참고문헌
- International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 2004;431:931-945. https://doi.org/10.1038/nature03001
- ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004;306:636-640. https://doi.org/10.1126/science.1105136
- Alberts B. The end of "small science"? Science 2012;337:1583. https://doi.org/10.1126/science.1230529
- Decoding ENCODE. Nat Chem Biol 2012;8:871. https://doi.org/10.1038/nchembio.1107
- ENCODE Project Consortium, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, et al. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011;9:e1001046. https://doi.org/10.1371/journal.pbio.1001046
- ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007;447:799-816. https://doi.org/10.1038/nature05874
- Weinstock GM. ENCODE: more genomic empowerment. Genome Res 2007;17:667-668. https://doi.org/10.1101/gr.6534207
- Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, et al. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res 2012;22:1735-1747. https://doi.org/10.1101/gr.136366.111
- Maher B. ENCODE: the human encyclopaedia. Nature 2012; 489:46-48. https://doi.org/10.1038/489046a
- Karlin S, McGregor J. The evolutionary development of modifier genes. Proc Natl Acad Sci U S A 1972;69:3611-3614. https://doi.org/10.1073/pnas.69.12.3611
- ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489: 57-74. https://doi.org/10.1038/nature11247
- Cockerill PN. Structure and function of active chromatin and DNase I hypersensitive sites. FEBS J 2011;278:2182-2210. https://doi.org/10.1111/j.1742-4658.2011.08128.x
- Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 2011;21:1757-1767. https://doi.org/10.1101/gr.121541.111
- Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Genomics: ENCODE explained. Nature 2012;489:52-55. https://doi.org/10.1038/489052a
- Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U. Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res 2012;22:1711-1722. https://doi.org/10.1101/gr.135129.111
- Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012;489: 83-90. https://doi.org/10.1038/nature11212
- Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, et al. The accessible chromatin landscape of the human genome. Nature 2012;489:75-82. https://doi.org/10.1038/nature11232
- Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, et al. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res 2012;22:1680-1688. https://doi.org/10.1101/gr.136101.111
- Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res 2006;16:1505- 1516. https://doi.org/10.1101/gr.5560806
- Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008;18:1051-1063. https://doi.org/10.1101/gr.076463.108
- Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Determinants of nucleosome organization in primary human cells. Nature 2011;474:516-520. https://doi.org/10.1038/nature10002
- Carey M, Smale ST. Micrococcal nuclease-Southern blot assay: I. MNase and restriction digestions. CSH Protoc 2007;2007: pdb.prot4890.
- Lee TI, Young RA. Transcription of eukaryotic protein-coding genes. Annu Rev Genet 2000;34:77-137. https://doi.org/10.1146/annurev.genet.34.1.77
- Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, et al. Architecture of the human regulatory network derived from ENCODE data. Nature 2012;489:91-100. https://doi.org/10.1038/nature11245
- Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 2012;22: 1790-1797. https://doi.org/10.1101/gr.137323.112
- Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res 2012;22:1748-1759. https://doi.org/10.1101/gr.136127.111
- Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, et al. Personal and population genomics of human regulatory variation. Genome Res 2012;22:1689-1697. https://doi.org/10.1101/gr.134890.111
- Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, et al. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol 2012; 13:R49. https://doi.org/10.1186/gb-2012-13-9-r49
- Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, et al. Systematic localization of common disease- associated variation in regulatory DNA. Science 2012; 337:1190-1195. https://doi.org/10.1126/science.1222794
- 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;473:43-49. https://doi.org/10.1038/nature09906
- Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 2009;458:362-366. https://doi.org/10.1038/nature07667
피인용 문헌
- Genome-wide analysis of histone modifications in latently HIV-1 infected T cells vol.28, pp.12, 2014, https://doi.org/10.1097/QAD.0000000000000309
- Epigenetics: Relevance and Implications for Public Health vol.35, pp.1, 2014, https://doi.org/10.1146/annurev-publhealth-032013-182513
- Common variants of NFE2L2 gene predisposes to acute respiratory distress syndrome in patients with severe sepsis vol.19, pp.1, 2015, https://doi.org/10.1186/s13054-015-0981-y
- Prostate cancer epigenetic biomarkers: next-generation technologies vol.34, pp.13, 2015, https://doi.org/10.1038/onc.2014.111
- Altered expression of LINC-ROR in cancer cell lines and tissues vol.37, pp.2, 2016, https://doi.org/10.1007/s13277-015-3933-x
- Identification of the early and late responder genes during the generation of induced pluripotent stem cells from mouse fibroblasts vol.12, pp.2, 2017, https://doi.org/10.1371/journal.pone.0171300
- Histone H3 Acetyl K9 and Histone H3 Tri Methyl K4 as Prognostic Markers for Patients with Cervical Cancer vol.18, pp.3, 2017, https://doi.org/10.3390/ijms18030477
- Polymorphisms with High Myopia vol.2017, pp.2314-6141, 2017, https://doi.org/10.1155/2017/3024156
- Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information vol.15, pp.S1, 2014, https://doi.org/10.1186/1471-2105-15-S1-S2