PaperPlayer biorxiv genetics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.01.232512v1?rss=1

Authors: Jang, J. K., Gladstein, A., Das, A., Cisco, Z., McKim, K.

Abstract:

Meiosis in female oocytes lack centrosomes, the major microtubule-organizing center, which may make them especially vulnerable to aneuploidy. In the acentrosomal oocytes of Drosophila, meiotic spindle assembly depends on the chromosomal passenger complex (CPC). Aurora B is the catalytic component of the CPC while the remaining subunits regulate its localization. Using an inhibitor of Aurora B activity, Binucleine 2, we found that continuous Aurora B activity is required to maintain the oocyte spindle during meiosis I. Furthermore, the necessity of a kinase for spindle regulation suggests that spindle dynamics is regulated by phosphatases. Our result have shown that the protein complex Protein Phosphatase 2A (PP2A) opposes CPC activity, probably by dephosphorylating spindle associated proteins such as the Kinesins. PP2A exists in two varieties, B55 and B56. While both antagonize Aurora B, they typically exhibit different localization and function. B55 has only minor roles in meiosis I spindle function. The B56 subunit is encoded by two partially redundant paralogs in the Drosophila genome, wdb and wrd. Knocking down both B56 subunits showed they are critical for multiple functions during meiosis I, including maintaining sister centromere and arm cohesion, end-on microtubule attachments, and the metaphase I arrest in oocytes. We found that WDB recruitment to the centromeres depends on BubR1, MEI-S332, and kinetochore protein SPC105R. However, only SPC105R is required for cohesion maintenance during meiosis I. We propose that SPC105R promotes cohesion maintenance by recruiting two proteins that further recruit PP2A, MEI-S332, and the Soronin homolog Dalmatian.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.232926v1?rss=1

Authors: Bengani, H., Grozeva, D., Moyon, L., Bhatia, S., Louros, S. R., Hope, J., Jackson, A., Prendergast, J., Owen, L. J., Naville, M., Rainger, J., Grimes, G., Halachev, M., Murphy, L. C., Boskovic, O. S., Heyningen, V. v., Kind, P., Abbott, C. M., Osterweil, E., Raymond, L., Roest Crollius, H., FitzPatrick, D.

Abstract:

Undiagnosed neurodevelopmental disease is significantly associated with rare variants in cis-regulatory elements (CRE) but demonstrating causality is challenging as target gene consequences may differ from a causative variant affecting the coding region. Here, we address this challenge by applying a procedure to discriminate likely diagnostic regulatory variants from those of neutral/low-penetrant effect. We identified six rare CRE variants using targeted and whole genome sequencing in 48 unrelated males with apparent X-linked intellectual disability (XLID) but without detectable coding region variants. These variants segregated appropriately in families and altered conserved bases in predicted CRE targeting known XLID genes. Three were unique and three were rare but too common to be plausibly causative for XLID. We compared the cis-regulatory activity of wild-type and mutant alleles in zebrafish embryos using dual-color fluorescent reporters. Two variants showed striking changes: one plausibly causative (FMR1CRE) and the other likely neutral/low-penetrant (TENM1CRE).These variants were knocked-in to mice and both altered embryonic neural expression of their target gene. Only Fmr1CRE mice showed disease-relevant behavioral defects. FMR1CRE is plausibly disease-associated resulting in complex misregulation of Fmr1/FMRP rather than loss-of-function. This is consistent both with absence of Fragile X syndrome in the probands and the observed electrophysiological anomalies in the FMR1CRE mouse brain. Although disruption of in vivo patterns of endogenous gene expression in disease-relevant tissues by CRE variants cannot be used as strong evidence for Mendelian disease association, in conjunction with extreme rarity in human populations and with relevant knock-in mouse phenotypes, such variants can become likely pathogenic.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.234005v1?rss=1

Authors: Gordenin, D. A., Klimczak, L. J., Randall, T. A., Saini, N., Li, J.-L.

Abstract:

Genomes of tens of thousands of SARS-CoV2 isolates have been sequenced across the world and the total number of changes (predominantly single base substitutions) in these isolates exceeds ten thousand. We compared the mutational spectrum in the new SARS-CoV-2 mutation dataset with the previously published mutation spectrum in hypermutated genomes of rubella - another positive single stranded (ss) RNA virus. Each of the rubella isolates arose by accumulation of hundreds of mutations during propagation in a single subject, while SARS-CoV-2 mutation spectrum represents a collection events in multiple virus isolates from individuals across the world. We found a clear similarity between the spectra of single base substitutions in rubella and in SARS-CoV-2, with C to U as well as A to G and U to C being the most prominent in plus strand genomic RNA of each virus. Of those, U to C changes universally showed preference for loops versus stems in predicted RNA secondary structure. Similarly, to what was previously reported for rubella, C to U changes showed enrichment in the uCn motif, which suggested a subclass of APOBEC cytidine deaminase being a source of these substitutions. We also found enrichment of several other trinucleotide-centered mutation motifs only in SARS-CoV-2 - likely indicative of a mutation process characteristic to this virus. Altogether, the results of this analysis suggest that the mutation mechanisms that lead to hypermutation of the rubella vaccine virus in a rare pathological condition may also operate in the background of the SARS-CoV-2 viruses currently propagating in the human population.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.235135v1?rss=1

Authors: Han, C., Yu, T., Qin, W., Liao, X., Huang, J., Liu, Z., Yu, L., Liu, X., Chen, Z., Yang, C., Wang, X., Mo, S., Zhu, G., Su, H., Mo, Z., Peng, T.

Abstract:

Background/Aims: Dietary aflatoxin B1 (AFB1) exposure, which induces DNA damage and codon 249 mutation of the TP53 gene, is one of the major risk factors for hepatocellular carcinoma (HCC). Hepatitis B virus (HBV) infection and AFB1 exert synergistic effects to promote carcinogenesis and TP53 R249S mutation in HCC. Methods: A genome-wide association study (GWAS) was conducted on 485 cases of HCC with chronic HBV infection, followed by a two-stage replication study on 270 cases with chronic HBV infection. Susceptibility variants for the TP53 R249S mutation in HCC were identified based on both GWAS and replication analysis. The associations of identified variants with expression levels of their located genes were validated in 20 paired independent samples. Results: Our results showed that TP53 R249S was significantly associated with ADAMTS18 rs9930984 (adjusted P = 4.84 x 10-6), WDR49 rs75218075 (adjusted P = 7.36 x 10-5) and SLC8A3 rs8022091 (adjusted P = 0.042). Additionally, ADAMTS18 mRNA expression was significantly higher in HCC tissue, compared with paired non-tumor tissue (P = 0.041) and patients carrying the TT genotype at rs9930984 showed lower ADAMTS18 expression in non-tumor tissue, compared with those carrying the GT genotype (P = 0.0028). Conclusions: TP53 expression is significantly associated with R249S mutation in HCC. Our collective results suggest that rs9930984, rs75218075 and rs8022091 are associated with susceptibility to the R249S mutation in cases of HCC exposed to AFB1 and HBV infection.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.235192v1?rss=1

Authors: Gifford, I., Dasgupta, A., Barrick, J. E.

Abstract:

Due to their universal presence and high sequence conservation, rRNA sequences are used widely in phylogenetics for inferring evolutionary relationships between microbes and in metagenomics for analyzing the composition of microbial communities. Most microbial genomes encode multiple copies of ribosomal RNA (rRNA) genes to supply cells with sufficient capacity for protein synthesis. These copies typically undergo concerted evolution that keeps their sequences identical, or nearly so, due to gene conversion, a type of intragenomic recombination that changes one copy of a homologous sequence to exactly match another. Widely varying rates of rRNA gene conversion have previously been estimated by comparative genomics methods and using genetic reporter assays. To more directly measure rates of rRNA intragenomic recombination, we sequenced the seven Escherichia coli rRNA operons in 15 lineages of cells that were evolved for ~13,750 generations with frequent single-cell bottlenecks that reduce the effects of selection. We identified 34 gene conversion events and estimate an overall rate of intragenomic recombination events between rRNA copies of 3.2 x 10-4 per generation or 5.3 x 10-5 per potential donor sequence. This rate varied only slightly from random expectations between different portions of the rRNA genes and between rRNA operons located at different locations in the genome. This accurate estimate of the rate of rRNA gene conversions fills a gap in our quantitative understanding of how ribosomal sequences and other multicopy elements diversify and homogenize during microbial genome evolution.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.03.235036v1?rss=1

Authors: Ghanta, K. S., Mello, C. C.

Abstract:

CRISPR genome editing has revolutionized genetics in many organisms. In the nematode Caenorhabditis elegans one injection into each of the two gonad arms of an adult hermaphrodite exposes hundreds of meiotic germ cells to editing mixtures, permitting the recovery of multiple indels or small precision edits from each successfully injected animal. Unfortunately, particularly for long insertions, editing efficiencies can vary widely, necessitating multiple injections, and often requiring co-selection strategies. Here we show that melting double stranded DNA (dsDNA) donor molecules prior to injection increases the frequency of precise homology-directed repair (HDR) by several fold for longer edits. We describe troubleshooting strategies that enable consistently high editing efficiencies resulting, for example, in up to 100 independent GFP knock-ins from a single injected animal. These efficiencies make C. elegans by far the easiest metazoan to genome edit, removing barriers to the use and adoption of this facile system as a model for understanding animal biology.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.02.233056v1?rss=1

Authors: Adolfi, A., Gantz, V. M., Jasinskiene, N., Lee, H.-F., Hwang, K., Bulger, E. A., Ramaiah, A., Bennett, J. B., Terradas, G., Emerson, J. J., Marshall, J. M., Bier, E., James, A. A.

Abstract:

The development of Cas9/gRNA-mediated gene-drive systems has bolstered the advancement of genetic technologies for controlling vector-borne pathogen transmission. These include population suppression approaches, genetic analogs of insecticidal techniques that reduce the number of vector insects, and population modification (replacement/alteration) approaches, which interfere with competence to transmit pathogens. We developed the first recoded gene-drive rescue system for population modification in the malaria vector, Anopheles stephensi, that relieves the load in females caused by integration of the drive into the kynurenine hydroxylase gene by rescuing its function. Non-functional resistant alleles are eliminated via a dominantly-acting maternal effect combined with slower-acting standard negative selection, and a functional resistant allele does not prevent drive invasion. Small cage trials show that single releases of gene-drive males robustly result in efficient population modification with >95% of mosquitoes carrying the drive within 5-11 generations over a range of initial release ratios.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.31.230565v1?rss=1

Authors: Rousseau, J., Mbakam, C. H., Guyon, A., Tremblay, G., Begin, F. G., Tremblay, J. P.

Abstract:

Base editing technique and PRIME editing techniques derived from the CRISPR/Cas9 discovery permit to modify selected nucleotides. We initially used the base editing technique to introduce in the APP gene the A673T mutation, which prevents the development of Alzheimer disease. Although the desired cytidine to thymidine mutation was inserted in up to 17% of the APP gene in HEK393T, there were also modifications of up to 20% of other nearby cytidines. More specific mutations of the APP gene were obtained with the PRIME editing technique. However, the best percentage of mutations was only 5.8%. The efficiency of the PRIME editing treatment was initially tested on the EMX1 gene. A single treatment produced the desired modification in 36% of the EMX1 gene. Three consecutive treatments increased the percentage of mutations to 50%. The PRIME editing technique was also used to insert specific point mutations in exons 9 and 35 of the DMD gene coding for the dystrophin gene and which is mutated in Duchenne Muscular Dystrophy (DMD). Up to 10% desired mutations of the DMD gene were obtained. Three repeated treatments increased the percentage of specific mutations to 16%. Given that there are thousands of nuclei inside a human muscle fiber and that the dystrophin nuclear domain is about 500 microns, this level of modifications would be sufficient to produce a phenotype improvement in DMD patients.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.30.228932v1?rss=1

Authors: Su, J., Zhao, J., Zhao, S., Shang, X., Pang, S., Chen, S., Liu, D., Kang, Z., Wang, X.

Abstract:

Due to the field soil changes, high density planting, and straw-returning methods, wheat common root rot (spot blotch) and Fusarium crown rot (FCR) have become severe threatens to global wheat productions. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these two devastating diseases have been poorly understood. This review summarizes the recent progress of genetic studies on wheat resistance to common root rot and Fusarium crown rot. Wheat germplasms with relative higher resistance are highlighted and genetic loci controlling the resistance to each of the disease are summarized.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.30.228825v1?rss=1

Authors: Madison, B. S., Flanagan, M. K., Nath, S., White, M. A.

Abstract:

Crossover frequency often differs substantially between sexes (i.e. heterochiasmy). Although this phenomenon is widespread throughout taxa, the mechanisms that lead to heterochiasmy remain unclear. One pattern that has emerged is that the overall length of the synaptonemal complex likely has a direct influence on the total number of crossovers in each sex. However, this has only been investigated in a handful of species. The threespine stickleback fish (Gasterosteus aculeatus) is an excellent species to explore whether synaptonemal complex length is associated with a difference in the total number of crossovers, as females have longer linkage maps than males. We used immunocytogenetics to quantify synaptonemal complex length in late pachytene female and male meiocytes. We found that females had synaptonemal complexes that were 1.65 times longer than males, which is remarkably similar to the length difference observed in a sex-specific linkage map constructed from a cross between two other populations. Our results support a model where chromosome axis length determines overall crossover frequency and establish the threespine stickleback as a useful species to explore the mechanistic basis of heterochiasmy.

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