Hackflex low cost Illumina sequencing library construction for high sample counts, bioRxiv, 2019-09-23
ABSTRACTWe developed Hackflex, a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 11 times more libraries for high-throughput Illumina sequencing to be generated at a fixed cost. We call this new method Hackflex. Quality of library preparation was tested by constructing libraries from E. coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. We demonstrated that Hackflex can produce high quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. Using Hackflex, we were able to achieve a per sample reagent cost of library prep of A$8.66, which is 8.23 times lower than the Standard Nextera Flex protocol at advertised retail price. An additional simple modification to the protocol enables a further price reduction of up to 11 fold or about A$6.50sample. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programs where sequencing large numbers of libraries is beneficial.
biorxiv genomics 200-500-users 2019Antibody against envelope protein from human endogenous retrovirus activates neutrophils in systemic lupus erythematosus, bioRxiv, 2019-09-21
AbstractNeutrophil activation and the formation of neutrophil extracellular trap (NET) are hallmarks of innate immune activation in systemic lupus erythematosus (SLE) and contribute to the systemic interferon signature. Here we report that the expression of an endogenous retrovirus (ERV) locus ERV-K102, encoding an envelope protein, was significantly elevated in SLE patient blood and was correlated with higher interferon status. Induction of ERV-K102 expression most strongly correlated with reduced transcript levels of epigenetic silencing factors. SLE IgG promoted phagocytosis of ERV-K102 envelope protein by neutrophils through immune complex formation. ERV immune complex phagocytosis resulted in subsequent NET formation consisting of DNA, neutrophil elastase, and citrullinated histone H3. Finally, analysis of anti-ERV-K102 IgG in SLE patients showed that IgG2 likely mediates this effect. Together, we identified an immunostimulatory ERV-K envelope protein elevated in SLE that may be a target of SLE IgG and able to promote neutrophil activation.eTOC summaryUsing ERVmap, the authors determined that the expression of ERV-K102 locus was elevated in SLE patient blood and correlated with the interferon signature. The envelope protein encoded by this locus activates human neutrophils through immune complex formation with SLE IgG.
biorxiv immunology 0-100-users 2019Gene capture by transposable elements leads to epigenetic conflict, bioRxiv, 2019-09-21
ABSTRACTPlant transposable elements (TEs) regularly capture fragments of host genes. When the host employs siRNAs to silence these TEs, siRNAs homologous to the captured regions may target both the TEs and the genes, potentially leading to their silencing. This epigenetic cross-talk establishes an intragenomic conflict silencing the TEs comes with the potential cost of silencing the genes. If the genes are important, however, natural selection will act to maintain function by moderating the silencing response. Such moderation may advantage the TEs. Here, we examined the potential for these epigenetic conflicts by focusing on three TE families in maize - Helitrons, Pack-MULEs and Sirevirus LTR retrotransposons. We documented 1,508 TEs with fragments captured from 2,019 donor genes and characterized the epigenetic profiles of both. Consistent with epigenetic conflict, donor genes mapped more siRNAs and were more methylated than ‘free’ genes that had no evidence of exon capture. However, these patterns differed between syntelog vs. transposed donor genes. Syntelog genes appeared to maintain function, consistent with moderation of the epigenetic response for important genes before reaching a deleterious threshold, while transposed genes bore the signature of silencing and potential pseudogenization. Intriguingly, transposed genes were overrepresented among donor genes, suggesting a link between capture and gene movement. We also investigated the potential for TEs to gain an advantage. TEs with captured fragments were older, mapped fewer siRNAs and had lower levels of methylation than ‘free’ TEs without gene fragments, but they showed no obvious evidence of increased copy numbers. Altogether, our results demonstrate that TE capture triggers an epigenetic conflict when genes are important, contrasting the loss of function for genes that are not under strong selective constraint. The evidence for an advantage to TEs is currently less obvious.
biorxiv genomics 0-100-users 2019A multi-tissue transcriptome analysis of human metabolites guides the interpretability of associations based on multi-SNP models for gene expression, bioRxiv, 2019-09-20
AbstractThere is particular interest in transcriptome-wide association studies (TWAS) - gene-level tests based on multi-SNP predictive models of gene expression - for identifying causal genes at loci associated with complex traits. However, interpretation of TWAS associations may be complicated by divergent effects of model SNPs on trait phenotype and gene expression. We developed an iterative modelling scheme for obtaining multi-SNP models of gene expression and applied this framework to generate expression models for 43 human tissues from the Genotype-Tissues Expression (GTEx) Project. We characterized the performance of single- and multi-SNP TWAS models for identifying causal genes in GWAS data for 46 circulating metabolites. We show that (a) multi-SNP models captured more variation in expression than the top cis-eQTL (median 2 fold improvement); (b) predicted expression based on multi-SNP models was associated (FDR<0.01) with metabolite levels for 826 unique gene-metabolite pairs, but, after step-wise conditional analyses, 90% were dominated by a single eQTL SNP; (c) amongst the 35% of associations where a SNP in the expression model was a significant cis-eQTL and metabolomic-QTL (met-QTL), 92% demonstrated colocalization between these signals, but interpretation was often complicated by incomplete overlap of QTLs in multi-SNP models; (d) using a “truth” set of causal genes at 61 met-QTLs, the sensitivity was high (67%), but the positive predictive value was low, as only 8% of TWAS associations at met-QTLs involved true causal genes. These results guide the interpretation of TWAS and highlight the need for corroborative data to provide confident assignment of causality.
biorxiv genomics 100-200-users 2019A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome, bioRxiv, 2019-09-20
AbstractComprehensive reference data is essential for accurate taxonomic and functional characterization of the human gut microbiome. Here we present the Unified Human Gastrointestinal Genome (UHGG) collection, a resource combining 286,997 genomes representing 4,644 prokaryotic species from the human gut. These genomes contain over 625 million protein sequences used to generate the Unified Human Gastrointestinal Protein (UHGP) catalogue, a collection that more than doubles the number of gut protein clusters over the Integrated Gene Catalogue. We find that a large portion of the human gut microbiome remains to be fully explored, with over 70% of the UHGG species lacking cultured representatives, and 40% of the UHGP missing meaningful functional annotations. Intra-species genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which were specific to individual human populations. These freely available genomic resources should greatly facilitate investigations into the human gut microbiome.
biorxiv microbiology 200-500-users 2019Correlative three-dimensional super-resolution and block face electron microscopy of whole vitreously frozen cells, bioRxiv, 2019-09-20
AbstractLiving cells function through the spatial compartmentalization of thousands of distinct proteins serving a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) has emerged as a pathway to directly view nanoscale protein relationships to the underlying global ultrastructure, but has traditionally suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional correlative cryogenic SR and focused ion beam milled block-face EM across entire vitreously frozen cells that addresses these issues by preserving native ultrastructure and enabling independent SR and EM workflow optimization. Application to a variety of biological systems revealed a number of unexpected protein-ultrastructure relationships and underscored the value of a comprehensive multimodal view of ultrastructural variability across whole cells.
biorxiv cell-biology 500+-users 2019