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Int. J. Mol. Sci. 2019, 20(2), 242; https://doi.org/10.3390/ijms20020242

Chromosome Conformation Capture Reveals Two Elements That Interact with the PTBP3 (ROD1) Transcription Start Site

1
Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Department of Molecular Oncology and Genetics, 85-796 Bydgoszcz, Poland
2
The Ludwik Rydygier Collegium Medicum, Department of Thoracic Surgery And Tumours, Nicolaus Copernicus University, 85-796 Bydgoszcz, Poland
3
Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
*
Author to whom correspondence should be addressed.
Received: 1 November 2018 / Revised: 31 December 2018 / Accepted: 3 January 2019 / Published: 9 January 2019
(This article belongs to the Special Issue Epigenetic Alterations in Age-Associated Diseases and Cancers)
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Abstract

The long-range control of gene expression is facilitated by chromatin looping and can be detected using chromosome conformation capture—3C. Here we focus on the chromatin architecture of the PTBP3 (Polypyrimidine tract binding protein 3) locus to evaluate its potential role in regulating expression of the gene. PTBP3 expression in prostate cancer cell lines is found significantly higher compared to skin fibroblasts using real-time PCR (p < 0.05) and digital droplet PCR (p < 0.01). Exploration of the chromatin spatial architecture of a nearly 200-kb fragment of chromosome 9 encompassing the PTBP3 gene identified two elements located 63 kb upstream and 48 kb downstream of PTBP3, which looped specifically to the PTBP3 promoter. These elements contain histone acetylation patterns characteristic of open chromatin regions with active enhancers. Our results reveal for the first time that long-range chromatin interactions between the −63 kb and +48 kb loci and the PTBP3 promoter regulate the expression of this gene in prostate cancer cells. These interactions support an open chromatin form for the PTBP3 locus in cancer cells and the three-dimensional structural model proposed in this paper. View Full-Text
Keywords: chromatin conformation; PTBP3; ROD1 (Regulator Of Differentiation 1); cancer epigenetic; gene expression regulation; prostate cancer chromatin conformation; PTBP3; ROD1 (Regulator Of Differentiation 1); cancer epigenetic; gene expression regulation; prostate cancer
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Kubiak, M.; Jurek, A.; Kamińska, K.; Kowalewski, J.; Huang, S.; Lewandowska, M.A. Chromosome Conformation Capture Reveals Two Elements That Interact with the PTBP3 (ROD1) Transcription Start Site. Int. J. Mol. Sci. 2019, 20, 242.

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