GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Harmston, Nathan ^a,b   Ing Simmons, Elizabeth ^a   Perry, Malcolm ^a   Barešić, Anja ^a   Lenhard, Boris ^a  

^a MRC CLINICAL SCIENCES CENTRE   (United Kingdom)

^b DUKE NUS MEDICAL SCHOOL   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN; CHROMOSOME; GENOME; ANIMAL; COMPUTER GRAPHICS; GENETIC DATABASE; GENETICS; GENOMICS; HUMAN; K-562 CELL LINE; METABOLISM; MOLECULAR GENETICS; MOUSE; PROCEDURES; SOFTWARE; THYMOCYTE;

CHROMATIN;

ANIMALS; CHROMATIN; COMPUTER GRAPHICS; DATABASES, GENETIC; GENOMICS; HUMANS; K562 CELLS; MICE; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; THYMOCYTES;

EID: 84946945344     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-2140-x     Document Type: Article

References (64)

1. Phillips-Cremins JE, Sauria MEG, Sanyal A, Gerasimova TI, Lajoie BR, Bell JSK, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell. 2013;153:1281-95.
2. Harmston N, Lenhard B. Chromatin and epigenetic features of long-range gene regulation. Nucleic Acids Res. 2013;41:7185-99.
3. Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013;49:773-82.
4. Shlyueva D, Stampfel G, Stark A. Transcriptional enhancers: From properties to genome-wide predictions. Nat Rev Genet. 2014;15:272-86.
5. Phillips-Cremins JE, Corces VG. Chromatin insulators: Linking genome organization to cellular function. Mol Cell. 2013;50:461-74.
6. Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, et al. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell. 2012;149:1233-44.
7. Chambeyron S, Bickmore WA. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev. 2004;18:1119-30.
8. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature. 2008;453:948-51.
9. Dorier J, Stasiak A. The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture. Nucleic Acids Res. 2010;38:7410-21.
10. Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet. 2010;42:53-61.
11. Amano T, Sagai T, Tanabe H, Mizushina Y, Nakazawa H, Shiroishi T. Chromosomal dynamics at the Shh locus: Limb bud-specific differential regulation of competence and active transcription. Dev Cell. 2009;16:47-57.
12. 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.
13. Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013;14:390.
14. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002;295:1306-11.
15. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 2006;38:1348-54.
16. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006;16:1299-309.
17. Kolovos P, van de Werken HJ, Kepper N, Zuin J, Brouwer RW, Kockx CE, et al. Targeted Chromatin Capture (T2C): A novel high resolution high throughput method to detect genomic interactions and regulatory elements. Epigenetics Chromatin. 2014;7:10.
18. Hughes JR, Roberts N, McGowan S, Hay D, Giannoulatou E, Lynch M, et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet. 2014;46:205-12.
19. 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.
20. Belton J-M, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: A comprehensive technique to capture the conformation of genomes. Methods. 2012;58:268.
21. Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148:84-98.
22. Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res. 2012;22:490-503.
23. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009;462:58-64.
24. 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.
25. Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012;489:109-13.
26. Stadhouders R, Thongjuea S, Andrieu-Soler C, Palstra R-J, Bryne JC, van den Heuvel A, et al. Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development. EMBO J. 2012;31:986-99.
27. Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 2013;504:306-10.
28. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576-89.
29. 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.
30. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11:R22.
31. Lin YC, Benner C, Mansson R, Heinz S, Miyazaki K, Miyazaki M, et al. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol. 2012;13:1196-204.
32. Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res. 2013;41:e132.
33. Scales M, Jäger R, Migliorini G, Houlston RS, Henrion MYR. visPIG--A web tool for producing multi-region, multi-track, multi-scale plots of genetic data. PLoS One. 2014;9:e107497.
34. Ay F, Bailey TL, Noble WS. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 2014;24:999-1011.
35. Paulsen J, Rødland EA, Holden L, Holden M, Hovig E. A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. Nucleic Acids Res. 2014;42(18):e143.
36. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80.
37. Lun ATL, Smyth GK. diffHic: A Bioconductor package to detect differential genomic interactions in Hi-C data. BMC Bioinformatics. 2015;16:258.
38. Servant N, Lajoie BR, Nora EP, Giorgetti L, Chen C-J, Heard E, et al. HiTC: Exploration of high-throughput "C" experiments. Bioinformatics. 2012;28:2843-4.
39. Mifsud B, Martincorena I, Darbo E, Sugar R, Schoenfelder S, Fraser P, Luscombe N: GOTHiC, a simple probabilistic model to resolve complex biases and to identify real interactions in Hi-C data. bioRxiv 2015:023317. http://dx.doi.org/10.1101/023317.
40. Walter C, Schuetzmann D, Rosenbauer F, Dugas M. Basic4Cseq: An R/Bioconductor package for analyzing 4C-seq data. Bioinformatics. 2014;30:3268-9.
41. Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EEM, Huber W. FourCSeq: Analysis of 4C sequencing data. Bioinformatics. 2015;31(19):3085-91. btv335.
42. Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013;9:e1003118.
43. Ay F, Noble WS. Analysis methods for studying the 3D architecture of the genome. Genome Biol. 2015;16:183.
44. Phanstiel DH, Boyle AP, Heidari N, Snyder MP. Mango: A bias-correcting ChIA-PET analysis pipeline. Bioinformatics. 2015;31(19):3092-8. btv336.
45. Heidari N, Phanstiel DH, He C, Grubert F, Jahanbanian F, Kasowski M, et al. Genome-wide map of regulatory interactions in the human genome. Genome Res. 2014;24:1905-17.
46. Hahne F, Durinck S, Ivanek R, Mueller A, Lianoglou S, Tan G, Parsons L: Gviz: Plotting Data and Annotation Information Along Genomic Coordinates. http://www.bioconductor.org/packages/2.14/bioc/html/Gviz.html.
47. Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014;42(Database issue):D764-70.
48. Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal. 2006;Complex Systems:1695.
49. Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, et al. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res. 2013;23:2066-77.
50. 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.
51. McCready PM, Hansen RK, Burke SL, Sands JF. Multiple negative and positive cis-acting elements control the expression of the murine CD4 gene. Biochim Biophys Acta. 1997;1351:181-91.
52. Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, et al. A map of the cis-regulatory sequences in the mouse genome. Nature. 2012;488:116-20.
53. FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature. 2014;507:462.
54. Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 2013;41:827.
55. Decker S, Finter J, Forde AJ, Kissel S, Schwaller J, Mack TS, et al. PIM kinases are essential for chronic lymphocytic leukemia cell survival (PIM2/3) and CXCR4-mediated microenvironmental interactions (PIM1). Mol Cancer Ther. 2014;13:1231-45.
56. Damm F, Chesnais V, Nagata Y, Yoshida K, Scourzic L, Okuno Y, et al. BCOR and BCORL1 mutations in myelodysplastic syndromes and related disorders. Blood. 2013;122:3169-77.
57. Gattei V, Degan M, Gloghini A, De Iuliis A, Improta S, Rossi FM, et al. CD30 ligand is frequently expressed in human hematopoietic malignancies of myeloid and lymphoid origin. Blood. 1997;89:2048-59.
58. Ramirez-Herrick AM, Mullican SE, Sheehan AM, Conneely OM. Reduced NR4A gene dosage leads to mixed myelodysplastic/myeloproliferative neoplasms in mice. Blood. 2011;117(9):2681-90.
59. Kadkhodaei B, Ito T, Joodmardi E, Mattsson B, Rouillard C, Carta M, et al. Nurr1 is required for maintenance of maturing and adult midbrain dopamine neurons. J Neurosci. 2009;29:15923-32.
60. Sekiya T, Kashiwagi I, Inoue N, Morita R, Hori S, Waldmann H, et al. The nuclear orphan receptor Nr4a2 induces Foxp3 and regulates differentiation of CD4+ T cells. Nat Commun. 2011;2:269.
61. Han Y-F, Cao G-W. Role of nuclear receptor NR4A2 in gastrointestinal inflammation and cancers. World J Gastroenterol. 2012;18:6865-73.
62. Shimamoto T, Ohyashiki JH, Ohyashiki K, Kawakubo K, Kimura N, Nakazawa S, et al. GATA-1, GATA-2, and stem cell leukemia gene expression in acute myeloid leukemia. Leukemia. 1994;8:1176-80.
63. Yabumoto K, Ohno H, Doi S, Edamura S, Arita Y, Akasaka T, et al. Involvement of the BCL3 gene in two patients with chronic lymphocytic leukemia. Int J Hematol. 1994;59:211.
64. O'Neil J, Shank J, Cusson N, Murre C, Kelliher M. TAL1/SCL induces leukemia by inhibiting the transcriptional activity of E47/HEB. Cancer Cell. 2004;5:587-96.