The Genome-- Now in 3D!

• Certain gliomas have a nonsynonymous IDH1 mutation
  • 2-Hydroxyglutarate -> Inhibition of DNA demethylase
  • 3D-Rearrangement -> Oncogenesis

Flavahan et al. 2016–Nature

• Chromatin Capture (e.g. Hi-C) methods reveal 3D proximity
• ChIA-PET enables discovery of specific protein-mediated 3D loops
  
  
  Shlyueva et al. 2014

• ~60% of enhancers affect a gene that isn't the most proximal

• Cohesin subunit: SMC1 (Young)/RAD21 (Snyder)
• CTCF: Structural (~ ½ as many cells; better data)
• POL2: Transcriptionally active
  
  
  

• Tang et al. 2015 (Cell) looked at common variants in CTCF binding regions

• 97% pairs had a similar direction of RNA logFC as loop logFC.

• Predicting cell-specific 3D loops from ChIP-Seq data
• CRISPR Assay modifying loops
• Cancer topology clustering from methylation
• Comprehensive allele-specific looping

ChIA-PET Data in these cell lines–

• Naive & Primed Embryonic Stem Cell
• GM12878
• HeLa, Jurkat, MCF7, K562
  
  

Hi-C Data in these cell lines–

• GM12878
• IMR90
• Naive Embryonic Stem Cell

Courtney– Whole Genome Sequencing Data

• Look for rare variants in CTCF binding regions
  • Burden test
  • Identify loop anchors with potentially disrupted CTCF occupancy
  • Map genes contained in loop from reference cell lines
    
    
• Verify variant functionality with CTCF ChIP-Seq or 3C

Pat– ATAC-Seq, ChIP-Seq, etc.

• Look for differential chromantin accessibility (e.g. conditioned on common variant status)
  • Identify loop anchors with potentially disrupted CTCF occupancy
  • Map genes contained in loop from reference cell lines
  • Link distal enhancer regions to gene promoters using similar cell type (e.g. GM12878)

• Martin Aryee, PhD
  • Research Advisor
    
    
• Sarah Johnstone, MD, PhD
  
  
• Prathik Naidu, Sarah Shareef, and others!

• http://bit.ly/July7OMRF
• dnalandscaper.aryeelab.org