Zhaohui Steve Qin Department of Biostatistics and Bioinformatics Rollins School of Public Health Emory University 3D Chromosome Organization Statistical challenges and opportunities for analyzing Hi-C data

Transcription regulation

However … Long-range chromosomal interactions Transcriptional factory Chimeric events

Chromosome folding 4 How can a two meter long polymer fit into a nucleus of ten micrometer (10 -5 m) diameter? m

Chromosome folding 5

“… deep things in science are not found because they are useful; they are found because it was possible to find them” -- Robert Oppenheimer 6

Chromosome Conformation Capture (3C) Dekker et al. Science 2002 Naumova and Dekker J of Cell Science Fine scale: (0-kb)

3C-on-chip/Circular 3C (4C) 5C Naumova and Dekker J of Cell Science Fine scale: (0-kb) Intermediate: (0-Mb)

Naumova and Dekker J of Cell Science Fine scale: (0-kb) Whole genome Intermediate: (0-Mb)

10

11

12

chr1 chr2chr3chr4chr5chr6chr7chr8chr9chr1 0 chr1 1 chr1 2 chr1 3 chr1 4 chr1 5 chr1 6 chr1 7 chr1 8 chr1 9 chr2 0 chr2 1 chr2 2 chr X chrY chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr chr X chr Y

What are the main findings?

In Liberman-Aiden et al. Genomes can be decomposed of compartments A and B, Fractal globule, not equilibrium globule.

In Sexton et al. Genome partitioned into physical domains. Domain structure highly connected with epigenetic activities.

In Dixon et al. Topological domains. Stable across cell types. Highly conserved across species. Domain boundaries enriched with insulators.

In Hou et al. Differences between domain boundary and interior, in terms of gene density, TF and epigenetic factor concentration.

Challenges Quality control and pre-processing of the reads, Any bias in the data? and if so, how to normalize? Whether it is possible, and if so, how, to infer the 3-dimesnional chromosomal structure based on the Hi-C data?

20 Hi-C Data Preprocess Restriction enzyme cutting site Restriction enzyme cut fragment Self-ligation reads Dangling reads PCR amplification reads Random breaking reads Random break Valid reads Downstream analysis Imakaev et al. 2012

Systematic biases in the data 21 Yaffe and Tanay, 2011 Restriction enzyme GC content Mappability

Methods for Hi-C Bias Reduction Normalization (equal ‘visibility’, no assumption on biases)  Iterative correction and eigenvector decomposition (ICE) (Imakaev, et al, 2012)  Sequential component normalization (SCN) (Cournac, et al, 2012) Correction (posit a statistical model on biases)  Yaffe & Tanay’s method (Yaffe & Tanay, 2011) Fragment level (4KB, ), 420 parameters  HiCNorm (Hu et al, 2012) Any resolution level 1MB, 10 6, 3 parameters 22

Motivation and the key assumption 23 Number of paired-end reads spanning the two loci is inversely proportional to the 3D spatial distance between them (obtained from fluorescence in situ hybridization(FISH)). Lieberman-Aiden et al, 2009

Bayesian statistical model 24 : number of reads between loci and. : 3D Euclidian distance between loci and. : number of enzyme cut site in locus. : mean GC content in locus. : mean mappability score in locus.

Real Hi-C data from Lieberman-Aiden et al d(L2, L4) = , d(L2, L3) = , significant

mESC: Hind3 vs. Nco1 26

Two compartment model

Whole Chromosome Model 28 Lieberman-Aiden, et al, 2009 Naumova and Dekker, 2010

Other Features (Chromosome 2) 29 CompartmentGene densityGene expressionChromatin accessibility Lamina interaction DNA replication timeH3K36me3H3K27me3 H3K4me3 H3K9me3H3K20me3 RNA polymerase II

References Hu M, Deng K, Selvaraj S, Qin ZS, Ren B, Liu JS. (2012) HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics Hu M, Deng K, Qin ZS, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. (2012) Bayesian inference of three-dimensional chromosomal organization. PLoS Computational Biology. 9(1):e Hou C, Li L, Qin ZS, Corces, VG. (2012) Gene Density, Transcription and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains. Mol Cell (with preview article of Xu and Felsenfeld (2012) Order from Chaos in the Nucleus. Mol Cell ).. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS and Ren B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature

Acknowledgements 31 Ming Hu Ke Deng Jun S. Liu Jesse Dixon Siddarth Selvaraj Bing Ren Li Chunhui Hou Victor Corces