The covalent modification of nucleosomal histones has emerged as a major determinant of chromatin structure and gene activity. To understand the interplay between various histone modifications, including acetylation and methylation, we performed a genome-wide chromatin structure analysis in a higher eukaryote. We found a binary pattern of histone modifications among euchromatic genes, with active genes being hyperacetylated for H3 and H4 and hypermethylated at Lys 4 and Lys 79 of H3, and inactive genes being hypomethylated and deacetylated at the same residues. Furthermore, the degree of modification correlates with the level of transcription, and modifications are largely restricted to transcribed regions, suggesting that their regulation is tightly linked to polymerase activity.[Keywords: Epigenetics; chromatin; histone; Drosophila; chromatin immunoprecipitation; microarray] Supplemental material is available at http://www.genesdev.org.

Haematopoietic stem cells drive blood production, but their population size and lifetime dynamics have not been quantified directly in humans. Here we identified 129,582 spontaneous, genome-wide somatic mutations in 140 single-cell-derived haematopoietic stem and progenitor colonies from a healthy 59-year-old man and applied population-genetics approaches to reconstruct clonal dynamics. Cell divisions from early embryogenesis were evident in the phylogenetic tree; all blood cells were derived from a common ancestor that preceded gastrulation. The size of the stem cell population grew steadily in early life, reaching a stable plateau by adolescence. We estimate the numbers of haematopoietic stem cells that are actively making white blood cells at any one time to be in the range of 50,000-200,000. We observed adult haematopoietic stem cell clones that generate multilineage outputs, including granulocytes and B lymphocytes. Harnessing naturally occurring mutations to report the clonal architecture of an organ enables the high-resolution reconstruction of somatic cell dynamics in humans.

SummaryMultiple signatures of somatic mutations have been identified in cancer genomes. Exome sequences of 1,001 human cancer cell lines and 577 xenografts revealed most common mutational signatures, indicating past activity of the underlying processes, usually in appropriate cancer types. To investigate ongoing patterns of mutational-signature generation, cell lines were cultured for extended periods and subsequently DNA sequenced. Signatures of discontinued exposures, including tobacco smoke and ultraviolet light, were not generated in vitro. Signatures of normal and defective DNA repair and replication continued to be generated at roughly stable mutation rates. Signatures of APOBEC cytidine deaminase DNA-editing exhibited substantial fluctuations in mutation rate over time with episodic bursts of mutations. The initiating factors for the bursts are unclear, although retrotransposon mobilization may contribute. The examined cell lines constitute a resource of live experimental models of mutational processes, which potentially retain patterns of activity and regulation operative in primary human cancers.

The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic changes and consequent clonal expansions leading to cancer. As for most cancer types, however, understanding of the earliest phases of colorectal neoplastic change, which may occur in morphologically normal tissue, is comparatively limited. Here, we whole genome sequenced hundreds of normal crypts from 42 individuals. Signatures of multiple mutational processes were revealed, some ubiquitous and continuous, others only found in some individuals, in some crypts or during certain periods of life. Likely driver mutations were present in ~1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium. Colorectal cancers exhibit substantially elevated mutation burdens relative to normal cells. Sequencing normal colorectal cells provides quantitative insights into the genomic and clonal evolution of cancerdriver mutations, which conceivably are morphologically indistinguishable from normal cells, are similarly unclear. In large part, these deficiencies are due to the technical challenge of identifying somatic mutations in normal tissues, which are composed of myriad microscopic cell clones. Several different approaches have been adopted to address this 4-14 , revealing signatures of common somatic mutational processes in normal cells of the small and large intestine, liver, blood, skin, and nervous system. Thus far, however, studies have not been of sufficient scale to characterise variation in signature activity or detect less frequent processes 4-14. Remarkably high proportions of normal skin, oesophageal, and endometrial epithelial cells have been shown to be members of clones already carrying driver mutations 10,11,15,16 , and large mutant clones have been detected in blood 17-20. The extent of this phenomenon in the colon, an organ with a high cancer incidence, has not been investigated. Colonic epithelium is a contiguous cell sheet organised into ~15,000,000 crypts each composed of ~2,000 cells 21. Towards the base of each crypt resides a small number of stem cells ancestral to the maturing and differentiated cells in the crypt 22. These stem cells stochastically replace one another through a process of neutral drift 23,24 such that all stem cells, and thus all cells, in a crypt derive from a single ancestor stem cell that existed in recent years 25-27. The somatic mutations that were present in this ancestor are thus found in all ~2,000 descendant cells and can be revealed by DNA sequencing of an individual crypt. These stem cells are thought to be the cells of origin of colorectal cancers 28. To characterise the earliest stages of colorectal carcinogenesis, somatic mutation burdens, mutational signatures, clonal dynamics, and the frequency of driver mutations in normal colorectal epithelium were explored by sequencing individual colorect...

26The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for 27 understanding the successive somatic genetic changes and consequent clonal expansions 28 leading to cancer. As for most cancer types, however