29 NGS Hi-C 2017 9 1 1
n Hi-C l Chromosome Conformation Capture l Hi-C n Hi-C l Hi-C l l l l TAD l 3D 2
n Fastq Hi-C 3 n python python.py Hi-C 3
Bio-Linux-8.0.7_hm_kh.ova ~/HiC 1_mapping_read_to_genome 2_filtering_reads 3_normalization 4_convert_Juice 5_detect_TADs 6_modeling_3D python Results data fastq Index Bowtie2 ref fasta src 4
Hi-C ex. Hi-C 5
NGS n n l l l Reseq l RNA-seq l ChIP-seq l ATAC-seq l Hi-C l irep 6
Chromosome Conformation Capture (3C) Dekker, Job, et al. "Capturing chromosome conformation." Science 295.5558 (2002): 1306-1311. 3C-based method DNA 7
3C-based technologies de Wit, Elzo, and Wouter de Laat. "A decade of 3C technologies: insights into nuclear organization." Genes & development 26.1 (2012): 11-24. 8
4C: Chromosome conformation capture-on-chip viewpoint PCR NGS 4C-seq de Wit, Elzo, and Wouter de Laat. "A decade of 3C technologies: insights into nuclear organization." Genes & development 26.1 (2012): 11-24. 9
4C: Chromosome conformation capture-on-chip 4C-seq Hi-C validation Ke, Yuwen, et al. "3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis." Cell 170.2 (2017): 367-381. 10
Hi-C Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science 326.5950 (2009): 289-293. vs. Forward, Reverse 11
Hi-C i j (i, j) Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159.7 (2014): 1665-1680. 12
Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159.7 (2014): 1665-1680. 13
L2 Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159.7 (2014): 1665-1680. L1 L3 14
Topologically Associated Domains (TADs) TAD Akdemir, Kadir Caner, and Lynda Chin. "HiCPlotter integrates genomic data with interaction matrices." Genome biology 16.1 (2015): 198. 15
Topologically Associated Domains (TADs) Ke, Yuwen, et al. "3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis." Cell 170.2 (2017): 367-381. 16
Topologically Associated Domains (TADs) Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159.7 (2014): 1665-1680. Fudenberg, Geoffrey, et al. "Formation of chromosomal domains by loop extrusion. Cell reports 15.9 (2016): 2038-2049. 17
Nagano, Takashi, et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547 (2017): 61 67 18
Hi-C 1. 2. 3. meta3c Marbouty, Martial, et al. "Metagenomic chromosome conformation capture (meta3c) unveils the diversity of chromosome organization in microorganisms. Elife 3 (2014): e03318. 19
Hi-C n l Bin 10 100 20
Hi-C n excl. single cell Hi-C l 3 O'sullivan, Justin M., et al. "The statistical-mechanics of chromosome conformation capture. Nucleus 4.5 (2013): 390-398 21
Hi-C n excl. single cell Hi-C l Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159.7 (2014): 1665-1680. 22
Hi-C n 3C 1 1 l l Genome Architecture Mapping Beagrie, Robert A., et al. "Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543.7646 (2017): 519-524. 23
n Hi-C l Chromosome Conformation Capture l Hi-C n Hi-C l Hi-C l l l l TAD l 3D 24
Hi-C Trimmomatic, cutadapt, fastqc Bowtie2, BWA, Juicer, hiclib, HiCUP, HIPPIE Juicer, hiclib, HiCUP, HIPPIE, HOMER Juicer, hiclib, HIPPIE, HOMER TAD 3 Fit-Hi-C, GOTHiC, HOMER, HIPPIE, HiCCUPS HiCseg, TADbit, Arrowhead, TADtree, Armatus ChromSDE, ShRec3D, PASTIS 25
Bio-Linux-8.0.7_hm_kh.ova ~/HiC 1_mapping_read_to_genome 2_filtering_reads 3_normalization 4_convert_Juice 5_detect_TADs 6_modeling_3D python Results data fastq Index Bowtie2 ref fasta src 26
Results mv 27
In situ Hi-C Kilobase Hi-C 100 fastq 100GB Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159.7 (2014): 1665-1680. 28
~/HiC/data Rao, et al. 2014 Human B-Lymphocyte: GM12878 1000 $cd ~/HiC/data $ls l R1, R2 fastq 29
~/HiC/Ref hg19 http://hgdownload.cse.ucsc.edu/downloads.html FASTA 30
~/HiC/Index ~/HiC/Ref hg19 bowtie2-build Bowtie2 31
Hi-C Trimmomatic TAD 3 32
Hi-C $cd ~/HiC/1_mapping_read_to_genome TAD 3 33
Illumina http://assets.illumina.com/content/dam/illuminamarketing/images/technology/paired-end-sequencing-figure.gif 34
Hi-C Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science 326.5950 (2009): 289-293. 35
Hi-C R1, R2 R1 R2 36
Hi-C 1. 2. => R1, R2 Imakaev, Maxim, et al. "Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature methods 9.10 (2012): 999-1003. 37
1. R1, R2 R1, R2 3 I. R1, R2 II. a. LocusA, LocusB LocusB Locus A B b. III. 2. Iterative alignment method 38
Iterative alignment method Imakaev, Maxim, et al. "Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature methods 9.10 (2012): 999-1003. 39
$less mapping.py R1 R2 40
bp 35bp 41
$python mapping.py Bowtie2 Bowtie2 42
$ls l../data 43
$less parse_results.py HDF5 Biopython Restriction 44
$python parse_results.py $ls -l HDF5 HDFView python HDF5 45
Hi-C $cd ~/HiC/2_filtering_reads TAD 3 46
R1, R2 Hi-C Imakaev, Maxim, et al. "Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature methods 9.10 (2012): 999-1003. 47
$less filtering.py maximummoleculelength 400bp HDF5 48
$less filtering.py filterrsitestart(): DNA filterduplicates(): PCR duplicate filterlarge(): 10^5bp filterextreme(): 0.5% 49
$less filtering.py 1Mbp Bin raw read count 1Mbp 3,000 3,000 Bin 90% 80% 1000 50
$python filtering.py $ls -l 51
$less./statistics.txt 52
Hi-C $cd ~/HiC/3_normalization TAD 3 53
1. 2. Hi-C I. Ligation II. GC III. Mappability. ChIP-seq: INPUT RNA-seq: 1 Hi-C 54
Hi-C 1. Explicit GC Yaffe and Tanay 2011 HiCNorm 2. Implicit Vanilla coverage, ICE, Knight and Ruiz 2012 55
Raw heatmap Normalized heatmap Raw coverage Corrected coverage 56
k l! A #$ #! A #& # 57
k l 1 A #& # k l 1 A #$ # 58
1 # A #$ # A #* 1 # A #$ # A #+ k = Vanilla coverage normalization 1 # A #$ # A #& l! A #$ # 59
Vanilla coverage normalization i j i j GC implicit bias Explicit Imakaev, Maxim, et al. "Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature methods 9.10 (2012): 999-1003. Explicit Implicit 60
Iterative correction (ICE method) Vanilla coverage normalization Þ Vanilla coverage normalization matrix balancing ICE matrix balancing Knight and Ruiz 2012 61
$less normalize.py Raw read count Bin ICE 62
$python normalize.py heatmap.pdf 63
TAD 3D 19 $python submatrix.py $less norm_mat.txt 64
JuiceBox JuiceBox JuiceBox $cd ~/4_convert_Juice $less convert_to_juicetext.py $python convert_to_juicetext.py $less./forjuice.txt $./convert_to_juicehic.sh test.hic Juice 65
JuiceBox $./execute_juicebox.sh File => Open => Local test.hic Chromosomes Annotations ENCODE 66
Hi-C TAD 3 67
L2 L1 L3 Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159.7 (2014): 1665-1680. 68
Forcato, Mattia, et al. "Comparison of computational methods for Hi-C data analysis." Nature methods 14.7 (2017): 679. 69
Fit-Hi-C (Global background) Ay, Ferhat, Timothy L. Bailey, and William Stafford Noble. "Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome research 24.6 (2014): 999-1011. ICE p-value 70
HiCCUPS (Local background) Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159.7 (2014): 1665-1680. K&R p-value 71
Hi-C TAD $cd ~/HiC/5_detect_TADs 3 72
Topologically Associated Domains (TADs) Forcato, Mattia, et al. "Comparison of computational methods for Hi-C data analysis." Nature methods 14.7 (2017): 679. TAD TAD 73
TADtree Caleb Weinreb, Benjamin J. Raphael; Identification of hierarchical chromatin domains, Bioinformatics, Volume 32, Issue 11, 1 June 2016, Pages 1601 1609 TAD, sub-tad Python 74
TADtree Caleb Weinreb, Benjamin J. Raphael; Identification of hierarchical chromatin domains, Bioinformatics, Volume 32, Issue 11, 1 June 2016, Pages 1601 1609 TAD TAD TAD 75
$less./control_file.txt TAD Bin TAD TAD TAD 76
TADtree $python TADtree.py./control_file.txt./output/chr19 N TAD proportion_duplicates.txt TAD BED Bin 77
TAD TAD DNA TAD TAD Forcato, Mattia, et al. "Comparison of computational methods for Hi-C data analysis. Nature methods 14.7 (2017): 679. Ke, Yuwen, et al. "3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis." Cell 170.2 (2017): 367-381. 78
Hi-C TAD 3 $cd ~/HiC/6_modeling_3D 79
3D Hi-C Serra, et al. 2015 1. 2. a. b. 80
3D 1. https://ja.wikipedia.org/wiki/ 2. 81
82
D #,. = 1 A #,. 1 α=1 Ai,j = 0 Di,j => Þ Shortest-path reconstruction ShRec3D Lesne, et al. 2014 MATLAB 83
Shortest-path reconstruction Bin 84
Shortest-path reconstruction Floyd-Warshall 85
$less./convert_contact_to_distance.py Python NetworkX 19 19 $python./convert_contact_to_distance.py../3_normalization/norm_mat.txt dist.npy 86
3 Multi-dimensional scaling; MDS 16S PCoA MDS 16S MDS OK 3 87
3 $less./modeling_3d.py dist.npy MDS $python modeling_3d.py 88
Dekker, Job, et al. "Capturing chromosome conformation." science 295.5558 (2002): 1306-1311. de Wit, Elzo, and Wouter de Laat. "A decade of 3C technologies: insights into nuclear organization." Genes & development 26.1 (2012): 11-24. Ke, Yuwen, et al. "3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis." Cell 170.2 (2017): 367-381. Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." science 326.5950 (2009): 289-293. Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping."cell 159.7 (2014): 1665-1680. Akdemir, Kadir Caner, and Lynda Chin. "HiCPlotter integrates genomic data with interaction matrices." Genome biology 16.1 (2015): 198. Fudenberg, Geoffrey, et al. "Formation of chromosomal domains by loop extrusion." Cell reports 15.9 (2016): 2038-2049. Nagano, Takashi, et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547 (2017): 61 67 Marbouty, Martial, et al. "Metagenomic chromosome conformation capture (meta3c) unveils the diversity of chromosome organization in microorganisms." Elife 3 (2014): e03318. O'sullivan, Justin M., et al. "The statistical-mechanics of chromosome conformation capture." Nucleus 4.5 (2013): 390-398. Beagrie, Robert A., et al. "Complex multi-enhancer contacts captured by genome architecture mapping." Nature 543.7646 (2017): 519-524. 89
Imakaev, Maxim, et al. "Iterative correction of Hi-C data reveals hallmarks of chromosome organization." Nature methods 9.10 (2012): 999-1003. Yaffe, Eitan, and Amos Tanay. "Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture." Nature genetics 43.11 (2011): 1059-1065. Hu, Ming, et al. "HiCNorm: removing biases in Hi-C data via Poisson regression." Bioinformatics 28.23 (2012): 3131-3133. Knight, Philip A., and Daniel Ruiz. "A fast algorithm for matrix balancing." IMA Journal of Numerical Analysis 33.3 (2013): 1029-1047. Forcato, Mattia, et al. "Comparison of computational methods for Hi-C data analysis." Nature methods 14.7 (2017): 679. Ay, Ferhat, Timothy L. Bailey, and William Stafford Noble. "Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts." Genome research 24.6 (2014): 999-1011. Caleb Weinreb, Benjamin J. Raphael; Identification of hierarchical chromatin domains, Bioinformatics, Volume 32, Issue 11, 1 June 2016, Pages 1601 1609 Serra, François, et al. "Restraint-based three-dimensional modeling of genomes and genomic domains." FEBS letters 589.20PartA (2015): 2987-2995. Lesne, Annick, et al. "3D genome reconstruction from chromosomal contacts." Nature methods 11.11 (2014): 1141-1143. 90