DNMT- and HDAC-inhibitors globally induce cryptic transcription start sites encoded in long terminal repeats
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1 DNMT- and HDAC-inhibitors globally induce cryptic transcription start sites encoded in long terminal repeats DGHO Jahrestagung, Stuttgart Germany Michael Daskalakis of Epigenomics and Cancer Risk Factors, C010 German Cancer Research Center Heidelberg
2 Offenlegung Interessenskonflikte 1. Anstellungsverhältnis oder Führungsposition Keine 2. Beratungs- bzw. Gutachtertätigkeit Keine 3. Besitz von Geschäftsanteilen, Aktien oder Fonds Keine 4. Patent, Urheberrecht, Verkaufslizenz Keine 5. Honorare Keine 6. Finanzierung wissenschaftlicher Untersuchungen Keine 7. Andere finanzielle Beziehungen Keine 8. Immaterielle Interessenkonflikte Keine
3 Page3 Epigenetic drug treatment Epigenetic changes are potentially reversible DNMT- and HDAC-inhibitors received FDA approval Mechanistic basis of clinical activity not fully understood Reactivation of epigenetically silenced TSGs Up-regulation of double stranded RNA molecules ( viral mimicry )
4 Page4 Omics approach to characterize the mode of action of epigenetic drugs Treatment DAC (DNA hypomethylation) SB939 (Histone acetylation) DAC+SB939 Next-generation sequencing Cap-analysis of gene expression (CAGE) Chromatin immunoprecipitation (ChIP) Whole-genome bisulfite (WGBS) Integrative data analysis TSS activity (CAGE) DNA methylation (WGBS) Chromatin modifications (ChIP)
5 Page5 Experimental outline
6 Page6 Epigenetic treatment globally alters TSS activity in cancer cells
7 Page7 Treatment-induced non-annotated transcripts (TINATs) arise after inhibition of epigenetic enzymes
8 Page8 TINAT expression in comparison with FANTOM5 data
9 Page9 Splicing event of TINATs
10 TINAT-exon fusion transcripts encode novel protein isoforms Page10 Translation: In silico prediction In vitro translation Polysome profiling MHC I binding Aberrant isoforms
11 Cell viability of NCI-H1299 cells using DOX-inducible TINAT-derived ORFs Page11
12 Global epigenomic reprogramming after DNMT or HDAC inhibition Page12 H2AK9ac H3K23ac
13 Cryptic transcripts (TINATs) predominantly arise from LTR12C elements Page13
14 LTR12C promoter region: putative NFY, SP1, and GATA2 binding sites Page14
15 10/1/2017 LTR12C Page15 expression upon epigenetic drug treatment and sirna-gata2 k.o. => GATA2 protein is required for LTR12C reactivation
16 Page16 Summary Genome wide reactivation of cryptic transcripts (TINATs) via epigenetic drug treatment (DNMTis and/or HDACis) TINATs arise from retroviral elements (mainly LTR12 family) Splicing events and protein coding potential of TINATs TINAT-exon fusion transcripts encode novel protein isoforms with predicted abnormal or immunogenic function Reactivation of ERV1 elements dependent on TFs (GATA2, NFY, others?)
17 Page17 of Epigenomics and Cancer Risk Factors David Brocks Christopher R. Schmidt Sara Laudato Daniel Lipka Christopher Oakes Clarissa Gerhäuser Yassen Assenov Alzbeta Ressnerova Md Saiful Islam Monika Helf Oliver Mücke Marion Bähr Karin Klimo Christoph Plass of Applied Bioinformatics/ of Theoretical Bioinformatics Charles Imbusch, Benedikt Brors Clinical Cooperation Unit Pediatric Oncology Ina Oehme Till Milde Olaf Witt Molecular Biology of the Cell II Holger Bierhoff, Ingrid Grummt of Stem Cells and Cancer (DKFZ) and HI-STEM ggmbh Simon Haas Marieke Essers Genome Organization & Function (DKFZ) and Bioquant Heidelberg Jan-Philipp Mallm Karsten Rippe Daofeng Li, Bo Zhang, Ting Wang Center of Molecular Biology Johanna Schott, Georg Stöcklin Dept. Hematology/Oncology Nadja Blagitko-Dorfs, Michael Lübbert Rainer Claus Jan Korbel Dept. Hematology/Oncology Lisa Pleyer, Richard Greil Institute of Pharmaceutical Sciences Chemical Epigenetics Group Manfred Jung
18 Thank you for your attention!
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