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DECIPHERING THE HISTONE CODE

DECIPHERING THE HISTONE CODE. E NRIQUE B LANCO. NUMBER OF SLIDES: 21 EXPECTED TIME: 25 minutes. TRANSCRIPTIONAL REGULATION. GENE REGULATORY ARCHITECTURE. Gene regulation can be coordinated in the genome into different levels: Individual genes Chromosomal domains Entire chromosomes

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DECIPHERING THE HISTONE CODE

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  1. DECIPHERING THE HISTONE CODE ENRIQUE BLANCO NUMBER OF SLIDES: 21 EXPECTED TIME: 25 minutes

  2. TRANSCRIPTIONAL REGULATION BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  3. GENE REGULATORY ARCHITECTURE Gene regulation can be coordinated in the genome into different levels: • Individual genes • Chromosomal domains • Entire chromosomes The regulatory code is constituted of different components: • Transcription factors • Regulatory sequences • Chromatin structure • Histone modification states BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  4. GENE PROMOTERS TSS TF1 TF2 TF3 TFn 5’ CTGCTGCATGATATCTTCTACGACACCATCATGCTAGGGGCTACTAGTCGTTACGTAGCTAGC TFBS1 TFBS2 TFBS3 TFBSn GENE 3’ PROXIMAL PROMOTER BASAL PROMOTER • TFBSs avg. length 6 - 15 bp • 1 TFBSs may recruit different TFs • 1 TF binds different TFBSs • Context constraints (space, compatibility) BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  5. ENHANCERS BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  6. CHROMATIN REMODELLING BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  7. NUCLEOSOMES AND HISTONES BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  8. HISTONE MODIFICATIONS BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  9. HISTONE H3 MODIFICATIONS BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  10. HISTONE PROFILES BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  11. HISTONE PROFILES (2) BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  12. ENHANCERS AND HISTONE MODIFICATIONS active poised BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  13. INSULATORS BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  14. PROMOTER ANALYSIS HNF1- binding sites (human) ------------AGTTAATCATTGGCC--------- -------------GTTAATTATTGGCAAATGTCCC- -------GTATGGGTTACTTATTCTCTCTTTGTTGA ------------GGTTAAGACTCTAAT--------- -------AGTCTAGTTAATAATCTACAATT------ ---------TGAGATTAATA---------------- ---------AATGATTAAAA---------------- -------------GTCAAACATTAAC---------- ----------CCGATTAACCATTAACCCCCACCCC- -------------GTTAATCAGAAAA---------- GGATGTATGTAGAATTACATAAGAA----------- -------------CTTACTCAATAAC---------- Sequence Logo (consensus) BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  15. OVERPREDICTION BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  16. COREGULATED GENES ? CONDITION 1 CONDITION 2 BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  17. IMPROVEMENTS: HISTONE MODIFICATIONS active poised BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  18. BROWSING ChIP-SEQ INFORMATION: UCSC BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  19. BROWSING ChIP-SEQ INFORMATION: modENCODE BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  20. BROWSING RNA-SEQ INFORMATION: FLYBASE BIOINFORMATICS ENVIRONMENTS ENRIQUE BLANCO 2011 eblanco@ub.edu

  21. DECIPHERING THE HISTONE CODE ENRIQUE BLANCO NUMBER OF SLIDES: 21 EXPECTED TIME: 25 minutes

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