Open Access Highly Accessed Research article

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

Petri Pehkonen1, Lynn Welter-Stahl2, Janine Diwo2, Jussi Ryynänen1, Anke Wienecke-Baldacchino2, Sami Heikkinen1, Eckardt Treuter3, Knut R Steffensen3 and Carsten Carlberg1*

Author Affiliations

1 School of Medicine, Institute of Biomedicine, University of Eastern Finland, FIN-70210 Kuopio, Finland

2 Life Sciences Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg

3 Department of Biosciences and Nutrition, Karolinska Institutet, S-14183 Huddinge, Sweden

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BMC Genomics 2012, 13:50  doi:10.1186/1471-2164-13-50

Published: 31 January 2012

Additional files

Additional file 1:

Figure S1. Validation of LXR antibody. Protein extracts from livers of WT, LXRα-/-, LXRβ-/- and LXRαβ-/- mice [73] (A) or from HeLa cells, which were transfected with the empty pSG5 expression vector as control and pSG5 expressing human LXRα or LXRβ, respectively, using FuGENE 6 transfection reagent (Roche) (B), were separated on 8% sodium dodecyl sulfate (SDS) polyacrylamide gels. Western blotting using anti-LXR antibody was then performed using standard procedures.

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Additional file 2:

Table S1. LXR binding locations in a human macrophage-type cell line. Columns indicate the chromosome, start and end locations of ChIP-Seq peaks, peak length and summit, P-values from Poisson distribution, FE in comparison to IgG, FDR value and information on which sample peak was detected (T09- or vehicle-treated). Information regarding to any peak present in both samples is presented in two separate rows.

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Additional file 3:

Figure S2. Distribution of genomic LXR binding sites to genomic elements. A Distribution of LXR binding locations from the high stringent set of peaks to different genomic elements. Unique peaks represent binding locations present only in one of the two samples (disjoint areas of Venn diagram in Figure 1A) and in both samples (joint set of Venn diagram in Figure 1A). B Distribution of peaks around TSSs of closest genes.

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Additional file 4:

Figure S3. RE types present within the 202 high stringency LXR peak set. Proportions of high stringency set of peaks containing direct repeats (DRs), everted repeats (ERs) and inverted repeats (IRs). Search has been made with RSAT DNA-pattern tool [26] using RGKTCA half-site with indicated number of spacings.

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Additional file 5:

Table S2. Differentially expressed genes in a human macrophage-type cell line. Columns indicate the chromosome, start of the T09 target gene, log2 expression after T09- and vehicle-treatment, adjusted P-value for gene expression difference, gene name and FC. The detected LXR binding locations within proximal (± 100 kb) and distal (± 1 Mb) area from the respective gene TSS are displayed on the right side of the table.

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Additional file 6:

Table S3. Detailed information on all 112 LXR hotspots. Numbers of peaks and genes are indicated similarly as in Table 1. Additional columns indicate the tendency of each region having vast majority (> 2 times) of peaks in T09- (or vehicle-) treated sample versus vehicle- (or T09-) treated sample, the tendency of each region having majority (> 2 times) of up- (or down-) regulated genes versus down- (up-) regulated genes. Moreover, in separate columns up- and down-regulated genes, number of all genes, gene density and enriched GO terms (P < 0.05) are shown. Regions already shown in Table 1 are in bold.

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Additional file 7:

Figure S4. Enrichment statistics of LXR binding locations. The number of LXR peaks in one of the 112 hotspot regions (Figure 2) is compared with the number of all genes (A), the number of DE genes with adjusted P < 0.01 (B), the proportion of DE genes (C) and the density of DE genes (D).

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Additional file 8:

Figure S5. LXR target gene validation. PMA-differentiated THP-1 cells were treated for 4 h with vehicle (DMSO), 1 μM GW3965 (GW) or 1 μM T0901317 (T09), total RNA was extracted and qPCR was performed with primers specific for selected genes. The data were normalized to the expression of the housekeeping gene RPLP0 and fold inductions were calculated in reference to vehicle control. Columns indicate the means of four independent cell treatments and the bars represent standard deviations. Student's t-test was performed to determine the significance of the stimulation in reference to vehicle-treated control (** P < 0.01; *** P < 0.001).

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Additional file 9:

Table S4. Enrichment analysis for all LXR target genes. The analysis was performed using the DAVID tool [37] for all 1063 LXR target genes with P < 0.01 for differential expression. The columns indicate GO identifier, term name, count of associated target genes and the P-value and FDR for the enrichment.

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Additional file 10:

Table S5. qPCR primers used in the validation of gene expression microarray results of select genes.

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