Somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by overexpressing combinations of factors such as Oct4, Sox2, Klf4, and c-Myc. Reprogramming is slow and stochastic, suggesting the existence of barriers limiting its efficiency. Here we identify senescence as one such barrier. Expression of the four reprogramming factors triggers senescence by up-regulating p53, p16^INK4a, and p21^CIP1. Induction of DNA damage response and chromatin remodeling of the INK4a/ARF locus are two of the mechanisms behind senescence induction. Crucially, ablation of different senescence effectors improves the efficiency of reprogramming, suggesting novel strategies for maximizing the generation of iPS cells.

Sheep retroviruses can be used to map the selective preferences of early farmers and trace livestock movements across Europe.

CHD7 is one of nine members of the chromodomain helicase DNA–binding domain family of ATP–dependent chromatin remodeling enzymes found in mammalian cells. De novo mutation of CHD7 is a major cause of CHARGE syndrome, a genetic condition characterized by multiple congenital anomalies. To gain insights to the function of CHD7, we used the technique of chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP–Seq) to map CHD7 sites in mouse ES cells. We identified 10,483 sites on chromatin bound by CHD7 at high confidence. Most of the CHD7 sites show features of gene enhancer elements. Specifically, CHD7 sites are predominantly located distal to transcription start sites, contain high levels of H3K4 mono-methylation, found within open chromatin that is hypersensitive to DNase I digestion, and correlate with ES cell-specific gene expression. Moreover, CHD7 co-localizes with P300, a known enhancer-binding protein and strong predictor of enhancer activity. Correlations with 18 other factors mapped by ChIP–seq in mouse ES cells indicate that CHD7 also co-localizes with ES cell master regulators OCT4, SOX2, and NANOG. Correlations between CHD7 sites and global gene expression profiles obtained from Chd7^+/+, Chd7^+/−, and Chd7^−/− ES cells indicate that CHD7 functions at enhancers as a transcriptional rheostat to modulate, or fine-tune the expression levels of ES–specific genes. CHD7 can modulate genes in either the positive or negative direction, although negative regulation appears to be the more direct effect of CHD7 binding. These data indicate that enhancer-binding proteins can limit gene expression and are not necessarily co-activators. Although ES cells are not likely to be affected in CHARGE syndrome, we propose that enhancer-mediated gene dysregulation contributes to disease pathogenesis and that the critical CHD7 target genes may be subject to positive or negative regulation. The gene encoding chromodomain helicase DNA–binding protein 7 (CHD7) is required for normal mammalian development. In humans, genetic mutations in CHD7 lead to CHARGE syndrome, a disorder characterized by multiple birth defects. In previous studies, CHD7 was shown to localize to the cell nucleus and bind to specific sites on chromatin. However, the genome-wide distribution of CHD7 on chromatin and its function are not known. Here, we identified 10,483 sites on chromatin bound by CHD7 in mouse embryonic stem cells. Many of these sites are gene enhancer elements suspected to be involved in turning on genes. We show CHD7 functions at these loci to fine-tune the levels of genes that are specifically expressed in mouse ES cells. This modulation is mediated through several proteins that bind together with CHD7 at enhancer elements and can occur in either direction. These findings suggest CHARGE syndrome is the result of key genes that are improperly expressed during development. These key genes are currently unknown but are likely to be tissue-specific and may be upregulated or downregulated in response to CHD7 mutation.