The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but a similar reference has lacked for epigenomic studies. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection to-date of human epigenomes for primary cells and tissues. Here, we describe the integrative analysis of 111 reference human epigenomes generated as part of the program, profiled for histone modification patterns, DNA accessibility, DNA methylation, and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically-relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation, and human disease.

We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes. By ChIP-seq, using 15.1 and 12.9 million uniquely mapped sequence reads, and an estimated false discovery rate of less than 0.001, we identified 41,582 and 11,004 putative STAT1-binding regions in stimulated and unstimulated cells, respectively. Of the 34 loci known to contain STAT1 interferon-responsive binding sites, ChIP-seq found 24 (71%). ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%.

DNA methylation and histone H3 lysine 9 trimethylation (H3K9me3) play important roles in silencing of genes and retroelements. However, a comprehensive comparison of genes and repetitive elements repressed by these pathways has not been reported. Here we show that in mouse embryonic stem cells (mESCs), the genes upregulated after deletion of the H3K9 methyltransferase Setdb1 are distinct from those derepressed in mESC deficient in the DNA methyltransferases Dnmt1, Dnmt3a, and Dnmt3b, with the exception of a small number of primarily germline-specific genes. Numerous endogenous retroviruses (ERVs) lose H3K9me3 and are concomitantly derepressed exclusively in SETDB1 knockout mESCs. Strikingly, ~15% of upregulated genes are induced in association with derepression of promoter-proximal ERVs, half in the context of "chimeric" transcripts that initiate within these retroelements and splice to genic exons. Thus, SETDB1 plays a previously unappreciated yet critical role in inhibiting aberrant gene transcription by suppressing the expression of proximal ERVs.

IntroductionHox proteins are homeodomain-containing transcription factors (TFs) that play a vital role in establishing body plan during development. In addition to this role in body planning, Hox proteins have been implicated in limb regeneration, wound healing, adipogenesis, and hematopoietic stem cell self-renewal. 1 Hoxa9, in particular, is expressed at high levels in early hematopoietic progenitor cells and promotes stem cell expansion. In contrast, Hoxa9 down-regulation is associated with hematopoietic differentiation. 2,3 In keeping with this role, Hoxa9 knock-out mice show defects in B and T-cell lymphopoiesis and myelopoiesis. 4 HOXA9 has been intensively studied because of its central role in human acute leukemias. [5][6][7][8] Early studies of BXH2 mice, which spontaneously develop acute myeloid leukemia (AML) as a result of endogenous retroviral integration, showed that overexpression of Hoxa9, as a result of integrations at the locus, is one of the most common genetic abnormalities in these leukemias. 9,10 Subsequent gene expression profiling studies showed that HOXA9 is expressed in many AMLs. Of 6817 genes tested, HOXA9 was the single most predictive marker for poor prognosis. 11 Certain subtypes of acute leukemias, particularly those with rearrangements of the mixed lineage leukemia (MLL) gene, show especially high expression of A cluster HOX genes, 5,6,8 which is critical for MLL fusion protein-mediated transformation. 12,13 However, deregulation of Hox expression also appears to play a central role in leukemias without MLL rearrangements, including AMLs associated with the CALM-AF10 translocation, fusions of HOXA9 to the nucleoporin gene NUP98 in a subset of leukemias with the t(7;11), 14,15 overexpression of CDX2 or CDX4 [16][17][18] and identified T-cell acute lymphoblastic leukemia cases with translocations between the TCR␤ and the HOXA9/HOXA10 locus. 19