (LXRs) are oxysterol sensing nuclear receptors with multiple effects on metabolism and immune cells. However, the complete genome-wide cistrome of LXR in cells of human origin has not yet been provided.

Results: We performed ChIP-seq in phorbol myristate acetate-differentiated THP-1 cells (macrophage-type) after stimulation with the potent synthetic LXR ligand T0901317 (T09). Microarray gene expression analysis was performed in the same cellular model. We identified 1357 genome-wide LXR locations (FDR < 1%), of which 526 were observed after T09 treatment. De novo analysis of LXR binding sequences identified a DR4-type element as the major motif. On mRNA level T09 up-regulated 1258 genes and repressed 455 genes. Our results show that LXR actions are focused on 112 genomic regions that contain up to 11 T09 target genes per region under the control of highly stringent LXR binding sites with individual constellations for each region. We could confirm that LXR controls lipid metabolism and transport and observed a strong association with apoptosis-related functions.

Conclusions: This first report on genome-wide binding of LXR in a human cell line provides new insights into the transcriptional network of LXR and its target genes with their link to physiological processes, such as apoptosis.The gene expression microarray and sequence data have been submitted collectively to the NCBI Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo under accession number GSE28319.

Show MeSH
Related in: MedlinePlus