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Figure S5. ChIP-seq analysis of FLAG-H1.3 in OV-3/H1.3(H) cells. from Histone H1.3 Suppresses H19 Noncoding RNA Expression and Cell Growth of Ovarian Cancer Cells

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posted on 2023-03-30, 22:30 authored by Magdalena Medrzycki, Yunzhe Zhang, Weijia Zhang, Kaixiang Cao, Chenyi Pan, Nathalie Lailler, John F. McDonald, Eric E. Bouhassira, Yuhong Fan

Figure S5. ChIP-seq analysis of FLAG-H1.3 in OV-3/H1.3(H) cells. A) Metagene analysis of H1.3 distribution on genes partitioned by gene expression levels (each group containing 20% of genes in genome) over a 10 kb region covering -5 kb to +5 kb of transcription start sites (TSS). On average, H1.3 exhibits the deepest dip at TSS of highly expressed genes (red) but no or minimal dip at TSS of inactive genes (blue). ChIP-seq was performed using anti-FLAG antibody in OV-3/H1.3(H) cells. B) Distribution of H1.3 along H19 (upper) and GAPDH (lower) loci in OV-3/H1.3(H) cells. Y axis: tag counts per 1000 bp window per 10 million mappable reads. IP-IN: normalized signal intensity of ChIP-seq subtracted by that of input-seq.

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ARTICLE ABSTRACT

Ovarian cancer is a deadly gynecologic malignancy for which novel biomarkers and therapeutic targets are imperative for improving survival. Previous studies have suggested the expression pattern of linker histone variants as potential biomarkers for ovarian cancer. To investigate the role of histone H1 in ovarian cancer cells, we characterize individual H1 variants and overexpress one of the major somatic H1 variants, H1.3, in the OVCAR-3 epithelial ovarian cancer cell line. We find that overexpression of H1.3 decreases the growth rate and colony formation of OVCAR-3 cells. We identify histone H1.3 as a specific repressor for the noncoding oncogene H19. Overexpression of H1.3 suppresses H19 expression, and knockdown of H1.3 increases its expression in multiple ovarian epithelial cancer cell lines. Furthermore, we demonstrate that histone H1.3 overexpression leads to increased occupancy of H1.3 at the H19 regulator region encompassing the imprinting control region (ICR), concomitant with increased DNA methylation and reduced occupancy of the insulator protein CTCF at the ICR. Finally, we demonstrate that H1.3 overexpression and H19 knockdown synergistically decrease the growth rate of ovarian cancer cells. Our findings suggest that H1.3 dramatically inhibits H19 expression, which contributes to the suppression of epithelial ovarian carcinogenesis. Cancer Res; 74(22); 6463–73. ©2014 AACR.