Histone signature of metanephric mesenchyme cell lines

Nathan McLaughlin

Xiao Yao

Yuwen Li

Zubaida Saifudeen

Samir El-Dahr

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^{Department of Pediatrics; The Renal and Hypertension Center of Excellence; Tulane University School of Medicine; New Orleans, LA USA}

^{Department of Biomedical Sciences Program; The Renal and Hypertension Center of Excellence; Tulane University School of Medicine; New Orleans, LA USA}

^{The Renal and Hypertension Center of Excellence; Tulane University School of Medicine; New Orleans, LA USA}

^{Correspondence to: Samir S El-Dahr, Email:}ude.enalut@rhadles

Received 2013 Jun 5; Revised 2013 Jul 11; Accepted 2013 Jul 15.

Abstract

The metanephric mesenchyme (MM) gives rise to nephrons, the filtering units of the mature kidney. The MM is composed of uninduced (Six2^/Lhx1^low) and induced (Wnt-stimulated, Six2^/Lhx1^high) cells. The global epigenetic state of MM cells is unknown, partly due to technical difficulty in isolating sufficient numbers of homogenous cell populations. We therefore took advantage of two mouse clonal cell lines representing the uninduced (mK3) and induced (mK4) metanephric mesenchyme (based on gene expression profiles and ability to induce branching of ureteric bud). ChIP-Seq revealed that whereas H3K4me3 active region “peaks” are enriched in metabolic genes, H3K27me3 peaks decorate mesenchyme and epithelial cell fate commitment genes. In uninduced mK3 cells, promoters of “stemness” genes (e.g., Six2, Osr1) are enriched with H3K4me3 peaks; these are lost in induced mK4 cells. ChIP-qPCR confirmed this finding and further demonstrated that G9a/H3K9me2 occupy the promoter region of Six2 in induced cells, consistent with the inactive state of transcription. Conversely, genes that mark the induced epithelialized state (e.g., Lhx1, Pax8), transition from a non-permissive to an active chromatin signature in mK3 vs. mK4 cells, respectively. Importantly, stimulation of Wnt signaling in uninduced mK3 cells provokes an active chromatin state (high H3K4me3, low H3K27me3), recruitment of β-catenin, and loss of pre-bound histone methyltransferase Ezh2 in silent induced genes followed by activation of transcription. We conclude that the chromatin signature of uninduced and induced cells correlates strongly with their gene expression states, suggesting a role of chromatin-based mechanisms in MM cell fate.

Keywords: kidney development, nephron progenitors, histone modifications, histone methylation, metanephric mesenchyme cells, ChIP-Seq

Abstract

Acknowledgments

The Authors acknowledge Steve Potter (Univ. of Cincinnati) for the mouse metanephric mesenchyme mK3 and mK4 cell lines. ChIP-Seq bioinformatics and statistical analyses were performed in collaboration with GenPathways. This work was supported by NIH grants 1P50 {"type":"entrez-nucleotide","attrs":{"text":"DK096373","term_id":"187408880","term_text":"DK096373"}}DK096373–01 (Pediatric Center of Excellence in Nephrology) and {"type":"entrez-nucleotide","attrs":{"text":"DK079886","term_id":"187540818","term_text":"DK079886"}}DK079886, and 1P20 RR017659. We acknowledge the assistance of the Renal and Hypertension Center and The Louisiana Cancer Research Consortium Microscopy and FACS Cores. E.K. is supported by a medical student research grant from the American Society of Nephrology. This work was performed as a part of Ph.D. thesis (N.M.).

Acknowledgments

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Disclosure of Potential Conflicts of Interest

Supplemental Materials

Supplemental materials may be found here: www.landesbioscience.com/journals/epigenetics/article/25753

Supplemental Materials

Footnotes

Previously published online: www.landesbioscience.com/journals/epigenetics/article/25753

Footnotes

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