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Timeline of Epigenetic Changes Induced by Ethanol (Etoh) in Hepg2 and HL60

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Timeline of Epigenetic Changes Induced by Ethanol (Etoh) in Hepg2 and HL60 Timeline of Epigenetic Changes Induced by Ethanol (EtOH) in HepG2 and HL60 Sophia Sayeed Qureshi This thesis is submitted in partial fulfilment of the requirements for the degree of Master of Science Department of Biological Science University of Bergen November 2019 1 Acknowledgements This project is a collaboration between the Department of Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Bergen and Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Science, University of Bergen. I would like to express my gratitude to various people that have, for better and for worse, been journeying with me in this thesis. First, I would like thank my supervisors; Professor Stephanie Le Hellard for letting me a part of the group and for her positive attitude, Anne-Kristin Stavrum for her never-ending patience and Anja Torsvik for her amazing knowledge in cell culture (and helping my cells to live) An honourable mention to Andrea, Carla and Jonelle, for helping me and occasionally making me laugh. Working with all of you has indeed been an immensely educational experience! To all family and friends, who in one way or another shared their support, either morally, academically or technically, thank you. Lastly, I would like to thank myself for rising from numerous mental breakdowns & crying sessions throughout my academic career, and for writing this thesis! Sophia, you did good! Sophia Sayeed Qureshi, 2019 - Bergen 2 Table of contents Acknowledgements ...........................................................................................................................2 1. Abstract .....................................................................................................................................5 2. Abbreviations ............................................................................................................................6 3. List of Figures............................................................................................................................8 4. List of Tables ........................................................................................................................... 10 5. Introduction ............................................................................................................................ 11 5.1 What is DNA? ........................................................................................................................ 11 5.2 DNAs association within the cell ........................................................................................... 12 5.3 Gene function ........................................................................................................................ 13 5.4 Transcription of DNA into mature mRNA ........................................................................... 15 5.5 Translation of mature mRNA into protein ........................................................................... 16 5.6 Epigenetics ............................................................................................................................. 17 5.6.1 DNA Methylation............................................................................................................ 18 5.6.2 Active DNA demethylation ............................................................................................. 19 5.6.3 Passive DNA demethylation ........................................................................................... 20 5.6.4 Histone variants .............................................................................................................. 21 5.7 Environmental epigenetics .................................................................................................... 22 5.7.1 Epigenetics after exposure of environmental chemicals and toxins .............................. 22 5.7.2 Nutritional epigenetics .................................................................................................... 23 5.7.3 Behavioural epigenetics .................................................................................................. 24 5.8 Profile of DNA methylation with microarray technology .................................................... 25 6. Aim of the thesis ...................................................................................................................... 27 7. Materials .................................................................................................................................. 28 7.1 Genes ..................................................................................................................................... 29 8. Methods ................................................................................................................................... 30 8.1 Cell culture ............................................................................................................................ 30 8.1.1 – Cultivation of cells ....................................................................................................... 30 8.1.2 – Passage of cells ............................................................................................................. 30 8.1.3 – Cell counting ................................................................................................................ 30 8.1.4 – Thawing frozen cells .................................................................................................... 31 8.1.5 – Cryopreserving cells .................................................................................................... 31 8.1.6 – Mycoplasma testing ..................................................................................................... 31 8.2 Ethanol evaporation test and viability assays ................................................................. 33 8.2.1 – Measurement of ethanol evaporation .......................................................................... 33 3 8.2.2 – MTT assay ................................................................................................................... 33 8.2.3 – Trypan blue staining assay .......................................................................................... 34 8.3 Design of experiment and treatment ..................................................................................... 35 8.4 Purification and extraction of total RNA and genomic DNA ............................................... 37 8.5 Up-concentration of DNA ..................................................................................................... 38 8.6 Agarose gel electrophoresis ................................................................................................... 38 8.7 Methylation typing ................................................................................................................ 38 8.7.1 Principal component analysis (PCA) ............................................................................. 39 8.7.2 Factor analysis ................................................................................................................ 39 8.7.3 Spline analysis ................................................................................................................. 40 8.7.4 Profile searches ............................................................................................................... 40 8.7.5 Linear models for microarray ........................................................................................ 41 9. Results ..................................................................................................................................... 42 9.1 Determination of design & experimental parameters .......................................................... 42 9.1.1 Evaporation of ethanol (EtOH) ...................................................................................... 42 9.1.2 Cell viability and proliferation ....................................................................................... 43 9.2 Processing of data and performance of methylation analysis .............................................. 45 9.2.1 Principal component analysis (PCA) ............................................................................. 45 9.2.2 Quantile-quantile (Q-Q) plot .......................................................................................... 49 9.2.3 Spline analysis ................................................................................................................. 49 9.2.4 Factor analysis with linear models for microarray (limma).......................................... 51 9.2.5 Profile searches ............................................................................................................... 53 10. Discussion ............................................................................................................................ 63 10.1 Main findings ................................................................................................................... 63 10.2 Discussion of performed analyses ................................................................................ 65 10.3 Methodological considerations ........................................................................................ 66 11. Conclusion ..........................................................................................................................
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