Charting a tissue from single-cell transcriptomes, bioRxiv, 2018-10-30
AbstractMassively multiplexed sequencing of RNA in individual cells is transforming basic and clinical life sciences. However, in standard experiments, tissues must first be dissociated. Thus, after sequencing, information about the spatial relationships between cells is lost although this knowledge is crucial for understanding cellular and tissue-level function. Recent attempts to overcome this fundamental challenge rely on employing additional in situ gene expression imaging data which can guide spatial mapping of sequenced cells. Here we present a conceptually different approach that allows to reconstruct spatial positions of cells in a variety of tissues without using reference imaging data. We first show for several complex biological systems that distances of single cells in expression space monotonically increase with their physical distances across tissues. We therefore seek to map cells to tissue space such that this principle is optimally preserved, while matching existing imaging data when available. We show that this optimization problem can be cast as a generalized optimal transport problem and solved efficiently. We apply our approach successfully to reconstruct the mammalian liver and intestinal epithelium as well as fly and zebrafish embryos. Our results demonstrate a simple spatial expression organization principle and that this principle (or future refined principles) can be used to infer, for individual cells, meaningful spatial position probabilities from the sequencing data alone.
biorxiv systems-biology 100-200-users 2018Retinotopic maps of visual space in the human cerebellum, bioRxiv, 2018-10-29
While the cerebellum is instrumental for motor control, it is not traditionally implicated in vision. Here, we report the existence of 5 ipsilateral visual field maps in the human cerebellum. These maps are located within the oculomotor vermis and cerebellar nodes of the dorsal attention and visual networks. These findings imply that the cerebellum is closely involved in visuospatial cognition, and that its contributions are anchored in sensory coordinates.
biorxiv neuroscience 100-200-users 2018The architecture of cell differentiation in choanoflagellates and sponge choanocytes, bioRxiv, 2018-10-29
SUMMARYCollar cells are ancient animal cell types which are conserved across the animal kingdom [1] and their closest relatives, the choanoflagellates [2]. However, little is known about their ancestry, their subcellular architecture, or how they differentiate. The choanoflagellate Salpingoeca rosetta [3] expresses genes necessary for animal multicellularity and development [4] and can alternate between unicellular and multicellular states [3,5], making it a powerful model to investigate the origin of animal multicellularity and mechanisms underlying cell differentiation [6,7]. To compare the subcellular architecture of solitary collar cells in S. rosetta with that of multicellular “rosettes” and collar cells in sponges, we reconstructed entire cells in 3D through transmission electron microscopy on serial ultrathin sections. Structural analysis of our 3D reconstructions revealed important differences between single and colonial choanoflagellate cells, with colonial cells exhibiting a more amoeboid morphology consistent with relatively high levels of macropinocytotic activity. Comparison of multiple reconstructed rosette colonies highlighted the variable nature of cell sizes, cell-cell contact networks and colony arrangement. Importantly, we uncovered the presence of elongated cells in some rosette colonies that likely represent a distinct and differentiated cell type. Intercellular bridges within choanoflagellate colonies displayed a variety of morphologies and connected some, but not all, neighbouring cells. Reconstruction of sponge choanocytes revealed both ultrastructural commonalities and differences in comparison to choanoflagellates. Choanocytes and colonial choanoflagellates are typified by high amoeboid cell activity. In both, the number of microvilli and volumetric proportion of the Golgi apparatus are comparable, whereas choanocytes devote less of their cell volume to the nucleus and mitochondria than choanoflagellates and more of their volume to food vacuoles. Together, our comparative reconstructions uncover the architecture of cell differentiation in choanoflagellates and sponge choanocytes and constitute an important step in reconstructing the cell biology of the last common ancestor of the animal kingdom.
biorxiv evolutionary-biology 100-200-users 2018Bacterial contribution to genesis of the novel germ line determinant oskar, bioRxiv, 2018-10-26
New cellular functions and developmental processes can evolve by modifying the functions or regulation of preexisting genes, but the creation of new genes and their contributions to novel processes is less well understood. New genes can arise not only from mutations or rearrangements of existing sequences, but also via acquisition of foreign DNA, also called horizontal gene transfer (HGT). Here we present evidence that HGT contributed to the creation of a novel gene indispensable for reproduction in some insects. The oskar gene evolved to fulfil a crucial role in insect germ cell formation, but was long considered a novel gene with unknown evolutionary origins. Our analysis of over 100 Oskar sequences suggests that Oskar arose through a novel gene formation history involving fusion of eukaryotic and prokaryotic sequences. One of its two conserved domains (LOTUS), was likely present in the genome of a last common insect ancestor, while the second (OSK) domain appears to have been acquired through horizontal transfer of a bacterial GDSL-like lipase domain. Our evidence suggests that the bacterial contributor of the OSK domain may have been a germ line endosymbiont. This shows that gene origin processes often considered highly unusual, including HGT and de novo coding region evolution, can give rise to novel genes that can both participate in pre-existing gene regulatory networks, and also facilitate the evolution of novel developmental mechanisms.
biorxiv evolutionary-biology 100-200-users 2018Identifying loci under positive selection in complex population histories, bioRxiv, 2018-10-26
AbstractDetailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called Graph-aware Retrieval of Selective Sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish and human population genomic data containing multiple population panels related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in under-studied human populations, as well as muscle mass, milk production and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation due to inversions in the history of Atlantic codfish.
biorxiv evolutionary-biology 100-200-users 2018Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules, bioRxiv, 2018-10-26
AbstractDiverse ribonucleoprotein complexes control messenger RNA processing, translation, and decay. Transcripts in these complexes localize to specific regions of the cell and can condense into non-membrane-bound structures such as stress granules. It has proven challenging to map the RNA composition of these large and dynamic structures, however. We therefore developed an RNA proximity labeling technique, APEX-Seq, which uses the ascorbate peroxidase APEX2 to probe the spatial organization of the transcriptome. We show that APEX-Seq can resolve the localization of RNAs within the cell and determine their enrichment or depletion near key RNA-binding proteins. Matching the spatial transcriptome, as revealed by APEX-Seq, with the spatial proteome determined by APEX-mass spectrometry (APEX-MS) provides new insights into the organization of translation initiation complexes on active mRNAs, as well as exposing unanticipated complexity in stress granule composition, and provides a powerful and general approach to explore the spatial environment of macromolecules.
biorxiv genomics 100-200-users 2018