Genetic screens in isogenic mammalian cell lines without single cell cloning, bioRxiv, 2019-06-23
Isogenic pairs of cell lines, which differ by a single genetic modification, are powerful tools for understanding gene function. Generating such pairs for mammalian cells, however, is labor-intensive, time-consuming, and impossible in some cell types. Here we present an approach to create isogenic pairs of cells and screen them with genome-wide CRISPR-Cas9 libraries to generate genetic interaction maps. We queried the anti-apoptotic genes BCL2L1 and MCL1, and the DNA damage repair gene PARP1, via 25 genome-wide screens across 4 cell lines. For all three genes, we identify a rich set of both expected and novel buffering and synthetic lethal interactions. Further, we compare the interactions observed in genetic space to those found when targeting these genes with small molecules and identify hits that may inform the clinical uses for these inhibitors. We anticipate that this methodology will be broadly useful to comprehensively study genes of interest across many cell types.
biorxiv genetics 0-100-users 2019The effect of bioRxiv preprints on citations and altmetrics, bioRxiv, 2019-06-23
1.AbstractA potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact, an effect which has been empirically observed for preprints in physics, astronomy and mathematics deposited to arXiv. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences. We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently published in peer-reviewed journals. Citation data from Scopus and altmetric data from <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpAltmetric.com>Altmetric.com<jatsext-link> were used to compare citation and online sharing behaviour of bioRxiv preprints, their related journal articles, and non-deposited articles published in the same journals. We found that bioRxiv-deposited journal articles received a sizeable citation and altmetric advantage over non-deposited articles. Regression analysis reveals that this advantage is not explained by multiple explanatory variables related to the article and its authorship. bioRxiv preprints themselves are being directly cited in journal articles, regardless of whether the preprint has been subsequently published in a journal. bioRxiv preprints are also shared widely on Twitter and in blogs, but remain relatively scarce in mainstream media and Wikipedia articles, in comparison to peer-reviewed journal articles.
biorxiv scientific-communication-and-education 200-500-users 2019High genetic diversity can contribute to extinction in small populations, bioRxiv, 2019-06-22
AbstractHuman-driven habitat fragmentation and loss has led to a proliferation of small and isolated plant and animal populations that may be threatened with extinction by genetic factors. The prevailing approach for managing these populations is to maintain high genetic diversity, which is often equated with fitness. Increasingly, this is being done using genetic rescue, where individuals from populations with high genetic diversity are translocated to small populations with high levels of inbreeding. However, the potentially negative consequences of this approach have recently been highlighted by the demise of the gray wolf population on Isle Royale, which only briefly recovered after genetic rescue by a migrant from the large mainland wolf population and then declined to the brink of extinction. Here, we use ecologically-motivated population genetic simulations to show that extinction risk in small populations is often increased by maximizing genetic diversity but is consistently decreased by minimizing deleterious variation. Surprisingly, we find that small populations that are founded or rescued by individuals from large populations with high genetic diversity have an elevated risk of extinction due to the high levels of recessive deleterious variation harbored by large populations. By contrast, we show that genetic rescue or founding from small or moderate-sized populations leads to decreased extinction risk due to greater purging of strongly deleterious variants. Our findings challenge the traditional conservation paradigm that focuses on genetic diversity in assessing extinction risk in favor of a new view that emphasizes minimizing deleterious variation. These insights have immediate implications for managing small and isolated populations in the increasingly fragmented landscape of the Anthropocene.
biorxiv evolutionary-biology 100-200-users 2019High precision coding in visual cortex, bioRxiv, 2019-06-22
Single neurons in visual cortex provide unreliable measurements of visual features due to their high trial-to-trial variability. It is not known if this “noise” extends its effects over large neural populations to impair the global encoding of stimuli. We recorded simultaneously from ∼20,000 neurons in mouse primary visual cortex (V1) and found that the neural populations had discrimination thresholds of ∼0.34° in an orientation decoding task. These thresholds were nearly 100 times smaller than those reported behaviorally in mice. The discrepancy between neural and behavioral discrimination could not be explained by the types of stimuli we used, by behavioral states or by the sequential nature of perceptual learning tasks. Furthermore, higher-order visual areas lateral to V1 could be decoded equally well. These results imply that the limits of sensory perception in mice are not set by neural noise in sensory cortex, but by the limitations of downstream decoders.
biorxiv neuroscience 500+-users 2019Highly Multiplexed Spatial Mapping of Microbial Communities, bioRxiv, 2019-06-22
ABSTRACTMapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density and rich diversity of species in environmental microbiomes and the limitations of optical imaging technology. Here, we introduce High Phylogenetic Resolution microbiome mapping by Fluorescence In-Situ Hybridization (HiPR-FISH), a versatile and cost-effective technology that uses binary encoding and spectral imaging and machine learning based decoding to create micron-scale maps of the locations and identities of hundreds of microbial species in complex communities. We demonstrate the ability of 10-bit HiPR-FISH to distinguish 1023 E. coli strains, each fluorescently labeled with a unique binary barcode. HiPR-FISH, in conjunction with custom algorithms for automated probe design and segmentation of single-cells in the native context of tissues, reveals the intricate spatial architectures formed by bacteria in the human oral plaque microbiome and disruption of spatial networks in the mouse gut microbiome in response to antibiotic treatment. HiPR-FISH provides a framework for analyzing the spatial organization of microbial communities in tissues and the environment at single cell resolution.
biorxiv microbiology 0-100-users 2019Super-resolution Imaging Reveals 3D Structure and Organizing Mechanism of Accessible Chromatin, bioRxiv, 2019-06-22
Access to cis-regulatory elements packaged in chromatin is essential for directing gene expression and cell viability. Here, we report a super-resolution imaging strategy, 3D ATAC-PALM, that enables direct visualization of the entire accessible genome. We found that active chromosomal segments are organized into spatially-segregated accessible chromatin domains (ACDs). Rapid depletion of CTCF or Cohesin (RAD21 subunit) induced enhanced ACD clustering, reduced physical separation between intrachromosomal ACDs, and differentially regulated ACD compaction. Experimental perturbations and polymer modeling suggest that dynamic protein-protein and protein-DNA interactions within ACDs couple with loop extrusion to organize ACD topology. Dysorganization of ACDs upon CTCF or Cohesin loss alters transcription factor binding and target search dynamics in living cells. These results uncover fundamental mechanisms underpinning the formation of 3D genome architecture and its pivotal function in transcriptional regulation.
biorxiv molecular-biology 100-200-users 2019