The evolutionary dynamics and fitness landscape of clonal haematopoiesis, bioRxiv, 2019-03-07
Somatic mutations acquired in healthy tissues as we age are major determinants of cancer risk. Whether variants confer a fitness advantage or rise to detectable frequencies by chance, however, remains largely unknown. Here, by combining blood sequencing data from ∼50,000 individuals, we reveal how mutation, genetic drift and fitness differences combine to shape the genetic diversity of healthy blood (‘clonal haematopoiesis’). By analysing the spectrum of variant allele frequencies we quantify fitness advantages for key pathogenic variants and genes and provide bounds on the number of haematopoietic stem cells. Positive selection, not drift, is the major force shaping clonal haematopoiesis. The remarkably wide variation in variant allele frequencies observed across individuals is driven by chance differences in the timing of mutation acquisition combined with differences in the cell-intrinsic fitness effect of variants. Contrary to the widely held view that clonal haematopoiesis is driven by ageing-related alterations in the stem cell niche, the data are consistent with the age dependence being driven simply by continuing risk of mutations and subsequent clonal expansions that lead to increased detectability at older ages.
biorxiv genomics 100-200-users 2019Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin, bioRxiv, 2019-03-05
ABSTRACTThree-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function, however many of its physical features at the single-cell level remain underexplored. Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular ∼200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in post-replicative chromatin, but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.
biorxiv genomics 100-200-users 2019Chromatin arranges in filaments of blobs with nanoscale functional zonation, bioRxiv, 2019-03-05
Three-dimensional (3D) chromatin organisation plays a key role in regulating genome function in higher eukaryotes. Despite recognition that the genome partitions into ~1Mb-sized topological associated domains (TADs) based on ensemble Hi-C measurements, many features of the physical organisation at the single cell level remain underexplored. Using 3D super-resolution microscopy, we reveal a sequential curvilinear arrangement of globular chromatin domains with viscoelastic properties (‘blobs’) juxtaposed to an RNA-populated interchromatin (IC) network. Quantitative mapping of genome function markers uncovers a zonal distribution, with RNA-binding factors concentrated in the IC, confinement of structural proteins and transcriptionally activepermissive marks to chromatin domain surfaces, and enrichment of repressive marks towards the interior. This correlation between nanoscale topology and genome function is relaxed in postreplicative chromatin, accentuated in replicative senescence, persists upon ATP depletion and hyperosmolarity induced chromatin condensation and, remarkably, after inactivation of cohesin. Our findings support a model of a higher-order chromatin architecture on the size level of TADs that creates and modulates distinct functional environments through a combination of biophysical parameters such as density and ATP-driven processes such as replication and transcription, but independent of cohesin.
biorxiv genomics 0-100-users 2019A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution, bioRxiv, 2019-03-02
AbstractC. elegans is an animal with few cells, but a striking diversity of cell types. Here, we characterize the molecular basis for their specification by profiling the transcriptomes of 84,625 single embryonic cells. We identify 284 terminal and pre-terminal cell types, mapping most single cell transcriptomes to their exact position in C. elegans’ invariant lineage. We use these annotations to perform the first quantitative analysis of the relationship between lineage and the transcriptome for a whole organism. We find that a strong lineage-transcriptome correlation in the early embryo breaks down in the final two cell divisions as cells adopt their terminal fates and that most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state. Users can explore our data with a graphical application “VisCello”.
biorxiv genomics 100-200-users 2019CTCF confers local nucleosome resiliency after DNA replication and during mitosis, bioRxiv, 2019-03-01
The access of Transcription Factors (TFs) to their cognate DNA binding motifs requires a precise control over nucleosome positioning. This is especially important following DNA replication and during mitosis, both resulting in profound changes in nucleosome organization over TF binding regions. Using mouse Embryonic Stem (ES) cells, we show that the TF CTCF displaces nucleosomes from its binding site and locally organizes large and phased nucleosomal arrays, not only in interphase steady-state but also immediately after replication and during mitosis. While regions bound by other TFs, such as Oct4 and Sox2, display major rearrangement, the post-replication and mitotic nucleosome organization activity of CTCF is not likely to be unique Esrrb binding regions are also characterized by persistent nucleosome positioning. Therefore, we propose that selected TFs, such as CTCF and Esrrb, govern the inheritance of nucleosome positioning at gene regulatory regions throughout the ES cell-cycle.
biorxiv genomics 0-100-users 2019High-density spatial transcriptomics arrays for in situ tissue profiling, bioRxiv, 2019-03-01
AbstractTissue function relies on the precise spatial organization of cells characterized by distinct molecular profiles. Single-cell RNA-Seq captures molecular profiles but not spatial organization. Conversely, spatial profiling assays to date have lacked global transcriptome information, throughput or single-cell resolution. Here, we develop High-Density Spatial Transcriptomics (HDST), a method for RNA-Seq at high spatial resolution. Spatially barcoded reverse transcription oligonucleotides are coupled to beads that are randomly deposited into tightly packed individual microsized wells on a slide. The position of each bead is decoded with sequential hybridization using complementary oligonucleotides providing a unique bead-specific spatial address. We then capture, and spatially in situ barcode, RNA from the histological tissue sections placed on the HDST array. HDST recovers hundreds of thousands of transcript-coupled spatial barcodes per experiment at 2 μm resolution. We demonstrate HDST in the mouse brain, use it to resolve spatial expression patterns and cell types, and show how to combine it with histological stains to relate expression patterns to tissue architecture and anatomy. HDST opens the way to spatial analysis of tissues at high resolution.
biorxiv genomics 0-100-users 2019