- The physical role of chromatin organization in the central dogma
- Aberrations of chromatin organization in disease
- Chromatin conformation capture (3C)
- HiC: a genome-wide extension of 3C
- Analytical methods of HiC data
2019-12-06
Outline
Part 1: Chromosome conformation capture
Chromosome conformation capture
DNA molecules are three dimensional
- DNA is a double-stranded, helical polymer
- Chromosomes are contiguous strands of DNA
- Long strands folded up to take up small space
Chromatin across the length scales
Chromatin across the length scales
Chromatin across the length scales
Chromatin across the length scales
Regulation of gene expression is partially mediated by chromatin organization
Hubs of preferential chromatin interaction bring multiple distal regions together
- Hubs are called topologically associated domains (TADs)
TADs and loops are formed by looping factors
Current leading model of loop formation: loop extrusion
Current leading model of loop formation: loop extrusion
Aberrations of chromatin organization can cause disease
Brachydactly and polydactyly
- Structural variants lead to enhancer hijacking
- Misregulation in embryogenesis leads to developmental defects
Aberrations of chromatin organization can cause disease
Cancer
- Methylation of CTCF site in SDH-deficient gastro-intestinal stromal tumours
- Methylation blocked CTCF binding
- Enhancer hijacking to express FGF4 oncogene
Measuring chromatin organization
- Chromosome fixation
- Restriction digest
- Proximity ligation
Measure chromatin organization across with genome
- Biotinylation for pull down
- Shearing
- Sequencing
Visualizing interactions
- Bin genome
- Aggregate reads
- Squares are “preferential hubs”
Intra-sample normalization
Biases that exist between bins:
- GC content
- Number of restriction enzyme cut sites
- Mappability
Intra-sample normalization
- Doubly-stochastic, symmetric matrix
- “Equal visibility” between loci
Intra-sample normalization
Calling TADs
Calling Loops
cLoops
Current methods are still unclear
- Inter-sample normalization is not well-studied
- Almost as many methods as data resource papers
- Lots of similarities and differences from typical genome sequencing
Break
Workshop
Outline
Part 2: Workshop
- Quality control of raw HiC data
- Pre-processing HiC data
- Visualizing with
cooler
Workshop
Summary
Summary
Spatial organization of chromatin within cells affects gene regulation
Measurement by sequencing-based techniques
Pre-processing tools for HiC data
What I didn’t cover
- Microscopy-based measurements
- Compartmentalization
- Changes over cell division
- Single-cell extensions