Lieberman-Aiden et al. (2009) Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326:

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1 Lieberman-Aiden et al. (2009) Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326: : Understanding the 3D conformation of the genome can provide insight into chromatin structure, gene expression, and cellular processes. Imaging of painted chromosomes is laborious and only provides information about the spatial positions of a small number of markers at the time of imaging. Chromosome conformation capture (3C) can be used to identify pairs of loci that come into close contact, but is also locus-specific. This study introduces a new genome-wide version of 3C called Hi-C. Jay Taylor (ASU) APM Lecture 13 Fall / 19

2 Hi-C consists of six steps. Step 1: The DNA is crosslinked. Formaldehyde (CH 2 O) forms crosslinks between nucleic acids and proteins. Crosslinking mainly occurs between amino groups and nearby nitrogen atoms. Jay Taylor (ASU) APM Lecture 13 Fall / 19

3 Step 2: The crosslinked DNA is digested. Restriction endonucleases (REs) are bacterial enzymes that cut DNA at specific nucleotide sequences. This study used HindIII and NcoI which recognize the palindromic sequences 5 -A A G C T T-3 and 5 -C C A T G G-3. The human genome contains approximately 850,000 HindIII restriction sites. HindIII and NcoI both create DNA fragments with complementary 5 overhangs known as sticky ends. Jay Taylor (ASU) APM Lecture 13 Fall / 19

4 Step 3: The sticky ends are filled and marked with biotin. The reactive sticky ends are converted to less reactive blunt ends by the addition of nucleotides and DNA polymerase. The blunt ends are also marked with biotin (vitamin B7), which is incorporated as biotin-dctp. Jay Taylor (ASU) APM Lecture 13 Fall / 19

5 Step 4: The filled DNA ends are ligated. Ligases are enzymes that join dsdna strands together. T4 DNA ligase is specifically used to anneal blunt ends. By carrying out the reaction under very dilute conditions, ligation mainly occurs between the crosslinked DNA fragments. Ligation of HindIII fragments creates a new Nhel restriction site within the annealed region which is used for quality control. Jay Taylor (ASU) APM Lecture 13 Fall / 19

6 Step 5: The ligated DNA is purified and sheared into small fragments. Protein and RNA are separated from the DNA enzymatically and by centrifugation. Biotin is then removed from unligated ends using an exonuclease. The purified DNA is sheared into bp fragments using ultrasound. The biotinylated fragments are isolated by passage through a column containing streptavidin beads. Streptavidin is a bacterial enzyme with a very high affinity for biotin. Jay Taylor (ASU) APM Lecture 13 Fall / 19

7 Step 6: The purified fragments are sequenced with paired-ends. Paired-end sequencing works by sequencing each end of a short DNA fragment. The resulting reads are called paired ends and are bp long. This study used the Illumina platform with 76 bp reads. Each component of the ligated fragment was identified by aligning the corresponding end read to the reference human genome. Proximity and orientation relative to HindIII sites in the reference genome were used to confirm each alignment. Jay Taylor (ASU) APM Lecture 13 Fall / 19

8 Summary Statistics The authors created a Hi-C library using 25 million cells derived from an EBV-transformed human lymphoblastoid tissue culture. Sequencing of this library generated 8.4 million alignable read pairs. Of these, 6.7 million corresponded to long-range contacts between sites separated by > 20 kb (or on different chromosomes). Spatial proximity maps were constructed by dividing the genome into 1-Mb regions (loci) and setting m ij = number of ligation products between locus i and locus j. This overlap matrix averages over the spatial conformations of the genomes in the original sample of cells. Jay Taylor (ASU) APM Lecture 13 Fall / 19

9 Reproducibility The reproducibility of the Hi-C results was investigated by producing libraries for two separate experiments with HindIII and a third with NcoI. Since the contact matrices for all three libraries were highly-correlated (Pearson s r = and r = for C or D vs. B), the three data sets were combined. Jay Taylor (ASU) APM Lecture 13 Fall / 19

10 Chromosome Territories The contact matrix was used to estimate the contact probability I n (s) within each chromosome as a function of the genomic distance between loci. In each case, I n (s) decreases monotonically with s. However, intrachromosomal contact probabilities at all distances exceed the average contact probabilities between different chromosomes. The last observation is consistent with the existence of chromosome territories. Figure 2A Jay Taylor (ASU) APM Lecture 13 Fall / 19

11 Interchromosomal Contacts Fig. 2B is a heat map showing observed/expected numbers of interchromosomal contacts. Red indicates enrichment. Consistent with FISH studies, the map shows an excess of interactions between small, gene-rich chromosomes (16-17, 19-22). Chr. 18 is gene-poor and interacts less frequently with the other small chromosomes. FISH shows that chr. 18 localizes near the nuclear periphery. Figure 2B Jay Taylor (ASU) APM Lecture 13 Fall / 19

12 Spatial Compartmentalization of Chromosome 14 Fig. 3B plots the observed/expected contacts between loci in chr. 14 relative to the genome-wide averages (M ). Fig. 3C shows the Pearson correlation matrix C for the rows and columns of M. Red blocks are highly positively correlated. The plaid pattern suggests that chr. 14 is divided into two sets of loci such that contacts are enriched within sets but depleted between them. These sets were also identified using principal component analysis. Jay Taylor (ASU) APM Lecture 13 Fall / 19

13 Genome-Wide Spatial Compartmentalization Fig. 3D shows the correlation matrix for the intrachromosomal contact profiles of loci on chr. 14 versus chr. 20. The compartment labels A and B can be assigned to each chromosome so that sets of loci on different chromosomes carrying the same label have correlated contact profiles. This suggests that a common feature is responsible for compartmentalization of each chromosome. Jay Taylor (ASU) APM Lecture 13 Fall / 19

14 Loci belonging to the same compartment tend to be closer in space than those in different compartments. L1 and L3 are in A; L2 and L4 are in B. FISH shows that L3 is consistently closer to L1 than to L2. Likewise, L2 is closer to L4 than L3. Comparable results were found for 4 loci on chr. 22. Jay Taylor (ASU) APM Lecture 13 Fall / 19

15 The spatial compartments correspond to gene density and expression. Compartment A correlates with: gene density (ρ = 0.431); mrna expression (ρ = 0.476); DNAseI sensitivity (ρ = 0.651), which is a proxy for chromatin accessibility; H3K36 trimethylation (ρ = 0.601), which is an activating chromatin mark. In contrast, the Hi-C data shows that loci at a fixed genomic distance in compartment B interact more frequently than comparable loci in compartment A. Jay Taylor (ASU) APM Lecture 13 Fall / 19

16 Compartmentalization in Different Cell Types A separate Hi-C library was constructed for a sample of cells from a erythroleukemia cell line (K562) with an abnormal karyotype. The K562 compartments also are significantly correlated with open and closed chromatin states. Although the compartment patterns in K562 and GM06990 are similar (r = 0.732), many loci that are in the open compartment of one cell type are in the closed compartment of the other. Jay Taylor (ASU) APM Lecture 13 Fall / 19

17 The authors compare the results of the Hi-C experiment with the conformations predicted by two models of the structure of a chromosome. The equilibrium globule is a compact, highly-knotted configuration of a polymer at equilibrium in a poor solvent. The fractal globule is a non-equilibrium configuration formed by an unentangled polymer that passes through successive rounds of crumpling. Fig. 4C Jay Taylor (ASU) APM Lecture 13 Fall / 19

18 Chromatin packing is consistent with the fractal globule model. The intrachromosomal contact probability I (s) scales like s 1.08 for genomic distances between 500 kb and 7 Mb. 3D-FISH experiments indicate that physical distance scales like s 1/3 for genomic distances between 500 kb and 2 Mb. These results are consistent with simulated fractal globules but not with simulated equilibrium globules, e.g., I (s) s 1 for the former and like s 3/2 for the latter. Jay Taylor (ASU) APM Lecture 13 Fall / 19

19 Conclusions On the scale of several megabases, the Hi-C results are consistent with a fractal model of chromatin organization. More detailed analyses are needed to assess the extent to which this model describes human chromosomes (e.g., different models can give rise to the same power laws). The fractal globule model is attractive because it predicts that chromosomes are only weakly entangled or knotted, which would facilitate folding and unfolding during chromatin remodeling, gene activation, and the cell cycle. The Hi-C technique can be used to construct comprehensive interaction maps that should provide insight into gene regulation and chromosome crosstalk. Jay Taylor (ASU) APM Lecture 13 Fall / 19