Top 10 Biorxiv Papers Today in Genetics


2.051 Mikeys
#1. Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways
Anne E. Dodson, Scott Kennedy
Germ granules are biomolecular condensates that promote germ cell totipotency in most, if not all, animals. In C. elegans , MEG-3 and MEG-4 are two intrinsically disordered proteins that are redundantly required for the phase separations that drive germ granule assembly in germline blastomeres. Here, we show that animals lacking MEG-3/4 exhibit defects in dsRNA-mediated gene silencing (RNAi) that are due, at least in part, to defects in systemic RNAi. Interestingly, these RNAi defects are transgenerationally disconnected from meg-3/4 genotype: RNAi defects do not arise until 5-9 generations after animals become mutant for meg-3/4 , and RNAi defects persist for 9-11 generations after meg-3/4 genotype is restored to wild type. Similar non-Mendelian patterns of inheritance are associated with other mutations that disrupt germ granule formation, indicating that germ granule disruption is the likely cause of genotype/phenotype disconnects. Loss of germ granules is associated with the production of aberrant populations of endogenous...
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biorxivpreprint: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/zTNbZyOSfu #bioRxiv
biorxiv_genetic: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/sqXs3q8c66 #biorxiv_genetic
ProfJWHolloway: RT @biorxiv_genetic: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/sqXs3q8c66 #biorxiv_genetic
Eva3034385615: RT @biorxivpreprint: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/zTNbZyOSfu #bioRxiv
eileenamcl: RT @biorxivpreprint: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/zTNbZyOSfu #bioRxiv
BrettNixon13: RT @biorxivpreprint: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/zTNbZyOSfu #bioRxiv
schraderlab: RT @biorxivpreprint: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/zTNbZyOSfu #bioRxiv
ColinConine: RT @biorxivpreprint: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/zTNbZyOSfu #bioRxiv
sbotlite: RT @biorxivpreprint: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/zTNbZyOSfu #bioRxiv
SharmaLab_UCSC: RT @biorxivpreprint: Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways https://t.co/zTNbZyOSfu #bioRxiv
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Authors: 2
Total Words: 12509
Unqiue Words: 2914

2.023 Mikeys
#2. The laboratory domestication of zebrafish: from diverse populations to inbred substrains
Jaanus Suurvaeli, Andrew R Whiteley, Yichen Zheng, Karim Gharbi, Maria Leptin, Thomas Wiehe
The zebrafish (Danio rerio) is a model vertebrate widely used to study disease, development and other aspects of vertebrate biology. Most of the research is performed on laboratory strains, one of which has been fully sequenced in order to derive a reference genome. It is known that the laboratory strains differ genetically from each other, but so far no genome-scale survey of variation between the laboratory and wild zebrafish populations exists. Here we use Restriction-Associated DNA sequencing (RAD-seq) to characterize three different wild zebrafish lineages from a population genetic viewpoint, and to compare them to four common laboratory strains. For this purpose we combine new genome-wide sequence data obtained from natural samples in India, Nepal and Bangladesh with a previously published dataset. We measured nucleotide diversity, heterozygosity, allele frequency spectra and patterns of gene conversion, and find that wild fish are much more diverse than laboratory strains. Further, in wild zebrafish there is a clear signal...
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biorxivpreprint: The laboratory domestication of zebrafish: from diverse populations to inbred substrains https://t.co/nPeYquVx3V #bioRxiv
biorxiv_genetic: The laboratory domestication of zebrafish: from diverse populations to inbred substrains https://t.co/6tVwqy5QY3 #biorxiv_genetic
jamiracci: RT @biorxivpreprint: The laboratory domestication of zebrafish: from diverse populations to inbred substrains https://t.co/nPeYquVx3V #bio…
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Authors: 6
Total Words: 0
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2.015 Mikeys
#3. Assessment of a split homing based gene drive for efficient knockout of multiple genes
Nikolay P Kandul, Junru Liu, Anna Buchman, Valentino M Gantz, Ethan Bier, Omar S Akbari
Homing based gene drives (HGD) possess the potential to spread linked cargo genes into natural populations and are poised to revolutionize population control of animals. Given that host-encoded genes have been identified that are important for pathogen transmission, targeting these genes using guide RNAs as cargo genes linked to drives may provide a robust method to prevent transmission. However, effectiveness of the inclusion of additional guide RNAs that target separate host encoded genes has not been thoroughly explored. To test this approach, here we generated a split-HGD in Drosophila melanogaster that encoded a drive linked effector consisting of a second gRNA engineered to target a separate host encoded gene, which we term a gRNA-mediated effector (GME). This design enabled us to assess homing and knockout efficiencies of two target genes simultaneously, and also explore the timing and tissue specificity of Cas9 expression on cleavage/homing rates. We demonstrate that inclusion of a GME can result in high efficiency of...
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biorxivpreprint: Assessment of a split homing based gene drive for efficient knockout of multiple genes https://t.co/Ha7ngCEx6c #bioRxiv
biorxiv_genetic: Assessment of a split homing based gene drive for efficient knockout of multiple genes https://t.co/hpjJ8eVubz #biorxiv_genetic
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Authors: 6
Total Words: 10190
Unqiue Words: 2792

2.014 Mikeys
#4. Early diverging fungus Mucor circinelloides lacks centromeric histone CENP-A and displays a mosaic of point and regional centromeres
Maria I Navarro-Mendoza, Carlos Perez-Arques, Shweta Panchal, Francisco E Niolas, Stephen J Mondo, Promit Ganguly, Jasmyn Pangilinan, Igor V Grigoriev, Joe Heitman, Kaustuv Sanyal, Victoriano Garre
Centromeres are rapidly evolving across eukaryotes, despite performing a conserved function to ensure high fidelity chromosome segregation. CENP-A chromatin is a hallmark of a functional centromere in most organisms. Due to its critical role in kinetochore architecture, the loss of CENP-A is tolerated in only a few organisms, many of which possess holocentric chromosomes. Here, we characterize the consequence of the loss of CENP-A in the fungal kingdom. Mucor circinelloides, an opportunistic human pathogen, lacks CENP-A along with the evolutionarily conserved CENP-C, but assembles a monocentric chromosome with a localized kinetochore complex throughout the cell cycle. Mis12 and Dsn1, two conserved kinetochore proteins were found to bind nine short overlapping regions, each comprising an ~200-bp AT-rich sequence followed by a centromere-specific conserved motif that echoes the structure of budding yeast point centromeres. Resembling fungal regional centromeres, these core centromere regions are embedded in large genomic expanses...
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biorxivpreprint: Early diverging fungus Mucor circinelloides lacks centromeric histone CENP-A and displays a mosaic of point and regional centromeres https://t.co/5nojCdznLm #bioRxiv
biorxiv_genetic: Early diverging fungus Mucor circinelloides lacks centromeric histone CENP-A and displays a mosaic of point and regional centromeres https://t.co/rsJzC9t0HL #biorxiv_genetic
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Authors: 11
Total Words: 0
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2.012 Mikeys
#5. Population genomics of the Viking world
Ashot Margaryan, Daniel John Lawson, Martin Sikora, Fernando Racimo, Simon Rasmussen, Ida Moltke, Lara Cassidy, Emil Jorsboe, Andres Ingason, Mikkel Winther Pedersen, Thorfinn Sand Korneliussen, Helene Wilhelmson, Magdalena Maria Bus, Peter de Barros Damgaard, Rui Martiniano, Gabriel Renaud, Claude Bherer, J. Victor Moreno-Mayar, Anna Katerina Fotakis, Marie Allen, Martyna Molak, Enrico Cappellini, Gabriele Scorrano, Alexandra Buzhilova, Allison Mary Fox, Anders Albrechtsen, Berit Schutz, Birgitte Skar, Caroline Ahlstrom Arcini, Ceri G. Falys, Charlotte Hedenstierna-Jonson, Dariusz Blaszczyk, Denis Pezhemsky, Gordon Turner-Walker, Hildur Gestsdottir, Inge Lundstrom, Ingrid Gustin, Ingrid Mainland, Inna Potekhina, Italo Maria Muntoni, Jade Cheng, Jesper Stenderup, Jilong Ma, Julie Gibson, Jyri Peets, Jorgen Gustafsson, Katrine Hojholt Iversen, Linzi Simpson, Lisa Mariann Strand, Louise Katherine Loe, Maeve Sikora, Marek Florek, Maria Vretemark, Mark Redknap, Monika Bajka, Tamara Pushkina, Morten Sovso, Natalia Grigoreva, Tom Christensen, Ole Thirup Kastholm, Otto Christian Uldum, Pasquale Favia, Per Holck, Raili Allmae, Sabine Sten, Simun Vilhelm Arge, Sturla Ellingvag, Vayacheslav Moiseyev, Wieslaw Bogdanowicz, Yvonne Magnusson, Ludovic Orlando, Daniel G. Bradley, Marie Louise Schjellerup Jorkov, Jette Arneborg, Niels Lynnerup, Neil Price, M. Thomas Pius Gilbert, Morten E. Allentoft, Jan Bill, Soren Michael Sindbek, Lotte Hedeager, Kristian Kristiansen, Rasmus Nielsen, Thomas Werge, Eske Willerslev
The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a...
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theladydharma: See? Even Vikings are mutts. @FerRacimo, and also @EaglePursuit thanks for the read: https://t.co/dR6HRBvzgc https://t.co/lOJMmtLfgk
henrysobie: #Population #Genomics of the #Viking #World #research #DNA #movement #migration #diversity #Europe #Denmark #Sweden #Norway https://t.co/kI9hsWRl8M https://t.co/f5qv36o2aF
NoahCarl90: RT @biorxiv_genetic: Population genomics of the Viking world https://t.co/RxI1yjz4gY #biorxiv_genetic
johanwadenback: RT @biorxiv_genetic: Population genomics of the Viking world https://t.co/RxI1yjz4gY #biorxiv_genetic
hugofgante: RT @biorxiv_genetic: Population genomics of the Viking world https://t.co/RxI1yjz4gY #biorxiv_genetic
JohanOrre: RT @biorxiv_genetic: Population genomics of the Viking world https://t.co/RxI1yjz4gY #biorxiv_genetic
MiguelSieck: RT @biorxiv_genetic: Population genomics of the Viking world https://t.co/RxI1yjz4gY #biorxiv_genetic
AltenaSjirk: RT @biorxiv_genetic: Population genomics of the Viking world https://t.co/RxI1yjz4gY #biorxiv_genetic
dvorikus: RT @biorxiv_genetic: Population genomics of the Viking world https://t.co/RxI1yjz4gY #biorxiv_genetic
RenatoPolimanti: RT @biorxiv_genetic: Population genomics of the Viking world https://t.co/RxI1yjz4gY #biorxiv_genetic
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Sample Sizes : [376, 2, 10, 43, 34, 6, 3, 23, 78, 17, 4, 29, 8, 33, 118, 42, 3, 16, 5, 7, 2, 21, 1675]
Authors: 85
Total Words: 12731
Unqiue Words: 4429

1.997 Mikeys
#6. Assessing by modeling the consequences of increased recombination in genomic selection of Oryza sativa and Brassica rapa.
Elise Tourrette, Rex Bernardo, Matthieu Falque, Olivier C. Martin
Recombination generates genetic diversity but the number of crossovers per meiosis is limited in most species. Previous studies showed that increasing recombination can enhance response to selection. However, such studies did not assume a specific method of modifying recombination. Our objective was to test whether two methods used to increase recombination in plants could increase the genetic gain in a population undergoing genomic selection. The first method, in Oryza sativa, used a mutant of anti-crossover genes to increase global recombination without affecting the recombination landscape. The second one uses the ploidy level of a cross between Brassica rapa and Brassica napus to increase the recombination particularly in pericentromeric regions. These recombination landscapes were used to model recombination while quantitative trait loci positions were based on the actual gene distribution. We simulated selection programs with initially a cross between two inbred lines, for two species. Increased recombination enhanced the...
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meiosis_papers: Assessing by modeling the consequences of increased recombination in genomic selection of Oryza sativa and Brassica rapa. | Martin O C https://t.co/gg288mlZnB
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Authors: 4
Total Words: 12587
Unqiue Words: 3303

1.997 Mikeys
#7. Variants in the degron of AFF3 cause a multi-system disorder with mesomelic dysplasia, horseshoe kidney and developmental and epileptic encephalopathy
Norine Voisin, Rhonda E. Schnur, Sofia Douzgou, Susan M. Hiatt, Cecilie F. Rustad, Natasha J. Brown, Dawn L. Earl, Boris Keren, Olga Levchenko, Sinje Geuer, David Amor, Alfredo Brusco, E. Martina Bebin, Gerarda Cappuccio, Joel Charrow, Nicolas Chatron, Gregory M. Cooper, Elena Dadali, Julien Delafontaine, Ennio Del Giudice, Ganka Douglas, Tara Funari, Giuliana Giannuzzi, Nicolas Guex, Delphine Heron, Øystein L. Holla, Anna C.E. Hurst, Jane Juusola, David Kronn, Alexander Lavrov, Crystle Lee, Else Merckoll, Anna Mikhaleva, Jennifer Norman, Sylvain Pradervand, Victoria Sanders, Fabio Sirchia, Toshiki Takenouchi, Akemi J. Tanaka, Heidi Taska-Tench, Elin Tønne, Kristian Tveten, Giuseppina Vitiello, Tomoko Uehara, Caroline Nava, Binnaz Yalcin, Kenjiro Kosaki, Dian Donnai, Stefan Mundlos, Nicola Brunetti-Pierri, Wendy K. Chung, Alexandre Reymond
The ALF transcription factor paralogs, AFF1, AFF2, AFF3 and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe a new autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its degradation. Consistent with a causative role of AFF3 variants, the mutated AFF3 proteins show reduced clearance. Ten affected individuals were identified, and present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe KIdney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for Seizures, H for Hypertrichosis, I for Intellectual disability and P for Pulmonary involvement), partially overlapping the AFF4 associated CHOPS syndrome. An eleventh individual with a microdeletion encompassing only the transactivation domain and degron motif of AFF3 exhibited overlapping clinical features. A zebrafish overexpression model that...
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Authors: 52
Total Words: 11072
Unqiue Words: 4583

1.997 Mikeys
#8. Identification of a major QTL and associated marker for high arabinoxylan fibre in white wheat flour
Alison Lovegrove, Luzie Wingen, Amy Plummer, Abigail Wood, Diana Passmore, Ondrej Kosik, Jackie Freeman, Rowan Mitchell, Mehmet Ulker, Karolina Tremmel-Bede Tremmel-Bede, Marianna Rakszegi, Zoltan Bedo, Gilles Charmet, Marie-Reine Petterant, Michelle Leverington Waite, Simon Simon Orford, Amanda Burridge, Till Pellny, Peter Shewry, Simon Griffiths
Dietary fibre (DF) has multiple health benefits, and wheat products are major sources of DF for human health. However, DF is depleted in white flour, which is most widely consumed, compared to wholegrain. The major type of DF in white wheat flour is the cell wall polysaccharide arabinoxylan (AX). Previous studies have identified the Chinese wheat cultivar Yumai 34 as having unusually high contents of AX in both water-soluble and insoluble forms. We have therefore used populations generated from crosses between Yumai 34 and four other wheat cultivars, three with average contents of AX (Ukrainka, Altigo and Claire) and one also having unusually high AX (Valoris), in order to map QTLs for soluble AX (determined as relative viscosity) of aqueous extracts of wholemeal flours) and total AX (determined by enzyme fingerprinting of white flour). A number of QTL were mapped, but most were only detected in one or two crosses. However, all four crosses showed strong QTLs for high RV/total AX on chromosome 1B, with Yumai 34 being the...
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biorxivpreprint: Identification of a major QTL and associated marker for high arabinoxylan fibre in white wheat flour https://t.co/g8dCjagLv8 #bioRxiv
biorxiv_genetic: Identification of a major QTL and associated marker for high arabinoxylan fibre in white wheat flour https://t.co/jZYsa2eokT #biorxiv_genetic
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Authors: 20
Total Words: 0
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1.997 Mikeys
#9. A Multistage Sequencing Strategy Pinpoints Many Novel and Candidate Disease Alleles for Orphan Disease Emery-Dreifuss Muscular Dystrophy and Supports Gene Misregulation as its Pathomechanism
Peter Meinke, Alastair R. W. Kerr, Rafal Czapiewski, Jose I. de las Heras, Elizabeth Harris, Heike Koelbel, Francesco Muntoni, Ulrike Schara, Volker Straub, Benedikt Schoser, Manfred Wehnert, Eric C. Schirmer
Limitations of genome-wide approaches for genetically-heterogenous orphan diseases led us to develop a new approach to identify novel Emery-Dreifuss muscular dystrophy (EDMD) candidate genes. We generated a primer library to genes: (I) linked to EDMD, (II) mutated in related muscular dystrophies, (III) highlighted from limited exome sequencing, (IV) encoding muscle-specific nuclear membrane proteins. Sequencing 56 unlinked EDMD patients yielded confirmed or strong candidate alleles from all categories, accounting for most remaining unlinked patients. Known functions of newly-linked genes argue the EDMD pathomechanism is from altered gene regulation and mechanotransduction through connectivity of candidates from the nuclear envelope to the plasma membrane.
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biorxivpreprint: A Multistage Sequencing Strategy Pinpoints Many Novel and Candidate Disease Alleles for Orphan Disease Emery-Dreifuss Muscular Dystrophy and Supports Gene Misregulation as its Pathomechanism https://t.co/cTDnna43Nm #bioRxiv
biorxiv_genetic: A Multistage Sequencing Strategy Pinpoints Many Novel and Candidate Disease Alleles for Orphan Disease Emery-Dreifuss Muscular ... https://t.co/zqekwSPuAT #biorxiv_genetic
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Authors: 12
Total Words: 9111
Unqiue Words: 2895

1.997 Mikeys
#10. Leveraging Gene Co-expression Patterns to Infer Trait-Relevant Tissues in Genome-wide Association Studies
Lulu Shang, Jennifer A. Smith, Xiang Zhou
Genome-wide association studies (GWASs) have identified many SNPs associated with various common diseases. Understanding the biological functions of these identified SNP associations requires identifying disease/trait relevant tissues or cell types. Here, we develop a network method, CoCoNet, to facilitate the identification of trait-relevant tissues or cell types. Different from existing approaches, CoCoNet incorporates tissue-specific gene co-expression networks constructed from either bulk or single cell RNA sequencing (RNAseq) studies with GWAS data for trait-tissue inference. In particular, CoCoNet relies on a covariance regression network model to express gene-level effect sizes for the given GWAS trait as a function of the tissue-specific co-expression adjacency matrix. With a composite likelihood-based inference algorithm, CoCoNet is scalable to tens of thousands of genes. We validate the performance of CoCoNet through extensive simulations. We apply CoCoNet for an in-depth analysis of four neurological disorders and four...
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Authors: 3
Total Words: 12142
Unqiue Words: 2899

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