PaperPlayer biorxiv genomics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.249870v1?rss=1

Authors: Halstead, M. M., Kern, C., Saelao, P., Wang, Y., Chanthavixay, G., Medrano, J. F., Van Eenennaam, A. L., Korf, I., Tuggle, C. K., Ernst, C. W., Zhou, H., ROSS, P. J.

Abstract:

Background: Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues. Results: Overall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions. Conclusions: The lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.249698v1?rss=1

Authors: Gal, C., Carelli, F. N., Appert, A., Cerrato, C., Huang, N., Dong, Y., Murphy, J., Ahringer, J.

Abstract:

The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z, and we find that DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses germline specific targets in the soma by facilitating H3K9me2 promoter marking. We further find that LIN-36 and LIN-15B differently regulate DREAM binding. In humans, THAP proteins have been implicated in cell cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.249656v1?rss=1

Authors: Feng, S., Lu, S., Grueber, W. B., Mann, R. S.

Abstract:

We describe a simple and efficient technique that allows scarless engineering of Drosophila genomic sequences near any landing site containing an inverted attP cassette, such as a MiMIC insertion. This 2-step method combines phiC31 integrase mediated site-specific integration and homing nuclease mediated resolution of local duplications, efficiently converting the original landing site allele to modified alleles that only have the desired change(s). Dominant markers incorporated into this method allow correct individual flies to be efficiently identified at each step. In principle, single attP sites and FRT sites are also valid landing sites. Given the large and increasing number of landing site lines available in the fly community, this method provides an easy and fast way to efficiently edit the majority of the Drosophila genome in a scarless manner. This technique should also be applicable to other species.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.250092v1?rss=1

Authors: Katsevich, E., Roeder, K.

Abstract:

Mapping gene-enhancer regulatory relationships is key to unraveling molecular disease mechanisms based on GWAS associations in non-coding regions. Recently developed CRISPR regulatory screens (CRSs) based on single cell RNA-seq (scRNA-seq) are a promising high-throughput experimental approach to this problem. However, the analysis of these screens presents significant statistical challenges, including modeling cell-level gene expression and correcting for sequencing depth. Using a recent large-scale CRS and its original analysis as a case study, we demonstrate weaknesses in existing analysis methodology, which lead to false positives as well as false negatives. To address these challenges, we propose SCEPTRE: analysis of single cell perturbation screens via conditional resampling. This novel method infers gene-enhancer associations by modeling the stochastic assortment of CRISPR gRNAs among cells instead of the gene expression, remaining valid despite arbitrary misspecification of the gene expression model. Applying SCEPTRE to the large-scale CRS, we demonstrate improvements in both sensitivity and specificity. We also discover 217 regulatory relationships not found in the original study, many of which are supported by existing functional data.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.249078v1?rss=1

Authors: Keenan, C. R., Coughlan, H. D., Iannarella, N., Johanson, T. M., Chan, W. F., Garnham, A. L., Smyth, G. K., Allan, R. S.

Abstract:

H3K9me3-dependent heterochromatin is critical for the silencing of repeat-rich pericentromeric regions and also has key roles in repressing lineage-inappropriate protein-coding genes in differentiation and development. Here, we investigate the molecular consequences of heterochromatin loss in cells deficient in both Suv39h1 and Suv39h2 (Suv39DKO), the major mammalian histone methyltransferase enzymes that catalyse heterochromatic H3K9me3 deposition. Unexpectedly, we reveal a predominant repression of protein-coding genes in Suv39DKO cells, with these differentially expressed genes principally in euchromatic (DNaseI-accessible, H3K27ac-marked) rather than heterochromatic (H3K9me3-marked) regions. Examination of the 3D nucleome reveals that transcriptomic dysregulation occurs in euchromatic regions close to the nuclear periphery in 3-dimensional space. Moreover, this transcriptomic dysregulation is highly correlated with altered 3-dimensional genome organization in Suv39DKO cells. Together, our results suggest that the nuclear lamina-tethering of Suv39-dependent H3K9me3 domains provides an essential scaffold to support euchromatic genome organisation and the maintenance of gene transcription for healthy cellular function.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.247692v1?rss=1

Authors: Malukiewicz, J., Cartwright, R. A., Curi, N. H., Dergam, J. A., Igayara, C. S., Moreira, S. B., Molina, C. V., Nicola, P. A., Noll, A., Passamani, M., Pereira, L. C., Pissinatti, A., Ruiz-Miranda, C. R., Silva, D. L., Stone, A. C., Zinner, D., Roos, C.

Abstract:

Background Callithrix marmosets are a relatively young non-human primate radiation, whose phylogeny is not yet fulllly resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed in this study to reconstruct a robust Callithrix phylogeny and divergence time estimates, as well as identify autochthonous and allochthonous Callithrix mitogenome lineages across Brazil. We sequenced 49 mitogenomes from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata) and anthropogenic hybrids (C. aurita x Callithrix sp., C. penicillata x C. jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously published Callithrix mtDNA genomes to analyze five Callithrix species in total. Results We report the complete sequence and organization of the C. aurita mtDNA genome. Phylogenetic analyses showed that C. aurita was the first to diverge within Callithrix 3.54 million years ago (MYA), while C. jacchus and C. penicillata lineages diverged most recently 0.5 MYA as sister clades. MtDNA clades of C. aurita, C. geoffroyi, and C. penicillata show intraspecific geographic structure, but C. penicillata clades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainly C. penicillata or C. jacchus mtDNA plotypes. The geographic origins of mtDNA haplotypes from hybrid and allochthonous Callithrix were broadly distributed across natural Callithrix ranges. Our phylogenetic results also evidence introgression of C. jacchus mtDNA into C. aurita. Conclusion Our robust Callithrix mitogenome phylogeny shows C. aurita lineages as basal and C. jacchus lineages among the most recent within Callithrix. We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochtonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonous Callithrix and autochthonous C. aurita. Our results encouragingly show that further development of genomic resources will allow to more clearly elucidate Callithrix evolutionary relationships and understand the dynamics.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.248526v1?rss=1

Authors: Lowther, C., Valkanas, E., Giordano, J. L., Wang, H. Z., Currall, B. B., O'Keefe, K., Collins, R. L., Zhao, X., Austin-Tse, C. A., Evangelista, E., Aggarwal, V., Lucente, D., Gauthier, L. D., Tolonen, C., Sahakian, N., An, J.-Y., Dong, S., Norton, M. E., MacKenzie, T., Devlin, B., Gilmore, K., Powell, B., Brandt, A., Vetrini, F., DiVito, M., Goldstein, D. B., Sanders, S. J., MacArthur, D. G., Hodge, J. C., O'Donnell-Luria, A., Rehm, H., Vora, N., Levy, B., Brand, H., Wapner, R., Talkowski, M. E.

Abstract:

Current prenatal and pediatric genetic evaluation requires three tests to capture balanced chromosomal abnormalities (karyotype), copy number variants (microarray), and coding variants (whole exome sequencing [WES] or targeted gene panels). Here, we explored the sensitivity, specificity, and added value of whole genome sequencing (WGS) to displace all three conventional approaches. We analyzed single nucleotide variants, small insertions and deletions, and structural variants from WGS in 1,612 autism spectrum disorder (ASD) quartet families (n=6,448 individuals) to benchmark the diagnostic performance of WGS against microarray and WES. We then applied these WGS variant discovery and interpretation pipelines to 175 trios (n=525 individuals) with a fetal structural anomaly (FSA) detected on ultrasound and pre-screened by karyotype and microarray. Analyses of WGS in ASD quartets identified a diagnostic variant in 7.5% of ASD probands compared to 1.1% of unaffected siblings (odds ratio=7.5; 95% confidence interval=4.5-13.6; P=2.8x10-21). We found that WGS captured all diagnostic variants detected by microarray and WES as well as five additional diagnoses, reflecting a 0.3% added yield over WES and microarray when combined. The WGS diagnostic yield was also inversely correlated with ASD proband IQ. Implementation in FSA trios identified a diagnostic variant not captured by karyotype or microarray in 12.0% of fetuses. Based on these data and prior studies, we estimate that WGS could provide an overall diagnostic yield of 47.6% in unscreened FSA referrals. We observed that WGS was sensitive to the detection of all classes of pathogenic variation captured by three conventional tests. Moreover, diagnostic yields from WGS were superior to any individual genetic test, warranting further evaluation as a first-tier diagnostic approach.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.247528v1?rss=1

Authors: Wang, S., Tao, Z., Wu, T., Liu, X.-S.

Abstract:

Summary: Mutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools are available for mutational signature analysis. However, most of them focus on specific type of mutation, or have limited scope of application. A pipeline tool for comprehensive mutational signature analysis is still lacking. Here we present Sigflow pipeline, which provides an one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution (SBS), doublet base substitution (DBS), small insertion and deletion (INDEL), and copy number alteration. A Docker image is constructed to solve the complex and time-consuming installation issues, and this enables reproducible research by version control of all dependent tools along with their environments. The Sigflow pipeline can be applied to both human and mouse genomes. Availability and implementation: Sigflow is an open source software under academic free license (AFL) v3.0 and it is freely available at https://github.com/ShixiangWang/sigminer.workflow or https://hub.docker.com/r/shixiangwang/sigflow. Contact: [email protected]

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.248286v1?rss=1

Authors: Kelley, E. R., Sleith, R. S., Matz, M. V., Wright, R. M.

Abstract:

Rampant coral disease, exacerbated by climate change and other anthropogenic stressors, threatens reefs worldwide, especially in the Caribbean. Physically isolated yet genetically connected reefs such as Flower Garden Banks National Marine Sanctuary (FGBNMS) may serve as potential refugia for degraded Caribbean reefs. However, little is known about the mechanisms and trade-offs of pathogen resistance in reef-building corals. Here we measure pathogen resistance in Montastraea cavernosa from FGBNMS. We identified individual colonies that demonstrated resistance or susceptibility to Vibrio spp. in a controlled laboratory environment. Long-term growth patterns suggest no trade-off between disease resistance and calcification. Predictive (pre-exposure) gene expression highlights subtle differences between resistant and susceptible genets, encouraging future coral disease studies to investigate associations between resistance and replicative age and immune cell populations. Predictive gene expression associated with long-term growth underscores the role of cation transporters and extracellular matrix remodelers, contributing to the growing body of knowledge surrounding genes that influence calcification in reef-building corals. Together these results demonstrate that coral genets from isolated sanctuaries such as FGBNMS can withstand pathogen challenges and potentially aid restoration efforts in degraded reefs. Furthermore, gene expression signatures associated with resistance and long-term growth help inform strategic assessment of coral health parameters.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.245308v1?rss=1

Authors: Du, X., Li, L., Liang, F., Liu, S., Zhang, W., Sun, S., Sun, Y., Fan, F., Wang, L., Liang, X., Qiu, W., Fan, G., Wang, O., Yang, W., Zhang, J., Xiao, Y., Wang, Y., Wang, D., Qu, S., Chen, F., Huang, J.

Abstract:

The importance of structural variants (SVs) on phenotypes and human diseases is now recognized. Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed, few benchmarking procedures are available to confidently assess their performances in biological and clinical research. To facilitate the validation and application of those approaches, our work established an Asian reference material comprising identified benchmark regions and high-confidence SV calls. We established a high-confidence SV callset with 8,938 SVs in an EBV immortalized B lymphocyte line, by integrating four alignment-based SV callers [from 109x PacBio continuous long read (CLR), 22x PacBio circular consensus sequencing (CCS) reads, 104x Oxford Nanopore long reads, and 114x optical mapping platform (Bionano)] and one de novo assembly-based SV caller using CCS reads. A total of 544 randomly selected SVs were validated by PCR and Sanger sequencing, proofing the robustness of our SV calls. Combining trio-binning based haplotype assemblies, we established an SV benchmark for identification of false negatives and false positives by constructing the continuous high confident regions (CHCRs), which cover 1.46Gb and 6,882 SVs supported by at least one diploid haplotype assembly. Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology, disease, and clinical diagnosis.

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