Browsing by Subject "DUPLICATIONS"

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  • Sironen, Anu; Uimari, Pekka; Venhoranta, Heli; Andersson, Magnus; Vilkki, Johanna (2011)
    ABSTRACT: BACKGROUND: Male infertility is an increasing problem in all domestic species including man. Localization and identification of genes involved in defects causing male infertility provide valuable information of specific events in sperm development. Sperm development is a complex process, where diploid spermatogonia develop into haploid, highly specialized spermatozoa. Correct expression and function of various genes and their protein products are required for production of fertile sperm. We have identified an infertility defect in Finnish Yorkshire boars caused by spermatogenic arrest. The aim of this study was to locate the disease associated region using genome wide screen with the PorcineSNP60 Beadchip and identify the causal mutation by candidate gene approach. RESULTS: In the Finnish Yorkshire pig population the spermatogenic arrest (SA) defect appears to be of genetic origin and causes severe degeneration of germ cells and total absence of spermatozoa. Genome wide scan with the PorcineSNP60 Beadchip localized the SA defect to porcine chromosome 12 in a 2 Mbp region. Sequencing of a candidate gene Tex14 revealed a 51 bp insertion within exon 27, which caused differential splicing of the exon and created a premature translation stop codon. The expression of Tex14 was markedly down regulated in the testis of a SA affected boar compared to control boars and no protein product was identified by Western blotting. The SA insertion sequence was also found within intron 27 in all analyzed animals, thus the insertion appears to be a possible duplication event. CONCLUSION: In this study we report the identification of a causal mutation for infertility caused by spermatogenic arrest at an early meiotic phase. Our results highlight the role of TEX14 specifically in spermatogenesis and the importance of specific genomic remodeling events as causes for inherited defects.
  • Lepelley, Alice; Della Mina, Erika; Van Nieuwenhove, Erika; Waumans, Lise; Fraitag, Sylvie; Rice, Gillian I.; Dhir, Ashish; Fremond, Marie-Louise; Rodero, Mathieu P.; Seabra, Luis; Carter, Edwin; Bodemer, Christine; Buhas, Daniela; Callewaert, Bert; de Lonlay, Pascale; De Somer, Lien; Dyment, David A.; Faes, Fran; Grove, Lucy; Holden, Simon; Hully, Marie; Kurian, Manju A.; McMillan, Hugh J.; Suetens, Kristin; Tyynismaa, Henna; Chhun, Stephanie; Wai, Timothy; Wouters, Carine; Bader-Meunier, Brigitte; Crow, Yanick J. (2021)
    Mitochondrial DNA (mtDNA) has been suggested to drive immune system activation, but the induction of interferon signaling by mtDNA has not been demonstrated in a Mendelian mitochondrial disease. We initially ascertained two patients, one with a purely neurological phenotype and one with features suggestive of systemic sclerosis in a syndromic context, and found them both to demonstrate enhanced interferon-stimulated gene (ISG) expression in blood. We determined each to harbor a previously described de novo dominant-negative heterozygous mutation in ATAD3A, encoding ATPase family AAA domain-containing protein 3A (ATAD3A). We identified five further patients with mutations in ATAD3A and recorded up regulated ISG expression and interferon alpha protein in four of them. Knockdown of ATAD3A in THP-1 cells resulted in increased interferon signaling, mediated by cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING). Enhanced interferon signaling was abrogated in THP-1 cells and patient fibroblasts depleted of mtDNA. Thus, mutations in the mitochondrial membrane protein ATAD3A define a novel type I interferonopathy.
  • Edger, Patrick P.; VanBuren, Robert; Colle, Marivi; Poorten, Thomas J.; Wai, Ching Man; Niederhuth, Chad E.; Alger, Elizabeth I.; Ou, Shujun; Acharya, Charlotte B.; Wang, Jie; Callow, Pete; McKain, Michael R.; Shi, Jinghua; Collier, Chad; Xiong, Zhiyong; Mower, Jeffrey P.; Slovin, Janet P.; Hytonen, Timo; Jiang, Ning; Childs, Kevin L.; Knapp, Steven J. (2017)
    Background: Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings: Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of similar to 7.9 million base pairs (Mb), representing a similar to 300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained similar to 24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome. Conclusions: Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.
  • Wang, Cui; Wang, Tong; Yin, Meiqi; Eller, Franziska; Liu, Lele; Brix, Hans; Guo, Weihua (2021)
    Polyploidization in plants is thought to have occurred as coping mechanism with environmental stresses. Polyploidization-driven adaptation is often achieved through interplay of gene networks involved in differentially expressed genes, which triggers the plant to evolve special phenotypic traits for survival. Phragmites australis is a cosmopolitan species with highly variable phenotypic traits and high adaptation capacity to various habitats. The species' ploidy level varies from 3x to 12x, thus it is an ideal organism to investigate the molecular evolution of polyploidy and gene regulation mediated by different numbers of chromosome copies. In this study, we used high-throughput RNAseq data as a tool, to analyze the gene expression profiles in tetraploid and octoploid P. australis. The estimated divergence time between tetraploid and octoploid P. australis was dated to the border between Pliocene and Pleistocene. This study identified 439 up- and 956 down-regulated transcripts in tetraploids compared to octoploids. Gene ontology and pathway analysis revealed that tetraploids tended to express genes responsible for reproduction and seed germination to complete the reproduction cycle early, and expressed genes related to defense against UV-B light and fungi, whereas octoploids expressed mainly genes related to thermotolerance. Most differentially expressed genes were enriched in chaperones, folding catalysts and protein processing in endoplasmic reticulum pathways. Multiple biased isoform usage of the same gene was detected in differentially expressed genes, and the ones upregulated in octoploids were related to reduced DNA methylation. Our study provides new insights into the role of polyploidization on environmental responses and potential stress tolerance in grass species.
  • Philips, Anju K.; Siren, Auli; Avela, Kristiina; Somer, Mirja; Peippo, Maarit; Ahvenainen, Minna; Doagu, Fatma; Arvio, Maria; Kaariainen, Helena; Van Esch, Hilde; Froyen, Guy; Haas, Stefan A.; Hu, Hao; Kalscheuer, Vera M.; Jarvela, Irma (2014)