A single-cell multiomics approach for simultaneous analysis of replication timing and gene expression

Analysis of a cell’s replication timing (RT) provides insight into how genes replicate, early or late, during the S-phase of the cell cycle. RT is cell-type specific, inheritable, and has been correlated to gene expression in normal and diseased states. However, most studies have been limited to somatic cells. Very little is known about RT control in early mouse embryos, and how it correlates with the start of transcription during zygote gene activation (ZGA), at the 2-cell stage. In this study, we develop an in-house single-cell multiomics approach to simultaneously analyze RT and gene expression in individual cells of the mouse 1-cell, 2-cell, and 4-cell embryos. We detect that RT is established at the 1-cell stage prior to ZGA. Surprisingly, we observe that the coordinated RT and gene expression control is different in early totipotent embryos, compared to previously published studies in somatic cells. Late replicating regions correlate with higher gene expression and open chromatin in the early developing embryos. Lastly, we perform an integrated pseudo time trajectory analysis combining RT and gene expression information per cell.

Mammalian DNA replication is a highly organized and regulated process. Large, Mb-sized regions are replicated at defined times along S-phase. Replication Timing (RT) is thought to play a role in shaping the mammalian genome by affecting mutation rates. Previous analyses relied on somatic RT profiles. However, only germline mutations are passed on to offspring and affect genomic composition. Therefore, germ cell RT information is necessary to evaluate the influences of RT on the mammalian genome. We adapted the RT mapping technique for limited amounts of cells, and measured RT from two stages in the mouse germline - primordial germ cells (PGCs) and spermatogonial stem cells (SSCs). RT in germline cells exhibited stronger correlations to both mutation rate and recombination hotspots density than those of RT in somatic tissues, emphasizing the importance of using correct tissues-of-origin for RT profiling. Germline RT maps exhibited stronger correlations to additional genetic features including GC-content, transposable elements (SINEs and LINEs), and gene density. GC content stratification and multiple regression analysis revealed independent contributions of RT to SINE, gene, mutation, and recombination hotspot densities. Together, our results establish a central role for RT in shaping multiple levels of mammalian genome composition.

Altered Transcription and Replication Driving MYC-Induced B and T Cell Leukemias

The spatiotemporal organization of DNA replication produces a highly robust and reproducible replication timing profile. Sequencing-based methods for assaying replication timing genome-wide have become commonplace, but regions of high repeat content in the human genome have remained refractory to analysis. Here, we report the first nearly-gapless telomere-to-telomere replication timing profiles in human, using the T2T-CHM13 genome assembly and sequencing data for five cell lines. We find that replication timing can be successfully assayed in centromeres and large blocks of heterochromatin. Centromeric regions replicate in mid-to-late S-phase and contain replication-timing peaks at a similar density to other genomic regions, while distinct families of heterochromatic satellite DNA differ in their bias for replicating in late S-phase. The high degree of consistency in centromeric replication timing across chromosomes within each cell line prompts further investigation into the mechanisms dictating that some cell lines replicate their centromeres earlier than others, and what the consequences of this variation are.

The organization of mammalian DNA replication is poorly understood. We have produced high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal, and embryonic stem (ES) cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy-number variations during S phase to produce replication timing profiles. We first obtained timing maps of 3% of the genome using high-density oligonucleotide tiling arrays and then extended the TimEX method genome-wide using massively parallel sequencing. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation, where replication forks progress unidirectionally from origins that can be hundreds of kilobases away. Absence of initiation in one transition region is shown at the molecular level by single molecule analysis of replicated DNA (SMARD). Comparison of ES and erythroid cells replication patterns revealed that these cells replicate about 20% of their genome in different quarters of S phase. Importantly, we detected a strong inverse relationship between timing of replication and distance to the closest expressed gene. This relationship can be used to predict tissue-specific timing of replication profiles from expression data and genomic annotations. We also provide evidence that early origins of replication are preferentially located near highly expressed genes, that mid-firing origins are located near moderately expressed genes, and that late-firing origins are located far from genes.

Deranged Transcription and Replication in MYC-Induced B and T Cell Leukemias

The transmission of genetic information relies on a coordinated network of cell cycle controls. Abnormalities in this network can result in genomic instability and lead to the transformation of normal cells into cancer cells. Chromosomal DNA replication is not only central to cellular division but also plays a crucial role in the maintenance of genomic integrity. DNA replication errors increase genetic instability, and may be a causative factor in diseases such as cancer and neuronal disorders. Replication in eukaryotes initiates from discrete genomic regions, termed origins, according to a strict, often tissue-specific, temporal program. The genetic program that controls activation of replication origins in mammalian cells has still not been elucidated. There is evidence that specification of replication sites and timing of replication are dynamic processes that are regulated by tissue-specific and developmental cues and that are responsive to epigenetic modifications. Here, we focus on the spatiotemporal regulation of DNA replication in the human genome. There is growing evidence that chromosome band patterns and epigenetic transformation of chromatin influence the timing of replication. On the basis of this evidence, we propose that the chromatin regions showing switches in replication timing from early to late in S phase are correlated with chromosome band boundaries. These chromatin regions generally display transitions in GC contents and include more non-B-form DNA structures than other genomic regions. We also examine here the effect of changes in replication timing on genomic stability and the possible role of replication timing in the etiology of diseases such as cancer. Replication timing assays are one of many promising techniques under investigation that may in future allow much earlier cancer detection than is possible today.

Modified allelic replication in lymphocytes of patients with neurofibromatosis type 1

Current temporal studies of DNA replication are either low-resolution or require complex cell synchronisation and/or sorting procedures. Here we introduce Nanotiming, a single-molecule, nanopore sequencing-based method producing high-resolution, telomere-to-telomere replication timing (RT) profiles of eukaryotic genomes by interrogating changes in intracellular dTTP concentration during S phase through competition with its analogue bromodeoxyuridine triphosphate (BrdUTP) for incorporation into replicating DNA. This solely demands the labelling of asynchronously growing cells with an innocuous dose of BrdU during one doubling time followed by BrdU quantification along nanopore reads. We demonstrate in S. cerevisiae model eukaryote that Nanotiming reproduces RT profiles generated by reference methods both in wild-type and mutant cells inactivated for known RT determinants. Nanotiming is simple, accurate, inexpensive, amenable to large-scale analyses, and has the unique ability to access RT of individual telomeres, revealing that Rif1 iconic telomere regulator selectively delays replication of telomeres associated with specific subtelomeric elements.

Stem cells have the unique ability to self-renew and differentiate into specialized cell types. Epigenetic mechanisms, including histones and their post-translational modifications, play a crucial role in regulating programs integral to a cell’s identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst stem cells (CySCs), the Drosophila testis provides an excellent in vivo model for studying adult stem cells. However, the small number of stem cells and cellular heterogeneity of this tissue have limited comprehensive genomic studies.In this study, we developed cell type-specific genomic techniques to analyze the transcriptome, histone modification patterns, and replication timing of GSC-like and CySC-like cells. Single cell RNA sequencing validated previous findings on GSC-CySC intercellular communication and revealed high expression of chromatin regulators in GSC-like cells. To characterize chromatin landscapes, we developed a cell-type-specific chromatin profiling assay to map H3K4me3-, H3K27me3-, and H3K9me3-enriched regions, corresponding to euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively. Finally, we determined cell type-specific replication timing profiles, integrating our in vivo datasets with published data using cultured cell lines. Our results reveal that GSC-like cells display a distinct replication program compared to somatic lineages, that aligns with chromatin state differences. Collectively, our integrated transcriptomic, chromatin, and replication datasets provide a comprehensive framework for understanding genome regulation differences between these in vivo stem cell populations, demonstrating the power of multi-omics in uncovering cell type-specific regulatory features.

Stem cells have the unique ability to self-renew and differentiate into specialized cell types. Epigenetic mechanisms, including histones and their post-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst stem cells (CySCs), the Drosophila testis provides an excellent in vivo model for studying adult stem cells. However, the small number of stem cells and the cellular heterogeneity of this tissue have limited comprehensive genomic studies. In this study, we develop cell-type-specific genomic techniques to analyze the transcriptome, histone modification patterns, and replication timing of germline stem cell (GSC)–like and somatic cyst stem cell (CySC)–like cells. Single-cell RNA sequencing validates previous findings on GSC–CySC intercellular communication and reveals a high expression of chromatin regulators in GSC-like cells. To characterize chromatin landscapes, we develop a cell-type-specific chromatin profiling assay to map H3K4me3-, H3K27me3-, and H3K9me3-enriched regions, corresponding to the euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively. Finally, we determine cell-type-specific replication timing profiles, integrating our in vivo data sets with published data using cultured cell lines. Our results reveal that GSC-like cells display a distinct replication program, compared with somatic lineages, that aligns with chromatin state differences. Collectively, our integrated transcriptomic, chromatin, and replication data sets provide a comprehensive framework for understanding genome regulation differences between these in vivo stem-cell populations, demonstrating the power of multiomics in uncovering cell-type-specific regulatory features.

Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early- and late-replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs.

Replication timing is a crucial aspect of genome regulation that is strongly correlated with chromatin structure, gene expression, DNA repair, and genome evolution. Replication timing is determined by the timing of replication origin firing, which involves activation of MCM helicase complexes loaded at replication origins. Nonetheless, how the timing of such origin firing is regulated remains mysterious. Here, we show that the number of MCMs loaded at origins regulates replication timing. We show for the first time in vivo that multiple MCMs are loaded at origins. Because early origins have more MCMs loaded, they are, on average, more likely to fire early in S phase. Our results provide a mechanistic explanation for the observed heterogeneity in origin firing and help to explain how defined replication timing profiles emerge from stochastic origin firing. These results establish a framework in which further mechanistic studies on replication timing, such as the strong effect of heterochromatin, can be pursued.

Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment.

Replication timing is a costly but powerful tool for characterizing cellular mechanisms that underlie chromatin organization, cancer epigenetics, and genomic instability. Genome-wide replication timing profiles reflect the temporal order of DNA synthesis during S phase and are closely linked to chromatin accessibility, transcriptional activity, and proliferative state. Prior work has demonstrated a robust inverse relationship between replication timing and DNA methylation at the domain scale, enabling methylation-based proxies to approximate replication timing in large cohorts where direct experimental measurement is impractical. Given the tight coupling between replication timing, chromatin structure, and cellular phenotype, we hypothesized that histologic morphology encodes information consistent with replication timing states. To test this hypothesis, we implemented Vision Transformer (ViT) architectures to predict replication timing proxies from whole-slide histopathology images. Patch-level embeddings were extracted using a pretrained ViT and aggregated through attention-based multiple instance learning to predict sample-level replication timing. In parallel, CellViT models were employed to perform cell-level prediction, enabling direct comparison between patch-based and cellular representations. Across both modeling strategies, statistically significant correlations were observed between image-derived features and methylation-based replication timing proxies. Patch-level models achieved correlations of approximately 46%, while cell-level models consistently reached correlations exceeding 50% on the validation cohort. Prediction error remained stable across folds, with mean absolute error and mean squared error values ranging between 0.4 and 0.6. These results demonstrate that replication timing–associated epigenomic states are reflected in tissue morphology and can be inferred using deep learning models applied to routine histopathology. This work establishes a feasible, noninvasive framework for replicosomic inference from whole-slide images and supports future efforts toward spatially resolved replication timing analysis and integrative modeling of replicative stress in cancer.