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Open chromatin features in topological domains and replication TTRs

Open chromatin features in topological domains and replication TTRs. Bob Thurman, UW 26 July, 2012 mouse ENCODE analysis call. 1. DNaseI at topo-domain boundaries. From Dixon et al., Nature. 2. Topo-domain boundary characteristics. CTCF. From Dixon et al., Nature (supplement) .

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Open chromatin features in topological domains and replication TTRs

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  1. Open chromatin features in topological domains and replication TTRs Bob Thurman, UW 26 July, 2012 mouse ENCODE analysis call 1

  2. DNaseI at topo-domain boundaries From Dixon et al., Nature 2

  3. Topo-domain boundary characteristics CTCF From Dixon et al., Nature (supplement) From Dixon et al., Nature 3

  4. DNaseI at topo-domain boundaries chr10 Smoothed DNaseI Smoothed DNaseI peaks Topo-domain boundaries DNaseI tag density 4

  5. DNaseI at topo-domain boundaries chr10 Smoothed DNaseI Smoothed DNaseI peaks Topo-domain boundaries DNaseI tag density 5

  6. DNaseI at topo-domain boundaries So it appears the boundaries are foci of regulatory activity. 6

  7. Explore Hi-C interactions from perspective of total interactions per locus, in addition to directionality index (DI) From Dixon et al., Nature 7

  8. Explore Hi-C interactions from perspective of total interactions per locus, in addition to directionality index (DI) Total interactions at locus = sum of two diagonals originating there (= sum across all columns of interaction matrix row) From Dixon et al., Nature 8

  9. Explore Hi-C total interactions per locus chr10 Smoothed DNaseI Topodomain boundaries Smoothed Hi-C total Interactions Hi-C total interactions DNaseI density 9

  10. Explore Hi-C total interactions per locus chr10 Smoothed DNaseI Topodomain boundaries Smoothed Hi-C total Interactions Hi-C total interactions DNaseI density 10

  11. Explore Hi-C total interactions per locus 11

  12. Explore Hi-C total interactions per locus 12

  13. From Dixon et al., Nature Interesting paradox that would like to understand better: Topo-domain boundaries clearly separate directionality of interactions: the left hand (A) does not talk to the right hand (B). And yet, boundaries appear to be foci of activity (H3K4me3, DNaseI, TSS). …and even enriched for interactions. 13

  14. From Dixon et al., Nature Interesting paradox that would like to understand better: Topo-domain boundaries clearly separate directionality of interactions: the left hand (A) does not talk to the right hand (B). And yet, boundaries appear to be foci of activity (H3K4me3, DNaseI, TSS). …and even enriched for interactions. Further possible interpretation: Boundary, which is open, contains key regulatory elements that are in dynamic physical contact with both A and B. 14

  15. DNaseI in and around TTR (timing transition region) boundaries From Tyrone and Ben… TTR 15

  16. From Tyrone and Ben… 16

  17. DNaseI in and around TTR boundaries 17

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