Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells, bioRxiv, 2019-01-25
AbstractThe epigenome plays a critical role in regulating gene expression in mammalian cells. However, understanding how cell-to-cell heterogeneity in the epigenome influences gene expression variability remains a major challenge. Here we report a novel method for simultaneous single-cell quantification of protein-DNA contacts with DamID and transcriptomics (scDamID&T). This method enables quantifying the impact of protein-DNA contacts on gene expression from the same cell. By profiling lamina-associated domains (LADs) in human cells, we reveal different dependencies between genome-nuclear lamina (NL) association and gene expression in single cells. In addition, we introduce the E. coli methyltransferase, Dam, as an in vivo marker of chromatin accessibility in single cells and show that scDamID&T can be utilized as a general technology to identify cell types in silico while simultaneously determining the underlying gene-regulatory landscape. With this strategy the effect of chromatin states, transcription factor binding, and genome organization on the acquisition of cell-type specific transcriptional programs can be quantified.
biorxiv molecular-biology 0-100-users 2019Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture, bioRxiv, 2019-01-24
AbstractThe proportion of phenotypic variance attributable to the additive effects of a given set of genotyped SNPs (i.e. SNP-heritability) is a fundamental quantity in the study of complex traits. Recent works have shown that existing methods to estimate genome-wide SNP-heritability often yield biases when their assumptions are violated. While various approaches have been proposed to account for frequency- and LD-dependent genetic architectures, it remains unclear which estimates of SNP-heritability reported in the literature are reliable. Here we show that genome-wide SNP-heritability can be accurately estimated from biobank-scale data irrespective of the underlying genetic architecture of the trait, without specifying a heritability model or partitioning SNPs by minor allele frequency andor LD. We use theoretical justifications coupled with extensive simulations starting from real genotypes from the UK Biobank (N = 337K) to show that, unlike existing methods, our closed-form estimator for SNP-heritability is highly accurate across a wide range of architectures. We provide estimates of SNP-heritability for 22 complex traits and diseases in the UK Biobank and show that, consistent with our results in simulations, existing biobank-scale methods yield estimates up to 30% different from our theoretically-justified approach.
biorxiv genomics 0-100-users 2019Behavior influences range limits and patterns of coexistence across an elevational gradient in tropical bird diversity, bioRxiv, 2019-01-24
Does competition influence patterns of coexistence between closely related taxa? Here we address this basic question in ecology by analyzing patterns of range overlap between related bird species (sister pairs) distributed along a Neotropical elevational gradient. We explicitly contrast the behavioral dimension of interspecific competition (interference competition) with similarity in resource acquisition traits (exploitative competition). We find that behavioral interactions are generally important in setting elevational range limits and preventing coexistence of closely related species. Specifically, close relatives that defend year-round territories tend to live in non-overlapping elevational distributions, while close relatives that do not defend territories tend to broadly overlap in distribution. In contrast, neither similarity in beak morphology nor evolutionary relatedness was associated with patterns of range limitation. Our main result is that interference competition can be an important driver of species ranges at the scale of entire diverse assemblages. Consequently, we suggest that behavioral dimensions of the niche should be more broadly incorporated in macroecological studies.
biorxiv ecology 0-100-users 2019Conduit integrity is compromised during acute lymph node expansion, bioRxiv, 2019-01-24
Lymph nodes (LNs) work as filtering organs, constantly sampling peripheral cues. This is facilitated by the conduit network, a parenchymal tubular-like structure formed of bundles of aligned extracellular matrix (ECM) fibrils ensheathed by fibroblastic reticular cells (FRCs). LNs undergo 5-fold expansion with every adaptive immune response and yet these ECM-rich structures are not permanently damaged. Whether conduit integrity and filtering functions are affected during cycles of LN expansion and resolution is not known. Here we show that the conduit structure is disrupted during acute LN expansion but FRC-FRC contacts remain intact. In homeostasis, polarised FRCs adhere to the underlying substrate to deposit ECM ba-solaterally. ECM production by FRCs is regulated by the C-type lectin CLEC-2, expressed by dendritic cells (DCs), at transcriptional and secretory levels. Inflamed LNs maintain conduit size-exclusion, but flow becomes leaky, which allows soluble antigens to reach more antigen-presenting cells. We show how dynamic communication between peripheral tissues and LNs changes during immune responses, and describe a mechanism that enables LNs to prevent inflammation-induced fibrosis.Highlights<jatslist list-type=bullet><jatslist-item>FRCs use polarized microtubule networks to guide matrix deposition<jatslist-item><jatslist-item>CLEC-2PDPN controls matrix production at transcriptional and post-transcriptional levels<jatslist-item><jatslist-item>FRCs halt matrix production and decouple from conduits during acute LN expansion<jatslist-item><jatslist-item>Conduits leak soluble antigen during acute LN expansion<jatslist-item>
biorxiv immunology 100-200-users 2019Genetic Identification of Cell Types Underlying Brain Complex Traits Yields Novel Insights Into the Etiology of Parkinson’s Disease, bioRxiv, 2019-01-24
AbstractGenome-wide association studies (GWAS) have discovered hundreds of loci associated with complex brain disorders, and provide the best current insights into the etiology of these idiopathic traits. However, it remains unclear in which cell types these variants are active, which is essential for understanding etiology and subsequent experimental modeling. Here we integrate GWAS results with single-cell transcriptomic data from the entire mouse nervous system to systematically identify cell types underlying psychiatric disorders, neurological diseases, and brain complex traits. We show that psychiatric disorders are predominantly associated with cortical and hippocampal excitatory neurons, and medium spiny neurons from the striatum. Cognitive traits were generally associated with similar cell types but their associations were driven by different genes. Neurological diseases were associated with different cell types, which is consistent with other lines of evidence. Notably, we found that Parkinson’s disease is not only genetically associated with dopaminergic neurons but also with serotonergic neurons and cells of the oligodendrocyte lineage. Using post-mortem brain transcriptomic data, we confirmed alterations in these cells, even at the earliest stages of disease progression. Our study provides an important framework for understanding the cellular basis of complex brain maladies, and reveals an unexpected role of oligodendrocytes in Parkinson’s disease.
biorxiv genomics 100-200-users 2019Mobile genetic element insertions drive antibiotic resistance across pathogens, bioRxiv, 2019-01-24
Mobile genetic elements contribute to bacterial adaptation and evolution; however, detecting these elements in a high-throughput and unbiased manner remains challenging. Here, we demonstrate a de novo approach to identify mobile elements from short-read sequencing data. The method identifies the precise site of mobile element insertion and infers the identity of the inserted sequence. This is an improvement over previous methods that either rely on curated databases of known mobile elements or rely on 'split-read' alignments that assume the inserted element exists within the reference genome. We apply our approach to 12,419 sequenced isolates of nine prevalent bacterial pathogens, and we identify hundreds of known and novel mobile genetic elements, including many candidate insertion sequences. We find that the mobile element repertoire and insertion rate vary considerably across species, and that many of the identified mobile elements are biased toward certain target sequences, several of them being highly specific. Mobile element insertion hotspots often cluster near genes involved in mechanisms of antibiotic resistance, and such insertions are associated with antibiotic resistance in laboratory experiments and clinical isolates. Finally, we demonstrate that mutagenesis caused by these mobile elements contributes to antibiotic resistance in a genome-wide association study of mobile element insertions in pathogenic Escherichia coli. In summary, by applying a de novo approach to precisely identify mobile genetic elements and their insertion sites, we thoroughly characterize the mobile element repertoire and insertion spectrum of nine pathogenic bacterial species and find that mobile element insertions play a significant role in the evolution of clinically relevant phenotypes, such as antibiotic resistance.
biorxiv microbiology 0-100-users 2019