7eb1787320e88d2379c594ccb40916a6 cells-13-01001.pdf 83963c5ba0f04c8bd690fd43915b419c0334a066 cells-13-01001.pdf cfa7ecaa80b837d033b5b6b766b60c4c63e652959727e96ddb133dda43dd4c12 cells-13-01001.pdf Title: Epigenetic Regulation of DLK1-DIO3 Region in Thyroid Carcinoma Subject: Non-coding RNAs (ncRNAs) have emerged as pivotal regulators in cellular biology, dispelling their former perception as ‘junk transcripts’. Notably, the DLK1-DIO3 region harbors numerous ncRNAs, including long non-coding RNAs (lncRNAs) and over 50 microRNA genes. While papillary thyroid cancer showcases a pervasive decrease in DLK1-DIO3-derived ncRNA expression, the precise mechanisms driving this alteration remain elusive. We hypothesized that epigenetic alterations underlie shifts in ncRNA expression during thyroid cancer initiation and progression. This study aimed to elucidate the epigenetic mechanisms governing DLK1-DIO3 region expression in this malignancy. We have combined the analysis of DNA methylation by bisulfite sequencing together with that of histone modifications through ChIP-qPCR to gain insights into the epigenetic contribution to thyroid cancer in cell lines representing malignancies with different genetic backgrounds. Our findings characterize the region’s epigenetic signature in thyroid cancer, uncovering distinctive DNA methylation patterns, particularly within CpG islands on the lncRNA MEG3-DMR, which potentially account for its downregulation in tumors. Pharmacological intervention targeting DNA methylation combined with histone deacetylation restored ncRNA expression. These results contribute to the understanding of the epigenetic mechanisms controlling the DLK1-DIO3 region in thyroid cancer, highlighting the combined role of DNA methylation and histone marks in regulating the locus’ expression. Keywords: thyroid cancer; epigenetics; methylation; ncRNAs Author: Letícia F. Alves, Isabelle N. da Silva, Diego C. de Mello, Cesar S. Fuziwara, Sonia Guil, Manel Esteller and Murilo V. 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Title: Cell Culture Destination: subsection.2.1 Item: Title: Methylation Array Destination: subsection.2.2 Item: Title: MAPK Pathway Inhibition Destination: subsection.2.3 Item: Title: TCGA Methylation Data Analysis Destination: subsection.2.4 Item: Title: Bisulfite-qPCR Destination: subsection.2.5 Item: Title: Overall Survival Analysis Destination: subsection.2.6 Item: Title: Treatment with 5-Aza-dC and TSA Destination: subsection.2.7 Item: Title: Quantitative Reverse Transcription PCR (RT-qPCR) Destination: subsection.2.8 Item: Title: Chromatin Immunoprecipitation (ChIP) for Histone Modifications Destination: subsection.2.9 Item: Title: Results Destination: section.3 Children: Item: Title: DNA Methylation of the DLK1-DIO3 Region Is Disrupted in Thyroid Cancer-Derived Cell Lines Destination: subsection.3.1 Item: Title: Hypermethylation of MEG3-DMR CGIs in Human Papillary Thyroid Carcinoma Samples from TCGA Destination: subsection.3.2 Item: Title: Silencing of MEG3 Is Mediated by DNA Methylation and Histone Acetylation Destination: subsection.3.3 Item: Title: Discussion Destination: section.4 Item: Title: Conclusions Destination: section.5 Item: Title: References Destination: appendix.A. Info: Title: Epigenetic Regulation of DLK1-DIO3 Region in Thyroid Carcinoma Author: Letícia F. Alves, Isabelle N. da Silva, Diego C. de Mello, Cesar S. Fuziwara, Sonia Guil, Manel Esteller and Murilo V. Geraldo Subject: Non-coding RNAs (ncRNAs) have emerged as pivotal regulators in cellular biology, dispelling their former perception as ‘junk transcripts’. Notably, the DLK1-DIO3 region harbors numerous ncRNAs, including long non-coding RNAs (lncRNAs) and over 50 microRNA genes. While papillary thyroid cancer showcases a pervasive decrease in DLK1-DIO3-derived ncRNA expression, the precise mechanisms driving this alteration remain elusive. We hypothesized that epigenetic alterations underlie shifts in ncRNA expression during thyroid cancer initiation and progression. This study aimed to elucidate the epigenetic mechanisms governing DLK1-DIO3 region expression in this malignancy. We have combined the analysis of DNA methylation by bisulfite sequencing together with that of histone modifications through ChIP-qPCR to gain insights into the epigenetic contribution to thyroid cancer in cell lines representing malignancies with different genetic backgrounds. Our findings characterize the region’s epigenetic signature in thyroid cancer, uncovering distinctive DNA methylation patterns, particularly within CpG islands on the lncRNA MEG3-DMR, which potentially account for its downregulation in tumors. Pharmacological intervention targeting DNA methylation combined with histone deacetylation restored ncRNA expression. These results contribute to the understanding of the epigenetic mechanisms controlling the DLK1-DIO3 region in thyroid cancer, highlighting the combined role of DNA methylation and histone marks in regulating the locus’ expression. 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