Epigenome Roadmap

Additional research which has received the NIH Roadmap Epigenomics funding

Nature

Ziller et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477-81 (2013)
(doi:10.1038/nature12433)

Jin F, et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290-4 (2013)
(doi:10.1038/nature12644)

Smith ZD, et al. DNA methylation dynamics of the human preimplantation embryo. Nature 511, 611-5 (2014) 
(doi:10.1038/nature13581)

Cheng, Y. et al. Principles of regulatory information conservation between mouse and human. Nature 515, 371-375 (2014)
(doi:10.1038/nature13985)

Nature Biotechnology

Selvaraj S, et al. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol. 31, 1111-8 (2013)
(doi:10.1038/nbt.2728)

Nature Cell Biology

Kang S, et al. Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis.  Nat Cell Biol. 17, 44-56 (2015)
(doi:10.1038/ncb3080)

Nature Chemical Biology

James LI, et al. Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. Nat Chem Biol. 9, 184-91 (2013)
(doi:10.1038/nchembio.1157)

Nature Communications

Zhang L, et al. Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nat Commun. 4:1517 (2013)
(doi:10.1038/ncomms2527)

Nature Genetics

Xie M, et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet. 45, 836-41 (2013)
(doi:10.1038/ng.2649)

Nature Methods

Diep D, et al. Library-free methylation sequencing with bisulfite padlock probes. Nat Methods 5, 270-2 (2012) 
(doi:10.1038/nmeth.1871)

Zhou, X, et al. Exploring long-range genome interaction data using the WashU Epigenome Browser. Nat Methods 10, 375-376 (2013)
(doi:10.1038/nmeth.2440)

Hattori T., et al. Recombinant antibodies to histone post-translational modifications. Nat Methods 10, 992–995 (2013) 
(doi:10.1038/nmeth.2605)

Kasinathan, S., et al. High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods 11, 203-9 (2014) 
(doi:10.1038/nmeth.2766)

Tome, J.M., et al.  Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling. Nat Methods 11, 683-8 (2014) 
(doi:10.1038/nmeth.2970)

Nature Protocols

Yu M, et al.  Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat Protoc. 7, 2159-70 (2012)
(doi: 10.1038/nprot.2012.137)

Nature Reviews Genetics

Mill, J., Heijmans, B.T. From promises to practical strategies in epigenetic epidemiology. Nat Rev Genet. 14, 585-94 (2013)
(doi:10.1038/nrg3405)

Nature Structural and Molecular Biology

Khare T, et al. 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nat Struct Mol Biol. 19, 1037-43 (2012)
(doi:10.1038/nsmb.2372)

Science

Maurano MT, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190-5 (2012) 
(doi:10.1126/science.1222794)

Cell

Clowney, E.J., et al. Nuclear aggregation of olfactory receptor genes governs their monogenic expression. Cell 151, 724-37 (2012) 
(doi:10.1016/j.cell.2012.09.043)

Yu, M., et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149, 1368-80 (2012)
(doi:10.1016/j.cell.2012.04.027)

Chaffer, C.L., et al. Poised Chromatin at the ZEB1 Promoter Enables Breast Cancer Cell Plasticity and Enhances Tumorigenicity. Cell 154, 61-74 (2013)  (doi:10.1016/j.cell.2013.06.005)

Loven, J., et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320-34 (2013) 
(doi:10.1016/j.cell.2013.03.036)

Whyte, W.A., et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307-19 (2013) 
(doi:10.1016/j.cell.2013.03.035)

Zhu, J., et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642-54 (2013) 
(doi:10.1016/j.cell.2012.12.033)

Stergachis, A.B., et al. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 154, 888-903 (2013)
(doi:10.1016/j.cell.2013.07.020)

Hnisz D, et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934-47 (2013) 
(doi:10.1016/j.cell.2013.09.053)

Xie et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134–1148 (2013)
(doi:10.1016/j.cell.2013.04.022)

Gifford, C.A.,  et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153, 1149-63 (2013)
(doi:10.1016/j.cell.2013.04.037)

Markenscoff-Papadimitriou, E., et al. Enhancer interaction networks as a means for singular olfactory receptor expression. Cell 159, 543-57 (2014) 
(doi:10.1016/j.cell.2014.09.033)

Genome Research

Zhang, B., et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 23, 1522-40 (2013)
(doi:10.1101/gr.156539.113)

Stevens, M., et al. Estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Genome Res. 23, 1541-53 (2013)
(doi:10.1101/gr.152231.112)

Nagarajan, R.P., et al. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Res. 24, 761-74 (2014)
(doi:10.1101/gr.164707.113)

Genome Biology

Davies, M.N., et al. Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol. 13, R43( 2012)
(doi:10.1186/gb-2012-13-6-r43)

Pidsley, R., et al. Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia. Genome Biol. 15, 483 (2014)
(doi:10.1186/s13059-014-0483-2)

Journal of Clinical Investigation

Santagata, S., et al. Taxonomy of breast cancer based on normal cell phenotype predicts outcome.  J Clin Invest. 124, 859-70 (2014). 
(doi:10.1172/JCI70941)

Human Molecular Genetics

Liu, Y., et al. Methylomics of gene expression in human monocytes. Hum Mol Genet 24, 5065-74 (2013)
(doi:10.1093/hmg/ddt356)

BMC Genomics

Pidsley, R., et al. A data-driven approach to preprocessing Illumina 450K methylation array data. 
BMC Genomics. 14:293 (2013)
(doi:10.1186/1471-2164-14-293)

Zhang, B., et al. Comparative DNA methylome analysis of endometrioid adenocarcinoma, uterine papillary serous carcinoma, and normal endometrium. BMC Genomics 15:868 (2014)
(doi:10.1186/1471-2164-15-868)

Genome Medicine

Whitaker, J.W., et al. An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype. Genome Medicine 5: 40 (2013) ​(doi:10.1186/gm444)

PLoS Genetics

Berko, E.R., et al. Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. PLoS Genet. 10(5):e1004402 (2014)
(doi:10.1371/journal.pgen.1004402)

Lim, A.S., et al. 24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex. PLoS Genet. 10(11):e1004792 (2014)
(doi:10.1371/journal.pgen.1004792)

Nucleic Acid Research

Zhu, Y., et al. Predicting enhancer transcription and activity from chromatin modifications. Nucleic Acids Research. 41: 10032-10043 (2013)
(doi:10.1093/nar/gkt826)

Bioinformatics

Wu, J., et al. SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics 27: 3010-3016 (2011)
(doi:10.1093/bioinformatics/btr508)

Wang, T., et al. STAR: An Integrated Solution to Management and Visualization of Sequencing Data. Bioinformatics. 29:3204-3210 (2013)
(doi:10.1093/bioinformatics/btt558)

Zhou, X., et al. methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser. Bioinformatics. 30:2206-7 (2014)
(doi:10.1093/bioinformatics/btu191)

Current Protocols in Bioinformatics

Zhou, X. and Wang, T. Using the Wash U Epigenome Browser to examine genome-wide sequencing data. Curr Protoc Bioinformatics. Chapter 10:Unit10.10 (2012)
(doi:10.1002/0471250953.bi1010s40) 

Cancer Informatics

Houseman, E.A., Ince, T.A. Normal cell-type epigenetics and breast cancer classification: a case study of cell mixture-adjusted analysis of DNA methylation data from tumors.  Cancer Inform. (Suppl 4):53-64 (2014)
(doi:10.4137/CIN.S13980)

Expert Review in Anticancer Therapy

Santagata, S., Ince, T.A. Normal cell phenotypes of breast epithelial cells provide the foundation of a breast cancer taxonomy. Expert Rev Anticancer Ther. 12:1385-9 ( 2014) 
(doi:10.1586/14737140.2014.956096)

Neurobiology of aging

Lunnon, K., et al. Blood methylomic signatures of presymptomatic dementia in elderly subjects with type 2 diabetes mellitus. Neurobiol Aging. Dec 24. pii: S0197-4580(14)00840-9 (2014)
(doi:10.1016/j.neurobiolaging.2014.12.023)

Condliffe, D, et al. Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's disease brain. Neurobiol Aging. 8:1850-4 (2014)
(doi:10.1016/j.neurobiolaging.2014.02.002)

JAMA Neurobiology

Yu, L., et al. Association of Brain DNA Methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 With Pathological Diagnosis of Alzheimer Disease. JAMA Neurol. 72:15-24 (2015)
(doi:10.1001/jamaneurol.2014.3049)

Translational Research 

Bennett, D.A., et al. Epigenomics of Alzheimer's disease. Transl Res. 165:200-220 (2015)
(doi:10.1016/j.trsl.2014.05.006)

American Journal of Medical Genetics B Neuropsychiatr Genet.

Lunnon, K., Mill, J. Epigenetic studies in Alzheimer's disease: current findings, caveats, and considerations for future studies. Am J Med Genet B Neuropsychiatr Genet. 162B :789-99 (2013)
(doi:10.1002/ajmg.b.32201)

Annals of the Rheumatic Diseases

Nakano, K., et al. DNA methylome signature in rheumatoid arthritis. Annals of the Rheumatic Diseases. 72: 110-117 (2013)
(doi:10.1136/annrheumdis-2012-201526)

Stem Cells

Jeffries, A.R., et al. Stochastic choice of allelic expression in human neural stem cells. Stem Cells 30:1938-47 (2012)
(doi:10.1002/stem.1155)

Methods 

Li. D, et al. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 72:29-40. (2014)
(doi:10.1016/j.ymeth.2014.10.032)

Whitaker, J.W., et al. Computational schemes for the prediction and annotation of enhancers from epigenomic assays. Methods 72: 86–94 (2015)
(doi:10.1016/j.ymeth.2014.10.008)