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Non-Coding RNA 2016, 2(3), 7; doi:10.3390/ncrna2030007

Promoter-Associated RNAs Regulate HSPC152 Gene Expression in Malignant Melanoma

1
Laboratory of Molecular Cell Biology, Centre for Cancer Research and Department of Medicine C, Chaim Sheba Medical Centre, Tel-Hashomer 52621, Israel
2
Functional Genomics Laboratory, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
3
Institute of Oncology, Sheba Medical Center, Tel Hashomer 52621, Israel
4
Molecular Pathology Unit, Institute of Pathology University Hospital Basel, CH-4031 Basel, Switzerland
Recent Address Centre for Cancer Research, Chaim Sheba Medical Centre, Tel-Hashomer 52621, Israel
*
Authors to whom correspondence should be addressed.
Academic Editor: George A. Calin
Received: 12 December 2015 / Revised: 13 June 2016 / Accepted: 19 June 2016 / Published: 30 June 2016
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Abstract

The threshold of 200 nucleotides (nt) conventionally divides non-coding RNAs (ncRNA) into long ncRNA (lincRNA, that have more than 200 nt in length) and the remaining ones which are grouped as “small” RNAs (microRNAs, small nucleolar RNAs and piwiRNAs). Promoter-associated RNAs (paRNAs) are generally 200–500 nt long and are transcribed from sequences positioned in the promoter regions of genes. Growing evidence suggests that paRNAs play a crucial role in controlling gene transcription. Here, we used deep sequencing to identify paRNA sequences that show altered expression in a melanoma cell line compared to normal melanocytes. Thousands of reads were mapped to transcription start site (TSS) regions. We limited our search to paRNAs adjacent to genes with an expression that differed between melanoma and normal melanocytes and a length of 200–500 nt that did not overlap the gene mRNA by more than 300 nt, ultimately leaving us with 11 such transcripts. Using quantitative real-time PCR (qRT-PCR), we found a significant correlation between the expression of the mRNA and its corresponding paRNA for two studied genes: TYR and HSPC152. Ectopic overexpression of the paRNA of HSPC152 (designated paHSPC) enhanced the expression of the HSPC152 mRNA, and an siRNA targeting the paHSPC152 decreased the expression of the HSPC152 mRNA. Overexpression of paHSPC also affected the epigenetic structure of its putative promoter region along with effects on several biologic features of melanoma cells. The ectopic expression of the paRNA to TYR did not have any effect. Overall, our work indicates that paRNAs may serve as an additional layer in the regulation of gene expression in melanoma, thus meriting further investigation. View Full-Text
Keywords: Promoter-Associated RNA; HSPC152; TYR; Melanoma Promoter-Associated RNA; HSPC152; TYR; Melanoma
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MDPI and ACS Style

Bonen, H.; Kol, N.; Shomron, N.; Leibowitz-Amit, R.; Quagliata, L.; Lorber, T.; Sidi, Y.; Avni, D. Promoter-Associated RNAs Regulate HSPC152 Gene Expression in Malignant Melanoma. Non-Coding RNA 2016, 2, 7.

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