PaperPlayer biorxiv genetics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.22.216143v1?rss=1

Authors: Toraason, E., Clark, C., Horacek, A., Glover, M. L., Salagean, A., Libuda, D. E.

Abstract:

During meiosis, the maintenance of genome integrity is critical for generating viable haploid gametes [1]. In meiotic prophase I, double-strand DNA breaks (DSBs) are induced and a subset of these DSBs are repaired as interhomolog crossovers to ensure proper chromosome segregation. DSBs in excess of the permitted number of crossovers must be repaired by other pathways to ensure genome integrity [2]. To determine if the sister chromatid is engaged for meiotic DSB repair during oogenesis, we developed an assay to detect sister chromatid repair events at a defined DSB site during Caenorhabditis elegans meiosis. Using this assay, we directly demonstrate that the sister chromatid is available as a meiotic repair template for both crossover and noncrossover recombination, with noncrossovers being the predominant recombination outcome. We additionally find that the sister chromatid is the exclusive recombination partner for DSBs during late meiotic prophase I. Analysis of noncrossover conversion tract sequences reveals that DSBs are processed similarly throughout prophase I and recombination intermediates remain central around the DSB site. Further, we demonstrate that the SMC-5/6 complex is required for long conversion tracts in early prophase I and intersister crossovers during late meiotic prophase I; whereas, the XPF-1 nuclease is required only in late prophase to promote sister chromatid repair. In response to exogenous DNA damage at different stages of meiosis, we find that mutants for SMC-5/6 and XPF-1 have differential effects on progeny viability. Overall, we propose that SMC-5/6 both processes recombination intermediates and promotes sister chromatid repair within meiotic prophase I, while XPF-1 is required as an intersister resolvase only in late prophase I.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.21.214452v1?rss=1

Authors: Almeida, M. P., Welker, J. M., Ekker, S. C., Clark, K. J., Essner, J. J., McGrail, M.

Abstract:

The Cre/lox recombinase system has been widely used for spatiotemporal control of gene expression in animal model systems, however, efficient methods to isolate zebrafish Cre drivers that reliably recapitulate endogenous expression patterns of known genes are in need. Here, we apply CRISPR/Cas9 double-strand breaks to direct targeted integration using short homology of a 2A-Cre recombinase transgene into the early coding region of proneural genes ascl1b, olig2 and neurod1. The pPRISM-2A-Cre targeting vector contains a linked lens-specific fluorescent secondary marker cassette for identification of transgenic embryos, and we observed high rates of germline transmission ranging from 10%-100% (2/20 olig2; 1/5 neurod1; 3/3 ascl1b). The established transgenic lines Tg(ascl1b-2A-Cre)is75, Tg(olig2-2A-Cre)is76, and Tg(neurod1-2A-Cre)is77 expressed functional Cre recombinase. in situ hybridization showed Cre expression reflected the pattern of the endogenous targeted proneural gene. In combination with Tg(ubi:loxP-EGFP-loxP-mCherry), each driver induced a switch from EGFP to mCherry expression in the expected proneural cell populations and their descendants, indicating efficient Cre-mediated recombination and excision of the floxed EGFP cassette. The results demonstrate Cre recombinase expression is driven by the native promoter and regulatory elements of the targeted genes. This approach provides a straightforward, efficient, and cost-effective method to generate cell type specific zebrafish Cre drivers whose spatial and temporal restricted expression mimics endogenous genes, surmounting the challenges associated with promoter BAC cloning and transposon mediated transgenesis.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.22.215376v1?rss=1

Authors: Schmitz, J., Abbondanza, F., Paracchini, S.

Abstract:

An efficient auditory system contributes to cognitive and psychosocial development. A right ear advantage in hearing thresholds (HT) has been described in adults and atypical patterns of left/right hearing threshold asymmetry (HTA) have been described for psychiatric and neurodevelopmental conditions. Previous genome-wide association studies (GWAS) on HT have mainly been conducted in elderly participants whose hearing is more likely to be affected by environmental effects. We analysed HT and HTA in a children population cohort (ALSPAC, n = 6,743, 7.6 years). Better hearing was associated with more advanced cognitive skills and higher socioeconomic status (SES). Mean HTA was negative (-0.28 dB), suggesting a left ear advantage in children but mainly driven by females (-0.48 dB in females v -0.09 dB in males). We performed the first GWAS on HT in children and the very first GWAS on HTA (n = 5,344). Single marker trait association analysis did not yield significant hits. Polygenic risk score (PRS) analysis revealed associations of PRS for schizophrenia with HT, which remained significant after controlling for SES and cognitive skills, and of PRS for autism spectrum disorders (ASD) with HTA. Gene-based analysis for HTA reached genome-wide significance for MCM5, which is implicated in axon morphogenesis. This analysis also highlighted other genes associated with contralateral axon crossing. Some of these genes have previously been reported for ASD. These results further support the hypothesis that pathways distinguishing the left/right axis of the brain (i.e. commissural crossing) contribute to both different types of asymmetries (i.e. HTA) and neurodevelopmental disorders.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.22.215939v1?rss=1

Authors: van Dongen, J., Hagenbeek, F. A., Suderman, M., Roetman, P. J., Sugden, K., Chiocchetti, A. G., Ismail, K., Mulder, R. H., Hafferty, J., Adams, M. J., Walker, R., Morris, S., Lahti, J., Kupers, L. K., Escaramis, G., Alemany, S., Bonder, M. J., Meijer, M., Ip, H. F., Jansen, R., Baselmans, B. M. L., Parmar, P., Lowry, E., Streit, F., Sirignano, L., Send, T., Frank, J., Jylhava, J., Wang, Y., Mishra, P. P., Colins, O. F., Corcoran, D., Poulton, R., Mill, J., Hannon, E., Arseneault, L., Korhonen, T., Vuoksimaa, E., Felix, J., Bakermans-Kranenburg, M., Campbell, A., Czamara, D., Binder, E., Corpel

Abstract:

DNA methylation profiles of aggressive behavior may capture lifetime cumulative effects of genetic, stochastic, and environmental influences associated with aggression. Here, we report the first large meta-analysis of epigenome-wide association studies (EWAS) of aggressive behavior (N=15,324 participants). In peripheral blood samples of 14,434 participants from 18 cohorts with mean ages ranging from 7 to 68 years, 13 methylation sites were significantly associated with aggression (alpha=1.2x10-7; Bonferroni correction). In cord blood samples of 2,425 children from five cohorts with aggression assessed at mean ages ranging from 4 to 7 years, 83% of these sites showed the same direction of association with childhood aggression (r=0.74, p=0.006) but no epigenome-wide significant sites were found. Top-sites (48 at a false discovery rate of 5% in the peripherl blood meta-analysis or in a combined meta-analysis of peripheral blood and cord blood) have been associated with chemical exposures, smoking, cognition, metabolic traits, and genetic variation (mQTLs). Three genes whose expression levels were associated with top-sites were previously linked to schizophrenia and general risk tolerance. At six CpGs, DNA methylation variation in blood mirrors variation in the brain. On average 44% (range=3-82%) of the aggression-methylation association was explained by current and former smoking and BMI. These findings point at loci that are sensitive to chemical exposures with potential implications for neuronal functions. We hope these results to be a starting point for studies leading to applications as peripheral biomarkers and to reveal causal relationships with aggression and related traits.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.22.215566v1?rss=1

Authors: Seike, T., Sakata, N., Shimoda, C., Niki, H., Furusawa, C.

Abstract:

Most sexually reproducing organisms have the ability to recognize individuals of the same species. In ascomycetes including yeasts, potential mating between cells of opposite mating-type depends on the molecular recognition of two peptidyl mating pheromones by their corresponding G-protein coupled receptors (GPCRs). Although such pheromone/receptor systems are likely to function in both mate choice and prezygotic isolation, very few studies have focus on the differences in pheromone/receptor system between mating types. The fission yeast Schizosaccharomyces pombe has two mating types (sexes), Plus (P) and Minus (M). Here we investigated the specificity of the two GPCRs, Mam2 and Map3, for their respective pheromones, P-factor and M-factor, in fission yeast. First, we switched GPCRs between S. pombe and the closely related species Schizosaccharomyces octosporus, which showed that SoMam2 (Mam2 of S. octosporus) is partially functional in S. pombe, whereas SoMap3 (Map3 of S. octosporus) is not interchangeable. Next, we swapped individual domains of Mam2 and Map3 with the respective domains in SoMam2 and SoMap3, which revealed differences between the receptors both in the intracellular regions that regulate the downstream signaling of pheromones and in the molecular recognition for pheromone binding. In particular, we demonstrated that two amino acid residues of Map3, F214 and F215, are essential for the specificity of M-factor recognition. Thus, the differences in these two GPCRs are likely to reflect the significantly distinct specificities of their respective pheromone/receptor systems; that is, the specificity of Map3 is more stringent than that of Mam2. We speculate that this sexual asymmetry might allow ascomycete fungi to generate novel prezygotic barriers within a population, while maintaining strong mate choice. Our genetic analyses also contribute to our understanding of the receptors that comprise the Class D GPCRs belonging to the fungal pheromone receptor family.

Author summaryCourtship signals play a key role in the fertilization processes of living beings from animals to microorganisms and, in particular, sex pheromones are involved in differentiating among species. On the other hand, changes in a pheromone/receptor system might also alter species-specificity during the selection of a mating partner, which is likely to facilitate prezygotic isolation. Here we demonstrate a distinct difference in the specificity of GPCRs for pheromones between cells of opposite mating-type in the fission yeast Schizosaccharomyces pombe, by conducting a comprehensive genetic analysis and comparison of these proteins between closely related fission yeast species. Our finding of sexual asymmetry due to the relative strictness of receptors in S. pombe suggests that it might be one of the driving forces behind the formation of new species. Such differences in pheromone/receptor interactions between the sexes may occur in a variety of life-forms such as insects and amphibians; hence, the findings of this study might be extended to other organisms. In addition, this study of S. pombe pheromone receptors sheds light on the functions of the unique Class D GPCRs.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.20.211441v1?rss=1

Authors: Goulielmaki, E., Tsekrekou, M., Batsiotos, N., Ascensao-Ferreira, M., Ledaki, E., Stratigi, K., Chatzinikolaou, G., Topalis, P., Kosteas, T., Altmuller, J., Demmers, J. A., Barbosa-Morais, N. L., Garinis, G. A.

Abstract:

RNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to spliceosomal U4 and U6 snRNAs and pre-mRNAs in developing livers. XAB2 depletion leads to aberrant intron retention, R-loop formation and DNA damage in cells. Studies in illudin S-treated cells and Csbm/m developing livers reveal that transcription-blocking DNA lesions trigger the release of XAB2 from all RNA targets tested. Immunoprecipitation studies reveal that XAB2 interacts with ERCC1-XPF and XPG endonucleases outside nucleotide excision repair and that the trimeric protein complex binds RNA:DNA hybrids under conditions that favor the formation of R-loops. Thus, XAB2 functionally links the spliceosomal response to DNA damage with R-loop processing with important ramifications for mammalian development and transcription-coupled DNA repair disorders.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.19.211375v1?rss=1

Authors: Carter, M., Gomez, S., Gritz, S., Larson, S., Silva-Herzog, E., Kim, H.-s., Schulz, D., Hovel-Miner, G. A.

Abstract:

Trypanosoma brucei is an early branching protozoan parasite that causes human and animal African Trypanosomiasis. Forward genetics approaches are powerful tools for uncovering novel aspects of Trypanosomatid biology, pathogenesis, and therapeutic approaches against trypanosomiasis. Here we have generated a T. brucei cloned ORFeome consisting of over 90% of the targeted 7,245 genes and used it to make an inducible Gain-of-Function parasite library broadly applicable to large-scale forward genetic screens. We conducted a proof of principle genetic screen to identify genes whose expression promotes survival in melarsoprol, a critical drug of last resort. The 57 genes identified as overrepresented in melarsoprol survivor populations included the rate-limiting enzyme for the biosynthesis of an established drug target (trypanothione), validating the tool. In addition, novel genes associated with gene expression, flagellum localization, and mitochondrion localization were identified and a subset of those genes increased melarsoprol resistance upon overexpression in culture. These findings offer new insights into Trypanosomatid basic biology, implications for drugs targets, and direct or indirect drug resistance mechanisms. This study generated a T. brucei ORFeome and Gain-of-Function parasite library, demonstrated the libraries usefulness in forward genetic screening, and identified novel aspects of melarsoprol resistance that will be the subject of future investigations. These powerful genetic tools can be used to broadly advance Trypanosomatid research.

IMPORTANCETrypanosomatid parasites threaten the health of over 1 billion people worldwide. Because their genomes are highly diverged from well-established eukaryotes, conservation is not always useful in assigning gene functions. However, it is precisely among the Trypanosomatid-specific genes that ideal therapeutic targets might be found. Forward genetics approaches are an effective way to identify novel gene functions. We used an ORFeome approach to clone a large percentage of Trypanosoma brucei genes and generate a Gain-of-Function parasite library. This library was used in a genetic screen to identify genes that promote resistance to the clinically significant, yet highly toxic drug, melarsoprol. Hits arising from the screen demonstrated the librarys usefulness in identifying known pathways and uncovered novel aspects of resistance mediated by proteins localized to the flagellum and mitochondrion. The powerful new genetic tools generated herein are expected to promote advances in Trypanosomatid biology and therapeutic development in the years to come.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.20.211565v1?rss=1

Authors: Formica, M., Storaci, A., Bertolini, I., Vaira, V., Vaccari, T.

Abstract:

Glioblastoma (GBM), a very aggressive and incurable tumor, often results from constitutive activation of EGFR (epidermal growth factor receptor) and of PI3K (phosphoinositide 3-kinase). To understand the role of autophagy in the pathogenesis of glial tumors in vivo, we used an established Drosophila melanogaster model of glioma based on overexpression in larval glial cells of an active human EGFR and of the PI3K homolog Dp110. Interestingly, the resulting hyperplastic glia expresses high levels of ref(2)P (refractory to Sigma P), the Drosophila homolog of p62/SQSTM1. However, cellular clearance of autophagic cargoes appears inhibited upstream of autophagosome formation. Remarkably, downregulation of subunits of the vacuolar-H+-ATPase (V-ATPase) prevents overgrowth, reduces PI3K signaling and restores clearance. Consistent with evidence in flies, neurospheres from patients with high V-ATPase subunit expression show inhibition of autophagy. Altogether, our data suggest that autophagy is repressed during glial tumorigenesis and that V-ATPase could represent a therapeutic target against GBM.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.20.212548v1?rss=1

Authors: Pownall, K. A., Pownall, K. A., Taylor, H. N., Stevison, L.

Abstract:

As individuals senesce, factors correlated with fitness, such as fecundity and longevity, decline. Increased age also alters recombination rates in a variety of taxa. Changes in individual recombination rate, or recombination rate plasticity, can increase meiotic errors. In Drosophila melanogaster, multiple studies on maternal age and recombination rate have found a characteristic pattern where rates initially increase, then decrease, then increase again relative to controls. Here, this phenomenon was investigated in D. pseudoobscura. First, fecundity and survivorship were investigated to guide the choice of treatment age. Then, a large-scale recombination analysis (N=23,559) was set up using three X-linked phenotypic markers. Recombination rate differences in two genomic intervals were measured in females aged to 7 days (control) and 35 days (selected treatment age) prior to mating, with progeny collection continuing for 12 days post-mating in 72 hour timepoints. Results revealed a 3.39% increase in recombination rate due to maternal age (p=0.025), for the first 72 hour time point in one of the two marker intervals. For both genomic intervals, recombination rates were higher in the age treatment for the first time point and lower in later time points of the experiment. Next, these data were used to investigate crossover interference, which decreased with maternal age in the first time point and increased in the last time point. Overall, these results suggest that the mechanisms responsible for recombination rate plasticity may differ between maternal age and stressors, such as temperature.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.20.211276v1?rss=1

Authors: Saez-Atienzar, S., Bandres-Ciga, S., Langston, R. G., Kim, J. J., Choi, S. W., Reynolds, R. H., The International ALS Genomics Consortium,, ITALSGEN,, Abramzon, Y., Dewan, R., Ahmed, S., Landers, J. E., Chia, R., Ryten, M., Cookson, M. R., Nalls, M. A., Chio, A., Traynor, B. J.

Abstract:

Despite the considerable progress in unraveling the genetic causes of amyotrophic lateral sclerosis (ALS), we do not fully understand the molecular mechanisms underlying the disease. We analyzed genome-wide data involving 78,500 individuals using a polygenic risk score approach to identify the biological pathways and cell types involved in ALS. This data-driven approach identified multiple aspects of the biology underlying the disease that resolved into broader themes, namely neuron projection morphogenesis, membrane trafficking, and signal transduction mediated by ribonucleotides. We also found that genomic risk in ALS maps consistently to GABAergic cortical interneurons and oligodendrocytes, as confirmed in human single-nucleus RNA-seq data. Using two-sample Mendelian randomization, we nominated five differentially expressed genes (ATG16L2, ACSL5, MAP1LC3A, PLXNB2, and SCFD1) within the significant pathways as relevant to ALS. We conclude that the disparate genetic etiologies of this fatal neurological disease converge on a smaller number of final common pathways and cell types.

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