Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated mutations in mtDNA are unclear. In this study, we analyzed somatic alterations in mtDNA from 1675 tumors. We identified 1907 somatic substitutions, which exhibited dramatic replicative strand bias, predominantly C > T and A > G on the mitochondrial heavy strand. This strand-asymmetric signature differs from those found in nuclear cancer genomes but matches the inferred germline process shaping primate mtDNA sequence content. A number of mtDNA mutations showed considerable heterogeneity across tumor types. Missense mutations were selectively neutral and often gradually drifted towards homoplasmy over time. In contrast, mutations resulting in protein truncation undergo negative selection and were almost exclusively heteroplasmic. Our findings indicate that the endogenous mutational mechanism has far greater impact than any other external mutagens in mitochondria and is fundamentally linked to mtDNA replication.DOI: http://dx.doi.org/10.7554/eLife.02935.001

Evidence for distinct human cancer stem cells (CSCs) remains contentious and the degree to which different cancer cells contribute to propagating malignancies in patients remains unexplored. In low- to intermediate-risk myelodysplastic syndromes (MDS), we establish the existence of rare multipotent MDS stem cells (MDS-SCs), and their hierarchical relationship to lineage-restricted MDS progenitors. All identified somatically acquired genetic lesions were backtracked to distinct MDS-SCs, establishing their distinct MDS-propagating function in vivo. In isolated del(5q)-MDS, acquisition of del(5q) preceded diverse recurrent driver mutations. Sequential analysis in del(5q)-MDS revealed genetic evolution in MDS-SCs and MDS-progenitors prior to leukemic transformation. These findings provide definitive evidence for rare human MDS-SCs in vivo, with extensive implications for the targeting of the cells required and sufficient for MDS-propagation.

Key Points Genome-wide binding profiles of FLI1, ERG, GATA2, RUNX1, SCL, LMO2, and LYL1 in human HSPCs reveals patterns of combinatorial TF binding. Integrative analysis of transcription factor binding reveals a densely interconnected network of coding and noncoding genes in human HSPCs.

While histone modifications have been implicated in many DNA-dependent processes, their precise role in DNA replication remains largely unknown. Here, we describe a very efficient, single-step method to specifically purify histones located around an origin of replication from S. cerevisiae. Using high-resolution mass spectrometry, we have obtained a comprehensive view of the histone modifications surrounding the origin of replication throughout the cell cycle. We have discovered that histone H3 and H4 acetylation is dynamically regulated around an origin of replication, at the level of multiply-acetylated histones. Furthermore, we find that this acetylation is required for efficient origin activation during S-phase. KeywordsDNA replication; histone modifications; mass spectrometry Eukaryotic DNA replication occurs in the context of chromatin. The fundamental unit of chromatin is the nucleosome, in which 147 base pairs of DNA tightly wrap around a histone octamer, consisting of the core histones H2A, H2B, H3 and H4 1 . The packaging of DNA into chromatin profoundly influences DNA-dependent processes such as transcription, replication, repair and recombination 2,3 . A large variety of covalent modifications are added to histones post-translationally, including acetylation, methylation, phosphorylation and ubiquitination, to influence DNA-dependent processes 4 .DNA replication occurs in the S-phase of the cell cycle and initiates at discrete sites on the chromosome called origins of replication (henceforth "origins"). DNA replication has been best studied in the budding yeast, Saccharomyces cerevisiae, where origins were first identified as autonomous replication sequence (ARS) elements in plasmid maintenance assays 5 . A number of protein complexes are assembled at an origin in a tightly regulated, temporally controlled manner over the cell cycle to initiate replication. Replication forks then travel bi-directionally outwards from the origin until the entire genome is replicated6.