Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.
Article
Google Scholar
Roadmap Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes. Nature. 2015;19:317–30.
Google Scholar
Henikoff S. ENCODE and our very busy genome. Nat Genet. 2007;39:817–8.
Article
CAS
PubMed
Google Scholar
Filion GJ, Van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, et al. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell. 2010;143:212–24.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes J, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods. 2012;9:473–6.
Article
CAS
PubMed Central
PubMed
Google Scholar
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010;107:21931–6.
Article
CAS
PubMed Central
PubMed
Google Scholar
Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011;470:279–83.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
Article
CAS
PubMed Central
PubMed
Google Scholar
Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker JR, et al. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Res. 2012;72:6319–24.
Article
CAS
PubMed
Google Scholar
He B, Chen C, Teng L, Tan K. Global view of enhancer-promoter interactome in human cells. Proc Natl Acad Sci U S A. 2014;111:E2191–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, et al. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res. 2013;23:777–88.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pastor WA, Stroud H, Nee K, Liu W, Pezic D, Manakov S, et al. MORC1 represses transposable elements in the mouse male germline. Nat Commun. 2014;5:5795.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bergman Y, Cedar H. DNA methylation dynamics in health and disease. Nat Struct Mol Biol. 2013;20:274–81.
Article
CAS
PubMed
Google Scholar
Thomassin H, Flavin M, Espinás ML, Grange T. Glucocorticoid-induced DNA demethylation and gene memory during development. EMBO J. 2001;20:1974–83.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462:315–22.
Article
CAS
PubMed Central
PubMed
Google Scholar
Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011;480:490–5.
CAS
PubMed
Google Scholar
Blattler A, Farnham PJ. Cross-talk between site-specific transcription factors and DNA methylation states. J Biol Chem. 2013;288:34287–94.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ooi L, Wood IC. Chromatin crosstalk in development and disease: lessons from REST. Nat Rev Genet. 2007;8:544–54.
Article
CAS
PubMed
Google Scholar
Gebhard C, Benner C, Ehrich M, Schwarzfischer L, Schilling E, Klug M, et al. General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res. 2010;70:1398–407.
Article
CAS
PubMed
Google Scholar
Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2012;44:40–6.
Article
CAS
PubMed Central
Google Scholar
Aran D, Sabato S, Hellman A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol. 2013;14:R21.
Article
PubMed Central
PubMed
Google Scholar
Hovestadt V, Jones DT, Picelli S, Wang W, Kool M, Northcott PA, et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature. 2014;510:537–41.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed Central
PubMed
Google Scholar
Aran D, Hellman A. DNA methylation of transcriptional enhancers and cancer predisposition. Cell. 2013;154:11–3.
Article
CAS
PubMed
Google Scholar
Wiench M, John S, Baek S, Johnson TA, Sung MH, Escobar T, et al. DNA methylation status predicts cell type-specific enhancer activity. EMBO J. 2011;30:3028–39.
Article
CAS
PubMed Central
PubMed
Google Scholar
Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45:1113–20.
Article
PubMed Central
PubMed
Google Scholar
The Cancer Genome Atlas. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330–7.
Article
Google Scholar
GENCODE gene annotations. [http://www.gencodegenes.org/releases/15.html]
Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9:215–6.
Article
CAS
PubMed Central
PubMed
Google Scholar
ENCODE_Project_Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.
Article
Google Scholar
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014;507:455–61.
Article
CAS
PubMed
Google Scholar
Kwasnieski JC, Fiore C, Chaudhari HG, Cohen BA. High-throughput functional testing of ENCODE segmentation predictions. Genome Res. 2014;24:1595–602.
Article
CAS
PubMed Central
PubMed
Google Scholar
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. 2010;42:806–10.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012;489:109–13.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014;42:D142–7.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013;41:D171–6.
Article
CAS
PubMed Central
PubMed
Google Scholar
Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, et al. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell. 2009;36:667–81.
Article
CAS
PubMed Central
PubMed
Google Scholar
Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, et al. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals iterchangeable roles of E2F family members. Genome Res. 2007;17:1550–61.
Article
CAS
PubMed Central
PubMed
Google Scholar
Shakya A, Callister C, Goren A, Yosef N, Garg N, Khoddami V, et al. Pluripotency transcription factor oct4 mediates stepwise nucleosome demethylation and depletion. Mol Cell Biol. 2015;35:1014–25.
Article
PubMed
Google Scholar
Lee DS, Shin JY, Tonge PD, Puri MC, Lee S, Park H, et al. An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator. Nat Commun. 2014;5:5619.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bresnick EH, Lee HY, Fujiwara T, Johnson KD, Keles S. GATA switches as developmental drivers. J Biol Chem. 2010;285:31087–93.
Article
CAS
PubMed Central
PubMed
Google Scholar
Brewer A, Pizzey J. GATA factors in vertebrate heart development and disease. Expert Rev Mol Med. 2006;8:1–20.
Article
PubMed
Google Scholar
Chou J, Provot S, Werb Z. GATA3 in development and cancer differentiation: cells GATA have it! J Cell Physiol. 2010;222:42–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Patient RK, McGhee JD. The GATA family (vertebrates and invertebrates). Curr Opin Genet Dev. 2002;12:416–22.
Article
CAS
PubMed
Google Scholar
Kouros-Mehr H, Bechis SK, Slorach EM, Littlepage LE, Egeblad M, Ewald AJ, et al. GATA-3 links tumor differentiation and dissemination in a luminal breast cancer model. Cancer Cell. 2008;13:141–52.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kouros-Mehr H, Kim JW, Bechis SK, Werb Z. GATA-3 and the regulation of the mammary luminal cell fate. Curr Opin Cell Biol. 2008;20:164–70.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yan W, Cao QJ, Arenas RB, Bentley B, Shao R. GATA3 inhibits breast cancer metastasis through the reversal of epithelial-mesenchymal transition. J Biol Chem. 2010;285:14042–51.
Article
CAS
PubMed Central
PubMed
Google Scholar
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, et al. Distinct predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics. 2007;39:311–8.
Article
CAS
PubMed
Google Scholar
Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, et al. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol. 2014;15:469.
Article
PubMed Central
PubMed
Google Scholar
Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D’Souza C, Fouse SD, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466:253–7.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kowalczyk MS, Hughes JR, Garrick D, Lynch MD, Sharpe JA, Sloane-Stanley JA, et al. Intragenic enhancers act as alternative promoters. Mol Cell. 2012;45:447–58.
Article
CAS
PubMed
Google Scholar
Raviram R, Rocha PP, Bonneau R, Skok JA. Interpreting 4C-Seq data: how far can we go? Epigenomics. 2014;6:455–7.
Article
CAS
PubMed Central
PubMed
Google Scholar
Eeckhoute J, Carroll JS, Geistlinger TR, Torres-Arzayus MI, Brown M. A cell-type-specific transcriptional network required for estrogen regulation of cyclin D1 and cell cycle progression in breast cancer. Genes & Dev. 2015;20:2513–26.
Article
Google Scholar
Yochum GS, Cleland R, Goodman RH. A genome-wide screen for beta-catenin binding sites identifies a downstream enhancer element that controls c-Myc gene expression. Mol Cell Biol. 2008;28:7368–79.
Article
CAS
PubMed Central
PubMed
Google Scholar
Konsavage Jr WM, Yochum GS. The myc 3’ wnt-responsive element suppresses colonic tumorigenesis. Mol Cell Biol. 2014;34:1659–69.
Article
PubMed Central
PubMed
Google Scholar
Rosenbauer F, Wagner K, Kutok JL, Iwasaki H, Le Beau MM, Okuno Y, et al. Acute myeloid leukemia induced by graded reduction of a lineage-specific transcription factor, PU.1. Nat Genet. 2004;36:624–30.
Article
CAS
PubMed
Google Scholar
Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet. 2011;43:964–8.
Article
CAS
PubMed Central
PubMed
Google Scholar
Frietze S, Wang R, Yao L, Tak YG, Ye Z, Gaddis M, et al. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biol. 2012;13:R52.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sur IK, Hallikas O, Vaharautio A, Yan J, Turunen M, Enge M, et al. Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science. 2012;338:1360–3.
Article
CAS
PubMed
Google Scholar
Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H, et al. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet. 2009;41:882–4.
Article
CAS
PubMed Central
PubMed
Google Scholar
The Cancer Genome Atlas. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012;489:519–25.
Article
Google Scholar
Massion PP, Taflan PM, Jamshedur Rahman SM, Yildiz P, Shyr Y, Edgerton ME, et al. Significance of p63 amplification and overexpression in lung cancer development and prognosis. Cancer Res. 2003;63:7113–21.
CAS
PubMed
Google Scholar
Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, et al. SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas. J Clin Invest. 2014;124:1636–45.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502:333–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Worsley Hunt R, Wasserman WW. Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets. Genome Biol. 2014;15:412.
Article
PubMed Central
PubMed
Google Scholar
Aguilera C, Nakagawa K, Sancho R, Chakraborty A, Hendrich B, Behrens A. c-Jun N-terminal phosphorylation antagonises recruitment of the Mbd3/NuRD repressor complex. Nature. 2011;469:231–5.
Article
CAS
PubMed
Google Scholar
Tupler R, Perini G, Green MR. Expressing the human genome. Nature. 2001;409:832–3.
Article
CAS
PubMed
Google Scholar
Razin SV, Borunova VV, Maksimenko OG, Kantidze OL. Cys2His2 zinc finger protein family: classification, functions, and major members. Biochemistry (Mosc). 2012;77:217–26.
Article
CAS
PubMed
Google Scholar
Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat Reviews Genetics. 2009;10:252–63.
Article
CAS
Google Scholar
Reynisdottir I, Arason A, Einarsdottir BO, Gunnarsson H, Staaf J, Vallon-Christersson J, et al. High expression of ZNF703 independent of amplification indicates worse prognosis in patients with luminal B breast cancer. Cancer Med. 2013;2:437–46.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kang X, Chen W, Kim RH, Kang MK, Park NH. Regulation of the hTERT promoter activity by MSH2, the hnRNPs K and D, and GRHL2 in human oral squamous cell carcinoma cells. Oncogene. 2009;28:565–74.
Article
CAS
PubMed Central
PubMed
Google Scholar
Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012;22:1748–59.
Article
CAS
PubMed Central
PubMed
Google Scholar
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;337:1190–5.
Article
CAS
PubMed Central
PubMed
Google Scholar
Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, et al. Epigenomic enhancer profiling defines a signature of colon cancer. Science. 2012;336:736–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hardison RC. Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. J Biol Chem. 2012;287:30932–40.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yao L, Tak YG, Berman BP, Farnham PJ. Functional annotation of colon cancer risk SNPs. Nat Commun. 2014;5:5114.
Article
CAS
PubMed Central
PubMed
Google Scholar
Fredriksson NJ, Ny L, Nilsson JA, Larsson E. Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. Nat Genet. 2014;46:1258–63.
Article
CAS
PubMed
Google Scholar
Huang FW, Hodis E, Xu MJ, Kryukov GV, Chin L, Garraway LA. Highly recurrent TERT promoter mutations in human melanoma. Science. 2013;339:957–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W. Genome-wide analysis of noncoding regulatory mutations in cancer. Nat Genet. 2014;46:1160–5.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011;43:768–75.
Article
CAS
PubMed Central
PubMed
Google Scholar
BioConductor. [http://www.bioconductor.org/]
ELMER source code. [https://github.com/lijingya/ELMER.git]
ELMER usage vignette. [https://github.com/lijingya/ELMER/blob/master/vignettes/vignettes.pdf]
ELMER user manual. [https://github.com/lijingya/ELMER/blob/master/inst/doc/ELMER_manual.pdf]
TCGA data access. [https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/]
TCGA pan-can analysis (Synapse).[https://www.synapse.org/#]
Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013;9:e1003118.
Article
CAS
PubMed Central
PubMed
Google Scholar
Epigenomics Roadmap data access. [https://sites.google.com/site/epigenomeroadmapawg/project-updates/finalsignaltracksandalignmentfiles]
FANTOM enhancer annotations. [http://enhancer.binf.ku.dk/presets/]
Alexa A, Rahnenfuhrer J. topGO: Enrichment analysis for Gene Ontology. R package version 2180. 2010. [http://www.bioconductor.org/packages/release/bioc/html/topGO.html]
Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27:1017–8.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012;22:1798–812.
Article
CAS
PubMed Central
PubMed
Google Scholar
Shannon P. MotifDb: An annotated collection of Protein-DNA binding sequence motifs. Bioconductor. 2014, R package version 1.8.0. [http://www.bioconductor.org/packages/release/bioc/html/MotifDb.html]
Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 2010;140:744–52.
Article
CAS
PubMed
Google Scholar