Induced pluripotent stem (iPS) cells are derived by epigenetic reprogramming, but their DNA methylation patterns have not yet been analyzed on a genome-wide scale. Here, we find substantial hypermethylation and hypomethylation of cytosine-phosphate-guanine (CpG) island shores in nine human iPS cell lines as compared to their parental fibroblasts. The differentially methylated regions (DMRs) in the reprogrammed cells (denoted R-DMRs) were significantly enriched in tissue-specific (T-DMRs; 2.6-fold, P < 10 −4 ) and cancer-specific DMRs (C-DMRs; 3.6-fold, P < 10 −4 ). Notably, even though the iPS cells are derived from fibroblasts, their R-DMRs can distinguish between normal brain, liver and spleen cells and between colon cancer and normal colon cells. Thus, many DMRs are broadly involved in tissue differentiation, epigenetic reprogramming and cancer. We observed colocalization of hypomethylated R-DMRs with hypermethylated C-DMRs and bivalent chromatin marks, and colocalization of hypermethylated R-DMRs with hypomethylated C-DMRs and the absence of bivalent marks, suggesting two mechanisms for epigenetic reprogramming in iPS cells and cancer.Correspondence should be addressed to G.Q.D. (George.Daley@childrens.harvard.edu) and A.P.F. (afeinberg@jhu.edu). 5 These authors contributed equally to this work. 6 These authors jointly supervised this work.Accession codes. NCBI GEO: Gene expression microarray data and CHARM microarray data have been submitted under accession number GSE18111.Note: Supplementary information is available on the Nature Genetics website. Here we used a similar approach to the question of iPS cell reprogramming, first comparing six human iPS cell lines to the fibroblasts from which they were derived using comprehensive high-throughput array-based relative methylation (CHARM) analysis 9 . This approach allows the interrogation of ~4.6 million CpG sites genome-wide using a custom designed NimbleGen HD2 microarray, including almost all CpG islands and shores in the human genome. Genomic DNA from iPS cells 3,5 , their parental fibroblasts and human embryonic stem (hES) cells (Online Methods) was digested with the enzyme McrBC, fractionated, labeled and hybridized to a CHARM array. AUTHOR CONTRIBUTIONSA total of 4,401 regions (including 96,404 CpG sites) were found to differ in iPS cell lines from the fibroblasts of origin (Table 1, Supplementary Table 1) at a false discovery rate (FDR) of 5%; we term these regions R-DMRs. Of these R-DMRs, DMRs that were hypermethylated in iPS cells compared to fibroblasts predominated over hypomethylated DMRs (60%:40%). Of the 4,401 DMRs, 1,969 were within 2 kb of the transcriptional start site of a gene.The genes that were associated with these R-DMRs showed functionally important features based on bioinformatic analyses. First, gene ontology (GO) annotation analysis of these genes revealed significant enrichment for genes involved in developmental and regulatory processes (Supplementary Table 2). For example, 38% of the genes that were hypomethylated in iPS ...

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.

In honeybee societies, distinct caste phenotypes are created from the same genotype, suggesting a role for epigenetics in deriving these behaviorally different phenotypes. We found no differences in DNA methylation between irreversible worker/queen castes, but substantial differences between nurses and forager subcastes. Reverting foragers back to nurses reestablished methylation levels for a majority of genes and provided the first evidence in any organism of reversible epigenetic changes associated with behavior.