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Unraveling intricate relationship between chromatin remodeling, transcription, and cancer

Unraveling intricate relationship between chromatin remodeling, transcription, and cancer b y Michael Tolstorukov Molecular Biology Department, Massachusetts General Hospital for Chromatin and Epigenetics in Cancer June 19-22, 2013 Atlanta, GA.

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Unraveling intricate relationship between chromatin remodeling, transcription, and cancer

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  1. Unraveling intricate relationship between chromatin remodeling, transcription, and cancer by Michael Tolstorukov Molecular Biology Department, Massachusetts General Hospital for ChromatinandEpigeneticsin Cancer June 19-22, 2013 Atlanta, GA

  2. -- mammalian Swi/Snf (Baf) complexcontains conserved core (green) and variant (blue) subunits -- mutation of the complexes is a frequent occurrence in cancer -- it is capable of mobilizing nucleosomes and remodeling chromatin in ATP-dependent manner TSS

  3. Experimental design Murine embryonic fibroblasts (MEFs) MEFs where either Snf5 or Brg1 subunit Wild typeMEFs is genetically deleted MNase digestion + High-throughput sequencing (Helicos, Illumina) Expression profiling (Affymetrix arrays) Data analysis and integration

  4. Global nucleosome occupancy profile at gene starts +1 -1 +2 +3 NDR

  5. Global nucleosome occupancy profile at gene starts +1 -1 +2 +3

  6. Global nucleosome occupancy profile at gene starts +1 -1 +2 +3

  7. Nucleosome phasing at gene starts +4 +2 +1 +3

  8. Nucleosome phasing at gene starts +4 +2 +1 +3 Spectral (Fourier) analysis confirms reduced nucleosomal repeat in Snf5- and Brg1-depleted samples

  9. Swi/Snf inactivation results in both up- and down-regulation of genes with a ‘net’ activation effect

  10. Swi/Snf inactivation results in both up- and down-regulation of genes with a ‘net’ activation effect 515 6 1 322

  11. Swi/Snf inactivation results in both up- and down-regulation of genes with a ‘net’ activation effect 515 6 1 322 Snf5/WT Brg1/WT 6.4 -6.4 fold-change, log2 Up-regulated Down-regulated

  12. Swi/Snf inactivation results in both up- and down-regulation of genes with a ‘net’ activation effect 793 > 491 > 1226 782

  13. Correlation between nucleosome density change and gene expression change upon Swi/Snf inactivation

  14. Gene ontology analysis Enriched gene ontology terms: Cell Cycle Process Cell Cycle Phase Mitotic Cell Cycle Cell Division DNA Metabolic Process Chromosome Segregation Genes that were UP-regulated upon Swi/Snf inactivation Regulation of Cell Motility Cell Migration Locomotion Genes that were DOWN-regulated upon Swi/Snf inactivation

  15. Is Swi/Snf present at the promoters where nucleosome occupancy is altered in mutant cells?

  16. 30% of the regions of Brg1 enrichment are located +/-3kb of TSS, while these regions constitute ~6% of the genome

  17. 30% of the regions of Brg1 enrichment are located +/-3kb of TSS, while these regions constitute ~6% of the genome

  18. Distribution of Brg1 tag density at TSS is bimodal Enriched in CpGi-genes, GO terms related to Cellular Metabolic Processes, Gene Expression Enriched in non-CpGi genes, GO terms related to Signaling Pathways, Sensory Perception

  19. Distribution of Brg1 tag density at TSS is bimodal Enriched in CpGi-genes, GO terms related to Cellular Metabolic Processes, Gene Expression Enriched in non-CpGi genes, GO terms related to Signaling Pathways, Sensory Perception

  20. Why do we observe only moderate correlation between loss of nucleosome occupancy and gene activation?

  21. An ‘array of positioned nucleosomes’ is specific for active, not silent genes

  22. Nucleosome positioning score [“-1”] + [“+1”] – [“NDR”] Score = [“baseline”]

  23. Nucleosome positioning score [“-1”] + [“+1”] – [“NDR”] Score = [“baseline”]

  24. Nucleosome positioning score [“-1”] + [“+1”] – [“NDR”] Score = [“baseline”]

  25. A model: TSS Tolstorukov, Sansam, Ping, et al. and Roberts, PNAS, 2013

  26. A model: TSS Altered transcription profile with net up-regulation effect, ultimately promoting cell proliferation Tolstorukov, Sansam, Ping, et al. and Roberts, PNAS, 2013

  27. Acknowledgements Dana-Farber Cancer Institute, Boston Children’s Hospital Charlie Roberts Courtney Sansam Ping Lu Edward Koellhoffer Katherine Helming Erik Tillman Julia Evans Boris Wilson Xi Wang Center for Biomedical Informatics, HMS Peter Park BurakAlver Funding: Poster B09

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