UNIVERSIDADE DE LISBOA Faculdade de Ciências Departamento de Biologia Vegetal The role of SETD2 in transcription and in DNA damage response Sílvia Filipa Camoeira Gonçalves de Carvalho Dissertação Mestrado em Biologia Molecular e Genética 2012 UNIVERSIDADE DE LISBOA Faculdade de Ciências Departamento de Biologia Vegetal The role of SETD2 in transcription and in DNA damage response Sílvia Filipa Camoeira Gonçalves de Carvalho Dissertação orientada pelo Doutor Sérgio Fernandes de Almeida e pelo Prof. Doutor Rui Gomes Mestrado em Biologia Molecular e Genética 2012 Content Content .................................................................................................................................................. ii List of Figures .......................................................................................................................................iv List of Abbreviations .............................................................................................................................. v Original Articles .................................................................................................................................. vii Sumário .............................................................................................................................................. viii Resumo .................................................................................................................................................ix Abstract ............................................................................................................................................... xiv Introduction ............................................................................................................................................ 1 1. Chromatin structure ........................................................................................................................ 1 2. Chromatin remodelling ................................................................................................................... 1 3. Transcription .................................................................................................................................. 2 3.1. The FACT complex is a major regulator of nucleosome dynamics ........................................... 3 4. DNA damage response ................................................................................................................... 4 4.1. DNA damage signalling ............................................................................................................ 4 4.2. p53 activation during the DNA damage repair .......................................................................... 5 5. Chromatin and cancer ..................................................................................................................... 6 5.1. Clear cell renal cell carcinoma ................................................................................................... 6 6. Aims of the study............................................................................................................................ 6 Results and Discussion ........................................................................................................................... 8 1. SETD2 role in transcription ............................................................................................................ 8 1.1. Downregulation of SETD2 affects RNAPII turnover at the transcription site ........................... 8 1.2. SETD2 prevents widespread intragenic transcription initiation ............................................... 10 1.3. SETD2 promotes FACT recruitment ....................................................................................... 12 2. SETD2 role in DNA damage response ......................................................................................... 13 2.1. ccRCC cell lines as an experimental model system to investigate the tumour suppressor role of SETD2 ............................................................................................................................................ 13 2.2. SETD2 is required for DNA damage repair ............................................................................. 14 2.3. SETD2 is required for ATM activation following DNA damage ............................................ 16 2.4. SETD2 is needed for proper DNA damage signalling ............................................................. 17 2.5. SETD2 regulates p53 activity during DNA damage repair ...................................................... 18 2.6. The role of SETD2 in DDR is independent from H3K36me3 ................................................. 19 Conclusion and Outlook ....................................................................................................................... 21 ii Material and Methods........................................................................................................................... 23 1. Cell culture ................................................................................................................................... 23 2. RNA interference .......................................................................................................................... 23 3. Western blot ................................................................................................................................. 23 4. Chromatin Immunoprecipitation ................................................................................................... 24 5. Fluorescence recovery after photobleaching (FRAP) ................................................................... 24 6. RNA-seq data analysis .................................................................................................................. 25 7. Comet assay .................................................................................................................................. 25 8. Immunofluorescence .................................................................................................................... 25 Acknowledgments ................................................................................................................................ 27 Bibliography......................................................................................................................................... 29 Annexes.................................................................................................................................................. I Annex I ................................................................................................................................................ I Annex II .............................................................................................................................................. II iii List of Figures Figure 1 SETD2 is a determinant of RNPII levels along the coding region of transcribed genes ........... 9 Figure 2 Genome-wide analysis of intragenic transcription initiation induced by SETD2 depletion.... 11 Figure 3 SETD2 is required for FACT recruitment .............................................................................. 12 Figure 4 SETD2 activity is reduced in mutant ccRCC ......................................................................... 13 Figure 5 SETD2 activity is required for DSBs repair ........................................................................... 15 Figure 6 SETD2 activity is required for ATM activation ..................................................................... 16 Figure 7 SETD2 activity is needed for DSBs signalling ....................................................................... 17 Figure 8 SETD2 is required for p53 activation ..................................................................................... 18 Figure 9 H3K36me3 levels do not change during the DDR ................................................................. 20 Figure 10 Proposed mechanism of SETD2 action as a regulator of transcription initiation and DDR .. 22 iv List of Abbreviations ATM Ataxia telangiectasia mutated ATMp ATM phosphorylated at Ser1981 ccRCC Clear cell renal cell carcinoma ChIP Chromatin immunoprecipitation CK2 Casein kinase 2 Ct Cycle threshold DDR DNA damage response DNA Deoxyribonucleic acid DNA-PKcs DNA-dependent protein kinase, catalytic subunit DSBs Double strand breaks FACT Facilitates chromatin transcription FBS Fetal bovine serum FRAP Fluorescence recovery after photobleaching h Hours H2Bub Histone H2B ubiquitinated H3K36me3 Histone H3 lysine 36 trimethylation MDM2 Mouse Double Minute 2 ITI Intragenic transcription initiation min Minutes MRN Mre11, Rad50 and Nbs1 MUT Mutant p21 Protein 21 p53 Protein 53 p53p Protein 53 phosphorylated at Ser15 RCC Renal cell carcinoma RNAi RNA interference RNAPII RNA polymerase II RNAPII-GFP RNA polymerase II fused to green fluorescent protein RT-qPCR Real time quantitative polymerase chain reaction PBS Phosphate buffered saline v s Seconds SDS-PAGE Sodium dodecyl sulphate polyacrylamide gel electrophoresis SETD2 SET domain containing 2 SPT6 Suppressor of Ty 6 homolog SPT16 Suppressor of Ty 16 homolog siRNA Small interfering RNA SSRP1 Structure specific recognition protein 1 Ser Serine U2OS Human osteosarcoma-derived cells VHL Von Hippel-Lindau WT Wild-type x Times γH2AX Histone H2AX phosphorylated at Ser139 vi Original Articles