Hi-C解析(2017NGSハンズオン講習会-2017年9月1日)
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- えりか めいこ
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1 29 NGS Hi-C
2 n Hi-C l Chromosome Conformation Capture l Hi-C n Hi-C l Hi-C l l l l TAD l 3D 2
3 n Fastq Hi-C 3 n python python.py Hi-C 3
4 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
5 Hi-C ex. Hi-C 5
6 NGS n n l l l Reseq l RNA-seq l ChIP-seq l ATAC-seq l Hi-C l irep 6
7 Chromosome Conformation Capture (3C) Dekker, Job, et al. "Capturing chromosome conformation." Science (2002): C-based method DNA 7
8 3C-based technologies de Wit, Elzo, and Wouter de Laat. "A decade of 3C technologies: insights into nuclear organization." Genes & development 26.1 (2012):
9 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):
10 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 (2017):
11 Hi-C Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science (2009): vs. Forward, Reverse 11
12 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 (2014):
13 Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell (2014):
14 L2 Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell (2014): L1 L3 14
15 Topologically Associated Domains (TADs) TAD Akdemir, Kadir Caner, and Lynda Chin. "HiCPlotter integrates genomic data with interaction matrices." Genome biology 16.1 (2015):
16 Topologically Associated Domains (TADs) Ke, Yuwen, et al. "3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis." Cell (2017):
17 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 (2014): Fudenberg, Geoffrey, et al. "Formation of chromosomal domains by loop extrusion. Cell reports 15.9 (2016):
18 Nagano, Takashi, et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547 (2017):
19 Hi-C meta3c Marbouty, Martial, et al. "Metagenomic chromosome conformation capture (meta3c) unveils the diversity of chromosome organization in microorganisms. Elife 3 (2014): e
20 Hi-C n l Bin
21 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):
22 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 (2014):
23 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 (2017):
24 n Hi-C l Chromosome Conformation Capture l Hi-C n Hi-C l Hi-C l l l l TAD l 3D 24
25 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
26 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
27 Results mv 27
28 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 (2014):
29 ~/HiC/data Rao, et al Human B-Lymphocyte: GM $cd ~/HiC/data $ls l R1, R2 fastq 29
30 ~/HiC/Ref hg19 FASTA 30
31 ~/HiC/Index ~/HiC/Ref hg19 bowtie2-build Bowtie2 31
32 Hi-C Trimmomatic TAD 3 32
33 Hi-C $cd ~/HiC/1_mapping_read_to_genome TAD 3 33
34 Illumina 34
35 Hi-C Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science (2009):
36 Hi-C R1, R2 R1 R2 36
37 Hi-C => R1, R2 Imakaev, Maxim, et al. "Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature methods 9.10 (2012):
38 1. R1, R2 R1, R2 3 I. R1, R2 II. a. LocusA, LocusB LocusB Locus A B b. III. 2. Iterative alignment method 38
39 Iterative alignment method Imakaev, Maxim, et al. "Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature methods 9.10 (2012):
40 $less mapping.py R1 R2 40
41 bp 35bp 41
42 $python mapping.py Bowtie2 Bowtie2 42
43 $ls l../data 43
44 $less parse_results.py HDF5 Biopython Restriction 44
45 $python parse_results.py $ls -l HDF5 HDFView python HDF5 45
46 Hi-C $cd ~/HiC/2_filtering_reads TAD 3 46
47 R1, R2 Hi-C Imakaev, Maxim, et al. "Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature methods 9.10 (2012):
48 $less filtering.py maximummoleculelength 400bp HDF5 48
49 $less filtering.py filterrsitestart(): DNA filterduplicates(): PCR duplicate filterlarge(): 10^5bp filterextreme(): 0.5% 49
50 $less filtering.py 1Mbp Bin raw read count 1Mbp 3,000 3,000 Bin 90% 80%
51 $python filtering.py $ls -l 51
52 $less./statistics.txt 52
53 Hi-C $cd ~/HiC/3_normalization TAD 3 53
54 1. 2. Hi-C I. Ligation II. GC III. Mappability. ChIP-seq: INPUT RNA-seq: 1 Hi-C 54
55 Hi-C 1. Explicit GC Yaffe and Tanay 2011 HiCNorm 2. Implicit Vanilla coverage, ICE, Knight and Ruiz
56 Raw heatmap Normalized heatmap Raw coverage Corrected coverage 56
57 k l! A #$ #! A #& # 57
58 k l 1 A #& # k l 1 A #$ # 58
59 1 # A #$ # A #* 1 # A #$ # A #+ k = Vanilla coverage normalization 1 # A #$ # A #& l! A #$ # 59
60 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): Explicit Implicit 60
61 Iterative correction (ICE method) Vanilla coverage normalization Þ Vanilla coverage normalization matrix balancing ICE matrix balancing Knight and Ruiz
62 $less normalize.py Raw read count Bin ICE 62
63 $python normalize.py heatmap.pdf 63
64 TAD 3D 19 $python submatrix.py $less norm_mat.txt 64
65 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
66 JuiceBox $./execute_juicebox.sh File => Open => Local test.hic Chromosomes Annotations ENCODE 66
67 Hi-C TAD 3 67
68 L2 L1 L3 Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell (2014):
69 Forcato, Mattia, et al. "Comparison of computational methods for Hi-C data analysis." Nature methods 14.7 (2017):
70 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): ICE p-value 70
71 HiCCUPS (Local background) Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell (2014): K&R p-value 71
72 Hi-C TAD $cd ~/HiC/5_detect_TADs 3 72
73 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
74 TADtree Caleb Weinreb, Benjamin J. Raphael; Identification of hierarchical chromatin domains, Bioinformatics, Volume 32, Issue 11, 1 June 2016, Pages TAD, sub-tad Python 74
75 TADtree Caleb Weinreb, Benjamin J. Raphael; Identification of hierarchical chromatin domains, Bioinformatics, Volume 32, Issue 11, 1 June 2016, Pages TAD TAD TAD 75
76 $less./control_file.txt TAD Bin TAD TAD TAD 76
77 TADtree $python TADtree.py./control_file.txt./output/chr19 N TAD proportion_duplicates.txt TAD BED Bin 77
78 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 (2017):
79 Hi-C TAD 3 $cd ~/HiC/6_modeling_3D 79
80 3D Hi-C Serra, et al a. b. 80
81 3D
82 82
83 D #,. = 1 A #,. 1 α=1 Ai,j = 0 Di,j => Þ Shortest-path reconstruction ShRec3D Lesne, et al MATLAB 83
84 Shortest-path reconstruction Bin 84
85 Shortest-path reconstruction Floyd-Warshall 85
86 $less./convert_contact_to_distance.py Python NetworkX $python./convert_contact_to_distance.py../3_normalization/norm_mat.txt dist.npy 86
87 3 Multi-dimensional scaling; MDS 16S PCoA MDS 16S MDS OK 3 87
88 3 $less./modeling_3d.py dist.npy MDS $python modeling_3d.py 88
89 Dekker, Job, et al. "Capturing chromosome conformation." science (2002): de Wit, Elzo, and Wouter de Laat. "A decade of 3C technologies: insights into nuclear organization." Genes & development 26.1 (2012): Ke, Yuwen, et al. "3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis." Cell (2017): Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." science (2009): Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping."cell (2014): 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): Nagano, Takashi, et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547 (2017): Marbouty, Martial, et al. "Metagenomic chromosome conformation capture (meta3c) unveils the diversity of chromosome organization in microorganisms." Elife 3 (2014): e O'sullivan, Justin M., et al. "The statistical-mechanics of chromosome conformation capture." Nucleus 4.5 (2013): Beagrie, Robert A., et al. "Complex multi-enhancer contacts captured by genome architecture mapping." Nature (2017):
90 Imakaev, Maxim, et al. "Iterative correction of Hi-C data reveals hallmarks of chromosome organization." Nature methods 9.10 (2012): Yaffe, Eitan, and Amos Tanay. "Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture." Nature genetics (2011): Hu, Ming, et al. "HiCNorm: removing biases in Hi-C data via Poisson regression." Bioinformatics (2012): Knight, Philip A., and Daniel Ruiz. "A fast algorithm for matrix balancing." IMA Journal of Numerical Analysis 33.3 (2013): 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): Caleb Weinreb, Benjamin J. Raphael; Identification of hierarchical chromatin domains, Bioinformatics, Volume 32, Issue 11, 1 June 2016, Pages Serra, François, et al. "Restraint-based three-dimensional modeling of genomes and genomic domains." FEBS letters PartA (2015): Lesne, Annick, et al. "3D genome reconstruction from chromosomal contacts." Nature methods (2014):
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