No abstract

A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ1. However, organizing the resulting taxonomy of cell types into lineage trees to understand developmental origin of cells remains challenging. Here we present LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)—a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.

Single-cell genomics and single-cell transcriptomics have recently emerged as powerful tools to study the biology of single cells at a genome-wide scale. However, a major challenge is to quantify both genomic DNA and mRNA from the same cell, which would allow direct comparison of genomic variation and transcriptome heterogeneity. Here we describe a method that allows the sequencing of genomic DNA and mRNA from the same cell without physical separation of the nucleic acids prior to amplification. We show that such an integrated strategy achieves efficiency similar to methods that sequence either genomic DNA or mRNA from single cells. We use this method to correlate DNA copy number variation to transcriptome variability among individual cells. Finally, we show that genes that display more cell-to-cell variability in transcript numbers are generally associated with reduced copy number loci and vice-versa, implying that copy number variations could potentially drive variability in gene expression between single cells.

Highlights d 20 mm resolution AP gene expression maps of C. elegans males and hermaphrodites d Resource for in silico identification of cell-and tissuespecific genes d Identification of sex-specific germline and sperm genes

With the exception of lamina-associated domains, the radial organization of chromatin in mammalian cells remains largely unexplored. Here, we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius that works by gradual enzymatic restriction of chromatin from the nuclear lamina towards the nucleus center, followed by sequencing of the generated cut sites. Using GPSeq, we mapped the radial organization of the human genome at 100 kb resolution, which revealed radial patterns of genomic and epigenomic features, gene expression, as well as A/B subcompartments. By combining radial information with chromosome contact frequencies measured by Hi-C, we substantially improved the accuracy of wholegenome structure modeling. Finally, we charted the radial topography of DNA double-strand breaks, germline variants and cancer mutations, and found that they have distinctive radial arrangements in A/B subcompartments. We conclude that GPSeq can reveal fundamental aspects of genome architecture.

We investigate the lifting of half-maximal four-dimensional gauged supergravities to compactifications of string theory. It is shown that a class of such supergravities can arise from compactifications of IIA string theory on manifolds of SU (2)-structure which may be thought of as K3 fibrations over T 2 . Examples of these SU (2)-structure backgrounds, as smooth K3 bundles and as compactifications with H-flux, are given and we also find evidence for a class of nongeometric, Mirror-fold backgrounds. By applying the duality between IIA string theory on K3 and Heterotic string theory on T 4 fibrewise, we argue that these SU (2)-structure backgrounds are dual to Heterotic compactifications on a class T 4 fibrations over T 2 . Examples of these fibrations as twisted tori, H-flux and T-fold compactifications are given. We also construct a new set of backgrounds, particular to Heterotic string theory, which includes a previously unknown class of Heterotic T-folds. A sigma model description of these backgrounds, from the Heterotic perspective, is presented in which we generalize the Bosonic doubled formalism to Heterotic string theory.

3 equal contribution 4 correspondence: janphilipp.junker@mdc-berlin.de (J.P.J.), a.vanoudenaarden@hubrecht.eu (A.v.O.) A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches, analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scartrace, a strategy for massively parallel whole-organism lineage tracing based on Cas9 induced genetic scars in the zebrafish.The timing of each cell division and the fate of the progeny define the lineage of an organism. Analysis of the lineage history of cell populations can reveal the developmental origin and the clonality of cell populations 1 . Genetically encoded fluorescent proteins are widely used as lineage markers 2,3 , but due to limited spectral resolution this approach has mostly been restricted to tracking the lineage of a relatively small subset of cells. Recent progress in live imaging has allowed for following many individual cells over time in optically transparent samples such as early fly and zebrafish embryos 4,5 . Nevertheless, direct observation of all cell divisions is generally only possible at the earliest developmental stages. RNA sequencing has emerged as a powerful method for systematic expression profiling of single cells and for computational inference of differentiation dynamics 6-8 . However, our ability to harness the enormous multiplexing capacity of high-throughput sequencing for lineage tracing has so far been lagging behind, despite pioneering studies in the hematopoietic system based on viral barcoding 9,10 or transposon

The adult zebrafish heart has a high capacity for regeneration following injury. However, the composition of the regenerative niche has remained largely elusive. Here, we dissected the diversity of activated cell states in the regenerating zebrafish heart based on single-cell transcriptomics and spatiotemporal analysis. We observed the emergence of several transient cell states with fibroblast characteristics following injury, and we outlined the proregenerative function of collagen-12-expressing fibroblasts. To understand the cascade of events leading to heart regeneration, we determined the origin of these cell states by high-throughput lineage tracing. We found that activated fibroblasts were derived from two separate sources: the epicardium and the endocardium. Mechanistically, we determined Wnt signalling as a regulator of the endocardial fibroblast response. In summary, our work identifies specialized activated fibroblast cell states that contribute to heart regeneration, thereby opening up possible approaches to modulating the regenerative capacity of the vertebrate heart.