Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution

Denoising Autoencoder Trained on Simulation-Derived Structures for Noise Reduction in Chromatin Scanning Transmission Electron Microscopy

Scanning transmission electron microscopy tomography with ChromEM staining (ChromSTEM), has allowed for the three-dimensional study of genome organization. By leveraging convolutional neural networks and molecular dynamics simulations, we have developed a denoising autoencoder (DAE) capable of postprocessing experimental ChromSTEM images to provide nucleosome-level resolution. Our DAE is trained on synthetic images generated from simulations of the chromatin fiber using the 1-cylinder per nucleosome (1CPN) model of chromatin. We find that our DAE is capable of removing noise commonly found in high-angle annular dark field (HAADF) STEM experiments and is able to learn structural features driven by the physics of chromatin folding. The DAE outperforms other well-known denoising algorithms without degradation of structural features and permits the resolution of α-tetrahedron tetranucleosome motifs that induce local chromatin compaction and mediate DNA accessibility. Notably, we find no evidence for the 30 nm fiber, which has been suggested to serve as the higher-order structure of the chromatin fiber. This approach provides high-resolution STEM images that allow for the resolution of single nucleosomes and organized domains within chromatin dense regions comprising of folding motifs that modulate the accessibility of DNA to external biological machinery.

Specific DNA binding of archaeal histones HMfA and HMfB

In archaea, histones play a role in genome compaction and are involved in transcription regulation. Whereas archaeal histones bind DNA without sequence specificity, they bind preferentially to DNA containing repeats of alternating A/T and G/C motifs. These motifs are also present on the artificial sequence "Clone20," a high-affinity model sequence for binding of the histones from Methanothermus fervidus. Here, we investigate the binding of HMfA and HMfB to Clone20 DNA. We show that specific binding at low protein concentrations (<30 nM) yields a modest level of DNA compaction, attributed to tetrameric nucleosome formation, whereas nonspecific binding strongly compacts DNA. We also demonstrate that histones impaired in hypernucleosome formation are still able to recognize the Clone20 sequence. Histone tetramers indeed exhibit a higher binding affinity for Clone20 than nonspecific DNA. Our results indicate that a high-affinity DNA sequence does not act as a nucleation site, but is bound by a tetramer which we propose is geometrically different from the hypernucleosome. Such a mode of histone binding might permit sequence-driven modulation of hypernucleosome size. These findings might be extrapolated to histone variants that do not form hypernucleosomes. Versatile binding modes of histones could provide a platform for functional interplay between genome compaction and transcription.

A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution

Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.

Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution

The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.

Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome

Nucleosome organization has been suggested to affect local mutation rates in the genome. However, the lack of de novo mutation and high-resolution nucleosome data has limited the investigation of this hypothesis. Additionally, analyses using indirect mutation rate measurements have yielded contradictory and potentially confounding results. Here, we combine data on >300,000 human de novo mutations with high-resolution nucleosome maps and find substantially elevated mutation rates around translationally stable (‘strong’) nucleosomes. We show that the mutational mechanisms affected by strong nucleosomes are low-fidelity replication, insufficient mismatch repair and increased double-strand breaks. Strong nucleosomes preferentially locate within young SINE/LINE transposons, suggesting that when subject to increased mutation rates, transposons are then more rapidly inactivated. Depletion of strong nucleosomes in older transposons suggests frequent positioning changes during evolution. The findings have important implications for human genetics and genome evolution.

Nucleosome organization has been suggested to affect local mutation rates in the genome. Here, the authors analyse data on >300,000 human de novo mutations and high-resolution nucleosome maps and provide evidence that nucleosome positioning stability modulates germline mutation rate variation across the human genome.

Local Determinants of the Mutational Landscape of the Human Genome

Large-scale chromatin features, such as replication time and accessibility influence the rate of somatic and germline mutations at the megabase scale. This article reviews how local chromatin structures -e.g., DNA wrapped around nucleosomes, transcription factors bound to DNA- affect the mutation rate at a local scale. It dissects how the interaction of some mutagenic agents and/or DNA repair systems with these local structures influence the generation of mutations. We discuss how this local mutation rate variability affects our understanding of the evolution of the genomic sequence, and the study of the evolution of organisms and tumors.

Invisible cities: segregated domains in the yeast genome with distinct structural and functional attributes

Recent advances in our understanding of the three-dimensional organization of the eukaryotic nucleus have rendered the spatial distribution of genes increasingly relevant. In a recent work (Tsochatzidou et al., Nucleic Acids Res 45:5818-5828, 2017), we proposed the existence of a functional compartmentalization of the yeast genome according to which, genes occupying the chromosomal regions at the nuclear periphery have distinct structural, functional and evolutionary characteristics compared to their centromeric-proximal counterparts. Around the same time, it was also shown that the genome of Saccharomyces cerevisiae is organized in topologically associated domains (TADs), which are largely associated with the replication timing. In this work, we proceed to investigate whether such units of three-dimensional genomic organization can be linked to transcriptional activity as a driving force for the shaping of genomic architecture. Through the application of a simple boundary-calling criterion in genome-wide 3C data, we define ~100 TAD-like domains which can be clustered in six different classes with radically different nucleosomal organizations, significant variations in transcription factor binding and uneven chromosomal distribution. Approximately ~20% of the genome is found to be confined in regions with "closed" chromatin structure around gene promoters. Most interestingly, we find both "open" and "closed" regions to be segregated, in the sense that they tend to avoid inter-chromosomal interactions. Our data further enforce the notion of a marked compartmentalization of the yeast genome in isolated territories, with implications in its function and evolution.

Large-scale SNP screenings identify markers linked with GCRV resistant traits through transcriptomes of individuals and cell lines in Ctenopharyngodon idella

Grass carp (Ctenopharyngodon idella) is an important economic species in freshwater aquaculture and its industry has been confined due to variety degeneration and frequent diseases. Marker-assisted selection is a feasible method for selective breeding of new varieties. Transcriptome data have greatly facilitated high-throughput single nucleotide polymorphism (SNP) marker discovery and phenotype association study. In this study, we gained a total of 25,981 and 5,775 high quality SNPs in two transcriptomes from individuals and cell lines, respectively. Comparative transcriptome analysis identified 413 and 832 grass carp reovirus (GCRV)-resistant-association SNPs as well as 1,381 and 1,606 GCRV-susceptible-association SNPs in individuals and cell lines, respectively. Integrated analysis indicated 22 genes with single SNP share common resistant/susceptible traits in two transcriptomes. Furthermore, we infected grass carp with GCRV, genotyping and association analyses were performed, and 9 in 22 SNPs were confirmed by PCR-RFLP. Meanwhile, mRNA expression profiles of 6 genes containing confirmed SNPs were examined by qRT-PCR. The results demonstrated that mRNA expressions were significant differences in resistant/susceptible individuals and cell lines. The present study develops an important strategy for high throughput screening of phenotype association genetic markers and the results will serve in grass carp breeding for GCRV resistance.

Evidence of selection for an accessible nucleosomal array in human

BACKGROUND

Recently, a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix has been used to reveal some enrichment of nucleosome-inhibiting energy barriers (NIEBs) nearby ubiquitous human "master" replication origins. Here we use this model to predict the existence of about 1.6 millions NIEBs over the 22 human autosomes.

RESULTS

We show that these high energy barriers of mean size 153 bp correspond to nucleosome-depleted regions (NDRs) in vitro, as expected, but also in vivo. On either side of these NIEBs, we observe, in vivo and in vitro, a similar compacted nucleosome ordering, suggesting an absence of chromatin remodeling. This nucleosomal ordering strongly correlates with oscillations of the GC content as well as with the interspecies and intraspecies mutation profiles along these regions. Comparison of these divergence rates reveals the existence of both positive and negative selections linked to nucleosome positioning around these intrinsic NDRs. Overall, these NIEBs and neighboring nucleosomes cover 37.5 % of the human genome where nucleosome occupancy is stably encoded in the DNA sequence. These 1 kb-sized regions of intrinsic nucleosome positioning are equally found in GC-rich and GC-poor isochores, in early and late replicating regions, in intergenic and genic regions but not at gene promoters.

CONCLUSION

The source of selection pressure on the NIEBs has yet to be resolved in future work. One possible scenario is that these widely distributed chromatin patterns have been selected in human to impair the condensation of the nucleosomal array into the 30 nm chromatin fiber, so as to facilitate the epigenetic regulation of nuclear functions in a cell-type-specific manner.

Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact

Deciphering the multitude of epigenomic and genomic factors that influence the mutation rate is an area of great interest in modern biology. Recently, chromatin has been shown to play a part in this process. To elucidate this relationship further, we integrated our own ultra-deep sequenced human nucleosomal DNA data set with a host of published human genomic and cancer genomic data sets. Our results revealed, that differences in nucleosome occupancy are associated with changes in base-specific mutation rates. Increasing nucleosome occupancy is associated with an increasing transition to transversion ratio and an increased germline mutation rate within the human genome. Additionally, cancer single nucleotide variants and microindels are enriched within nucleosomes and both the coding and non-coding cancer mutation rate increases with increasing nucleosome occupancy. There is an enrichment of cancer indels at the theoretical start (74 bp) and end (115 bp) of linker DNA between two nucleosomes. We then hypothesized that increasing nucleosome occupancy decreases access to DNA by DNA repair machinery and could account for the increasing mutation rate. Such a relationship should not exist in DNA repair knockouts, and we thus repeated our analysis in DNA repair machinery knockouts to test our hypothesis. Indeed, our results revealed no correlation between increasing nucleosome occupancy and increasing mutation rate in DNA repair knockouts. Our findings emphasize the linkage of the genome and epigenome through the nucleosome whose properties can affect genome evolution and genetic aberrations such as cancer.

Beyond xeroderma pigmentosum: DNA damage and repair in an ecological context. A tribute to James E. Cleaver

The ability to repair DNA is a ubiquitous characteristic of life on Earth and all organisms possess similar mechanisms for dealing with DNA damage, an indication of a very early evolutionary origin for repair processes. James E. Cleaver's career (initiated in the early 1960s) has been devoted to the study of mammalian ultraviolet radiation (UVR) photobiology, specifically the molecular genetics of xeroderma pigmentosum and other human diseases caused by defects in DNA damage recognition and repair. This work by Jim and others has influenced the study of DNA damage and repair in a variety of taxa. Today, the field of DNA repair is enhancing our understanding of not only how to treat and prevent human disease, but is providing insights on the evolutionary history of life on Earth and how natural populations are coping with UVR-induced DNA damage from anthropogenic changes in the environment such as ozone depletion.