Predicting chromatin organization using histone marks

Genome Biology

Volumn 16, Issue 1, 2015, Pages

  Huang, Jialiang ^a,b   Marco, Eugenio ^a,b,d   Pinello, Luca ^a,b   Yuan, Guo Cheng ^a,b,c  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c HARVARD STEM CELL INSTITUTE   (United States)

^d EDITAS MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; HISTONE H3; TRANSCRIPTION FACTOR CTCF; CHROMATIN;

ARTICLE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN INTERACTION HUBS; COMPUTER MODEL; COMPUTER PREDICTION; CONTROLLED STUDY; DNA SEQUENCE; ENHANCER REGION; HIGH THROUGHPUT SEQUENCING; HISTONE MODIFICATION; HUMAN; SINGLE NUCLEOTIDE POLYMORPHISM; TOPOLOGICALLY ASSOCIATED DOMAIN; CELL LINE; CHEMISTRY; COMPUTER SIMULATION; HISTONE CODE; METABOLISM; REGULATORY SEQUENCE;

CELL LINE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; COMPUTER SIMULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONE CODE; HUMANS; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

EID: 84940090292     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-015-0740-z     Document Type: Article

References (44)

1. Kouzarides T. Chromatin modifications and their function. Cell. 2007;128:693-705.
2. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129:823-37.
3. Jenuwein T, Allis CD. Translating the histone code. Science. 2001;293:1074-80.
4. Bernstein BE, Meissner A, Lander ES. The mammalian epigenome. Cell. 2007;128:669-81.
5. Rivera CM, Ren B. Mapping human epigenomes. Cell. 2013;155:39-55.
6. Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, et al. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012;13:R53.
7. Dekker J. Gene regulation in the third dimension. Science. 2008;319:1793-4.
8. Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013;14:390-403.
9. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289-93.
10. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376-80.
11. Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 2013;503:290-4.
12. Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159:1665-80.
13. Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015;518:331-6.
14. Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2012;30:90-8.
15. Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature. 2013;502:59-64.
16. Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet. 2011;43:630-8.
17. Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS. Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. Genome Res. 2015;25:544-57.
18. Yaffe E, Tanay A. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet. 2011;43:1059-65.
19. Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-Andre V, Sigova AA, et al. Super-enhancers in the control of cell identity and disease. Cell. 2013;155:934-47.
20. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 2010;28:495-501.
21. Roadmap Epigenomics C, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518:317-30.
22. Chipman HA, George EI, McCulloch RE. BART: Bayesian additive regression trees. Ann Appl Stat. 2010;4:266-98.
23. Zhou Q, Liu JS. Extracting sequence features to predict protein-DNA interactions: a comparative study. Nucleic Acids Res. 2008;36:4137-48.
24. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15:1034-50.
25. Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012;9:999-1003.
26. Ay F, Bailey TL, Noble WS. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 2014;24:999-1011.
27. Pope BD, Gilbert DM. The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture. J Mol Biol. 2013;425:4690-5.
28. Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 2014;515:402-5.
29. Sandhu KS, Li G, Poh HM, Quek YL, Sia YY, Peh SQ, et al. Large-scale functional organization of long-range chromatin interaction networks. Cell Rep. 2012;2:1207-19.
30. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010;28:1045-8.
31. Roadmap Epigenome Project. ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/roadmapepigenomics/ .
32. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011;473:43-9.
33. ENCODE Project. http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/ .
34. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
35. Peng C, Fu LY, Dong PF, Deng ZL, Li JX, Wang XT, et al. The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling. Nucleic Acids Res. 2013;41:e183.
36. Li W, Gong K, Li Q, Alber F, Zhou XJ. Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data. Bioinformatics. 2015;31:960-2.
37. PhastCons score. ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons44way/placentalMammals/ .
38. Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014;42:D1001-6.
39. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32:D493-6.
40. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, de Bakker PI. SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics. 2008;24:2938-9.
41. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841-2.
42. Adam Kapelner, Bleich J. bartMachine: Machine Learning with Bayesian Additive Regression Trees. arXiv. 2013, preprint arXiv:1312.2171.
43. HubPredictor. https://github.com/huangjialiangcn/HubPredictor .
44. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137.