Methylation of cytosines is an essential epigenetic modification in mammalian genomes, yet the rules that govern methylation patterns remain largely elusive. To gain insights into this process, we generated base-pair-resolution mouse methylomes in stem cells and neuronal progenitors. Advanced quantitative analysis identified low-methylated regions (LMRs) with an average methylation of 30%. These represent CpG-poor distal regulatory regions as evidenced by location, DNase I hypersensitivity, presence of enhancer chromatin marks and enhancer activity in reporter assays. LMRs are occupied by DNA-binding factors and their binding is necessary and sufficient to create LMRs. A comparison of neuronal and stem-cell methylomes confirms this dependency, as cell-type-specific LMRs are occupied by cell-type-specific transcription factors. This study provides methylome references for the mouse and shows that DNA-binding factors locally influence DNA methylation, enabling the identification of active regulatory regions.

DNA is packaged into chromatin, a highly compacted DNA-protein complex; therefore, all cellular processes that use the DNA as a template, including DNA repair, require a high degree of coordination between the DNA-repair machinery and chromatin modification/remodelling, which regulates the accessibility of DNA in chromatin. Recent studies have implicated histone acetyltransferase (HAT) complexes and chromatin acetylation in DNA repair; however, the precise underlying mechanism remains poorly understood. Here, we show that the HAT cofactor Trrap and Tip60 HAT bind to the chromatin surrounding sites of DNA double-strand breaks (DSBs) in vivo. Trrap depletion impairs both DNA-damage-induced histone H4 hyperacetylation and accumulation of repair molecules at sites of DSBs, resulting in defective homologous recombination (HR) repair, albeit with the presence of a functional ATM-dependent DNA-damage signalling cascade. Importantly, the impaired loading of repair proteins and the defect in DNA repair in Trrap-deficient cells can be counteracted by chromatin relaxation, indicating that the DNA-repair defect that was observed in the absence of Trrap is due to impeded chromatin accessibility at sites of DNA breaks. Thus, these data reveal that cells may use the same basic mechanism involving HAT complexes to regulate distinct cellular processes, such as transcription and DNA repair.

In mammals, fusion of two morphologically distinct gametes, oocytes and spermatozoa, leads to the formation of totipotent embryos. Acquisition of totipotency is thought to be mediated by extensive epigenetic reprogramming of parental genomes, affecting DNA methylation and histone modifications, and possibly replication timing and transcriptional activity in parental specific manners [1][2][3][4] . It is currently unclear to what extent differential reprogramming of maternal and paternal genomes is due to differences in chromatin states inherited from the oocyte and spermatozoon [4][5][6][7][8][9][10][11] . Beyond DNA methylation 1,2,6,12 , it is unknown which types of parental chromatin states are maintained or reprogrammed in early embryos. If certain parental chromatin states did escape reprogramming in the early embryo, such information could constitute an "intrinsic intergenerational epigenetic program directing gene expression in the next generation 13 . If these chromatin states also escaped reprogramming during gametogenesis, the inheritance program would function transgenerationally 13 . An increasing number of studies point to inter-or transgenerational transmission of acquired phenotypic traits that are related to temporal exposure of (grand-)parents to alternative instructive environmental cues [14][15][16][17][18] . Mechanistically, such phenotypic changes may be related to (transient) alterations of an intrinsic inheritance program.A role of histones and associated posttranslational modifications in maternal and paternal transmission of intrinsic or acquired epigenetic information is largely unknown 13 . In many metazoans, male germ cells undergo during their final differentiation into sperm an extensive chromatin remodeling process during which 3 genomic DNA becomes newly packaged into a highly condensed configuration by sperm specific proteins. In mammals, removal of histones is generally not complete 10,11,[19][20][21][22][23][24] . Furthermore, remaining histones have been reported to stay associated with the paternal genome during de novo chromatin formation in the zygote following fertilization 9 .We and others recently showed that histones lasting in human sperm are to some extent enriched at regulatory sequences of genes 10,11 . We also demonstrated that H3K4me3-and H3K27me3-marked histones are retained at promoters of specific sets of genes in mouse spermatozoa 11. The extent of evolutionary conservation of nucleosome retention at gene regulatory sequences in spermatozoa and the mechanistic principles of such retention are, however, unknown.To address conservation and to dissect the molecular logic underlying nucleosome retention, we determined the genome-wide nucleosome occupancy in mouse spermatozoa that only contain 1% residual histones. We show here that combinatorial effects of sequence composition, histone variants and histone modifications uniquely determine the packaging of sperm DNA. Nucleosomes in sperm mainly localize to unmethylated CpG-rich sequences in a histone variant specif...

PR-Set7/SET8 is a histone H4–lysine 20 methyltransferase required for normal cell proliferation. However, the exact functions of this enzyme remain to be determined. In this study, we show that human PR-Set7 functions during S phase to regulate cellular proliferation. PR-Set7 associates with replication foci and maintains the bulk of H4-K20 mono- and trimethylation. Consistent with a function in chromosome dynamics during S phase, inhibition of PR-Set7 methyltransferase activity by small hairpin RNA causes a replicative stress characterized by alterations in replication fork velocity and origin firing. This stress is accompanied by massive induction of DNA strand breaks followed by a robust DNA damage response. The DNA damage response includes the activation of ataxia telangiectasia mutated and ataxia telangiectasia related kinase–mediated pathways, which, in turn, leads to p53-mediated growth arrest to avoid aberrant chromosome behavior after improper DNA replication. Collectively, these data indicate that PR-Set7–dependent lysine methylation during S phase is an essential posttranslational mechanism that ensures genome replication and stability.

Distal regulatory elements, including enhancers, play a critical role in regulating gene activity. Transcription factor binding to these elements correlates with Low Methylated Regions (LMRs) in a process that is poorly understood. Here we ask whether and how actual occupancy of DNA-binding factors is linked to DNA methylation at the level of individual molecules. Using CTCF as an example, we observe that frequency of binding correlates with the likelihood of a demethylated state and sites of low occupancy display heterogeneous DNA methylation within the CTCF motif. In line with a dynamic model of binding and DNA methylation turnover, we find that 5-hydroxymethylcytosine (5hmC), formed as an intermediate state of active demethylation, is enriched at LMRs in stem and somatic cells. Moreover, a significant fraction of changes in 5hmC during differentiation occurs at these regions, suggesting that transcription factor activity could be a key driver for active demethylation. Since deletion of CTCF is lethal for embryonic stem cells, we used genetic deletion of REST as another DNA-binding factor implicated in LMR formation to test this hypothesis. The absence of REST leads to a decrease of hydroxymethylation and a concomitant increase of DNA methylation at its binding sites. These data support a model where DNA-binding factors can mediate turnover of DNA methylation as an integral part of maintenance and reprogramming of regulatory regions.

Topoisomerases are essential for DNA replication in dividing cells, but their genomic targets and function in postmitotic cells remain poorly understood. Here we show that a switch in the expression from Topoisomerases IIα (Top2α) to IIβ (Top2β) occurs during neuronal differentiation in vitro and in vivo. Genome-scale location analysis in stem cell-derived postmitotic neurons reveals Top2β binding to chromosomal sites that are methylated at lysine 4 of histone H3, a feature of regulatory regions. Indeed Top2β-bound sites are preferentially promoters and become targets during the transition from neuronal progenitors to neurons, at a time when cells exit the cell cycle. Absence of Top2β protein or its activity leads to changes in transcription and chromatin accessibility at many target genes. Top2β deficiency does not impair stem cell properties and early steps of neuronal differentiation but causes premature death of postmitotic neurons. This neuronal degeneration is caused by up-regulation of Ngfr p75, a gene bound and repressed by Top2β. These findings suggest a chromatin-based targeting of Top2β to regulatory regions in the genome to govern the transcriptional program associated with neuronal differentiation and longevity.epigenetic regulation | neurogenesis | gene expression | genomewide assays T opoisomerases are essential for solving topological problems arising from DNA-templated processes such as replication, transcription, recombination, chromatin remodeling, chromosome condensation, and segregation (1-5). The type I subfamily of topoisomerases achieves this task by passing one strand of the DNA through a break in the opposing strand; proteins in the type II subfamily pass a region of duplex strands from the same or a different molecule through a double-stranded gap generated in DNA (1-5). Mammalian cells encode two isozymes of type II enzymes that have highly homologous N-terminal ATPase and central core domains but differ at their C-termini (6). These two isozymes, Topoisomerases IIα (Top2α) and IIβ (Top2β), have almost identical enzymatic properties in vitro (7, 8); however, their expression patterns are dissimilar. Top2α is the main isoform expressed in proliferating cells, shows high expression in S/G2/M phases of the cell cycle, and plays important roles in DNA replication and chromosome condensation/segregation during the cell cycle (9-12).The cellular functions of Top2β are much less well understood. It is expressed in all mammalian cells throughout the cell cycle but is up-regulated robustly when cells reach a postmitotic state of terminal differentiation (13-15). For example, the postmitotic granule cells in the external germinal layer of the developing rat cerebellum show a transition from Top2α to Top2β (14), and blocking Top2β catalytic activity affects the expression of about one third of genes induced during differentiation of rat cerebellar granule neurons (16). Genetic deletion of Top2b in mice causes neural defects including aberrant axonal elongation and branching and perinatal death e...

Chromatin modifications at core histones including acetylation, methylation, phosphorylation and ubiquitination play an important role in diverse biological processes. Acetylation of specific lysine residues within the N terminus tails of core histones is arguably the most studied histone modification; however, its precise roles in different cellular processes and how it is disrupted in human diseases remain poorly understood. In the last decade, a number of histone acetyltransferases (HATs) enzymes responsible for histone acetylation, has been identified and functional studies have begun to unravel their biological functions. The activity of many HATs is dependent on HAT complexes, the multiprotein assemblies that contain one HAT catalytic subunit, adapter proteins, several other molecules of unknown function and a large protein called TRansformation/tRanscription domain-Associated Protein (TRRAP). As a common component of many HAT complexes, TRRAP appears to be responsible for the recruitment of these complexes to chromatin during transcription, replication and DNA repair. Recent studies have shed new light on the role of TRRAP in HAT complexes as well as mechanisms by which it mediates diverse cellular processes. Thus, TRRAP appears to be responsible for a concerted and context-dependent recruitment of HATs and coordination of distinct chromatin-based processes, suggesting that its deregulation may contribute to diseases. In this review, we summarize recent developments in our understanding of the function of TRRAP and TRRAP-containing HAT complexes in normal cellular processes and speculate on the mechanism underlying abnormal events that may lead to human diseases such as cancer.

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