Comparative levels of GH promoter methylation in mice.

<p><b>A.</b> Above, schematic of the relative position of CpGs in the mouse GH promoter. Middle, pairwise analysis comparing the levels of DNA methylation in wild type (WT) with dwarf (dw) mice (Snell) using bisulfite DNA sequencing. Bottom, combined bisulfite restriction analysis (CoBRA) of the CpG located at position −4 on the same samples. The proportion of non-methylated C nucleotide is indicated by the cleaved FokI products (blue arrow). <b>B.</b> The GH promoter becomes demethylated during mouse development and is coincident with GH gene expression. Above, schematic illustration of the developmental events relating to Pit-1-mediated induction of the GH gene and concomitant loss of GH promoter methylation. Below, pyrosequencing of bisulfite-treated genomic DNA extracted from mouse pituitary, selected from different days of mouse development (e14.5, P0.5 or P14.5) and displayed as the percent methylation of CpG sites in the mouse promoter.</p

Profiling gene expression from cells with knock-down levels of SmcHD1.

<p><b>A.</b> Retroviral shRNA directed towards SmcHD1 efficiently down-regulated SmcHD1 protein levels in HEK293 cells. shRNAs directed towards SmcHD1, a control shRNA or empty plasmid (pQCXIP) was used for retroviral infection HEK293 cells. NEs were prepared from stably infected cells and analyzed by immunoblot with an anti-SmcHD1 antibody. An anti-LSD1 antibody was used as an internal control for loading. <b>B.</b> A disproportionate number of genes were up-regulated on the X-chromosome in SmcHD1 knock-down cells. A pie chart was used to illustrate the percentage of genes on each chromosome that were up- or down- regulated in SmcHD1 knock-down cells. <b>C.</b> Heat map and hierarchal clustering of selected up- and down- regulated genes in SmcHD1 knock-down cells or cells infected with control non-specific NC5 shRNA. Below, scaling of the fold differences of the genes from cells. Intense red indicates up-regulation and intense blue indicates down-regulation.</p

The H19/Igf2 imprinted locus was dis-regulated following SmcHD1 knock-down.

<p><b>A.</b> A number of imprinted genes associated with BWS and SRS were dysregulated in SmcHD1 SH-SY5Y knock-down cells. A graphical representation of the H19/Igf2 locus on the human chromosome at position 11p15.5. Maternally imprinted genes are highlighted in blue, maternally expressed genes are in red, one of the placental-specific imprinted genes is colored in brown and not imprinted genes are in green. A non-coding RNA, Kcnq1ot1 is colored in blue and is typically expressed from the paternal chromosome presumably acting to silence genes normally expressed from the maternal chromosome (M) including Kcnq1 and Cdkn1c. Differentially DNA methylated regions (ICR1, KvDMR1 (ICR2)) are indicated by the trapezoids (solid indicates hypermethylation and open hypomethylation). <b>B.</b> mRNA quantitation of selected genes in the H19/Igf2 locus using RT-qPCR in SmcHD1 SH-SY5Y knock-down cells. The copy numbers are relative to and corrected using β-actin cDNA levels. * indicates P-values <0.05, ** P-values <0.01 and *** P-values <0.001 using an unpaired Students t-test.</p

Identification of a GH promoter DMR using mouse BAC transgenes.

<p><b>A.</b> A mouse BAC transgene encompassing GH gene was modified by homologous recombination to replace the mouse GH gene with the rat GH proximal promoter and the coding sequence for RFP. A second recombination event using the same BAC transgene was used to delete a putative distal LCR (ΔLCR- GH:RFP). Imaging of dissected mouse pituitary, illustrates RFP expression from the WT-GH:RFP but not ΔLCR-GH:RFP transgenic mice. <b>B.</b> WT-GH:RFP protein mirrored endogenous GH expression. Pituitaries were fixed and embedded in paraffin, the tissue sectioned and subjected to indirect immunofluorescence with anti-GH, anti-Prl and anti-TSHβ antibodies using Cy2-cojugated secondary antibodies. The images were merged with images of RFP expression. Note: RFP was nuclear while the hormones were localized to the cytoplasm. <b>C.</b> Pairwise analysis of the rat GH promoter methylation levels by bisulfite sequencing of pituitary DNA from WT-GH:RFP and ΔLCR-GH:RFP transgenic mice. The number indicates the relative position of the CpG from the transcriptional start site. The n-values indicate the number of clones sequenced from transgenic mice and used for the pairwise statistical analysis.</p

Inhibition of DNA methylation relieves transcriptional repression of GH and characterization of a methyl-DNA binding activity.

<p><b>A.</b> GH gene repression can be relieved by treatment with 5-azaC. Above, schematic illustration of the CpG sites location in the rat GH promoter (the CpGs are numbered according to their relative position from the transcriptional start site). Middle, bisulfite sequencing of genomic DNA extracted from pituitary derived-GH+ (GC cells) or GH− cells (MMQ cells). The level of DNA methylation is displayed as unmethylated (open circles) or methylated (solid circles) from individual clones. Lower, GH− cells (MMQ) were treated with 5-azaC and the level of gene expression compared using RT-qPCR. The solid bars represent 5-azaC treated cells and the open bars, cells cultured under normal conditions. <b>B.</b> A methyl-specific binding protein binds to a region of DNA derived from the mouse GH promoter. Above, DNA sequence of the double-stranded oligonucleotides used in the EMSA. The position of the CpGs relative to the transcriptional start site are indicated and the position of a previously described binding site for the thyroid hormone receptor (TR) is boxed. Lower left, EMSA with MMQ nuclear extracts comparing the bound proteins from either methylated (lane 2) or unmethylated DNA probes (lane 5). A methylated competitor DNA (M) reveals a specific upper methyl-DNA protein-binding component (Lane 3, arrow). Lower right, an EMSA competition assay with nuclear extracts from pituitary-derived cell lines (MMQ, GC and GHFT) as indicated. Methylated or unmethylated (U) competitor oligonucleotides were used to identify the upper shifted component representing a DNA bound protein. All nuclear extracts contained a methyl-DNA binding protein. <b>C.</b> Methylation of CpGs at position −8 and −7 were required for recruiting a methyl DNA binding protein. Above, schematic of the result from the competition assay illustrated below. The shaded area indicates CpGs essential for the methyl DNA binding protein. Below, an EMSA with MMQ nuclear extracts (NE) and a methylated DNA probe with various competitor oligonucleotides as indicated. <b>D.</b> The methyl-DNA binding activity observed with the GH DMR appears to be unique. The sequence of the oligonucleotides used in the competition assay are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097535#pone.0097535.s006" target="_blank">Table S1</a>. An EMSA with increasing amounts of MMQ NE (6 and 12 µg) and a methylated GH DMR probe optionally in the presence of competitor oligonucleotides (100X) as indicated.</p

A TRIP230-Retinoblastoma Protein Complex Regulates Hypoxia-Inducible Factor-1α-Mediated Transcription and Cancer Cell Invasion

Localized hypoxia in solid tumors activates transcriptional programs that promote the metastatic transformation of cells. Like hypoxia-inducible hyper-vascularization, loss of the retinoblastoma protein (Rb) is a trait common to advanced stages of tumor progression in many metastatic cancers. However, no link between the role of Rb and hypoxia-driven metastatic processes has been established. We demonstrated that Rb is a key mediator of the hypoxic response mediated by HIF1α/β, the master regulator of the hypoxia response, and its essential co-activator, the thyroid hormone receptor/retinoblastoma-interacting protein (TRIP230). Furthermore, loss of Rb unmasks the full co-activation potential of TRIP230. Using small inhibitory RNA approaches in vivo, we established that Rb attenuates the normal physiological response to hypoxia by HIF1α. Notably, loss of Rb results in hypoxia-dependent biochemical changes that promote acquisition of an invasive phenotype in MCF7 breast cancer cells. In addition, Rb is present in HIF1α-ARNT/HIF1β transcriptional complexes associated with TRIP230 as determined by co-immuno-precipitation, GST-pull-down and ChIP assays. These results demonstrate that Rb is a negative modulator of hypoxia-regulated transcription by virtue of its direct effects on the HIF1 complex. This work represents the first link between the functional ablation of Rb in tumor cells and HIF1α-dependent transcriptional activation and invasion

Effect of selective aryl hydrocarbon receptor modulators on estrogen-inducible transcription.

<p>The effect of 1 µM DiMNF on E2-inducible CAT-D expression in MCF7 and ECC-1 cells. Cells were treated with the indicated ligands for 24 h prior to RNA isolation. Gene expression was determined as described above. Error bars represent ± S.D. * p<0.05.</p

Effect of ARNT knockdown on ARNT, CAT-D and ERα protein levels.

<p>ECC-1 (<b>A and B</b>) and MCF7 (<b>C and D</b>) cells were transfected with either siSCX or siARNT and ligand treated as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029545#pone-0029545-g002" target="_blank">Figure 2</a>. (<b>A and C</b>) Representative Western blots of ARNT, CAT-D, ERα and α-tubulin protein levels. Bar graphs of CAT-D protein levels in ECC-1 (<b>B</b>) and MCF7 (<b>D</b>) cells after normalizing luminescence values to α-tubulin. Open bars represent ligand treatments after siRNA to scrambled negative control (siSCX) and closed (black) bars represent ligand treatments after siRNA to ARNT (siARNT). Experiments were performed three times with essentially identical outcomes.</p

Loss of ARNT shows a cell specific co-activator or co-repressor transcriptional function.

<p>ECC-1 cells (<b>A and B</b>) and MCF7 cells (<b>C and D</b>) were transfected with either scrambled siRNA (siSCX) or siRNA directed to ARNT (siARNT#1 or siARNT#3). Twenty-four hours after transfection, cells were treated with vehicle (DMSO), E2 (10 nM), TCDD (2 nM) or a combination of E2 and TCDD. Gene expression was determined by real-time RT-PCR after isolation and reverse transcription of total RNA. <i>CAT-D</i> and <i>pS2</i> expression were normalized to constitutively active 36B4 gene expression. (<b>E</b>) Western blot analysis of CAT-D protein levels in MCF7 and ECC-1 cells. Cells were treated with DMSO or E2 (10 nM) and varying concentrations of TCDD (10 pM, 50 pM, 100 pM, 500 pM, 1 nM or 5 nM). After 24 hours of treatment, whole cell lysates were harvested, and Western Blot assays were performed using antibodies directed against CAT-D and α-tubulin. Error bars represent ± S.D. * p<0.05.</p