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CRISPR AND Zebrafish

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https://www.readbyqxmd.com/read/28988229/studying-kidney-disease-using-tissue-and-genome-engineering-in-human-pluripotent-stem-cells
#1
Elena Garreta, Federico González, Núria Montserrat
Kidney morphogenesis and patterning have been extensively studied in animal models such as the mouse and zebrafish. These seminal studies have been key to define the molecular mechanisms underlying this complex multistep process. Based on this knowledge, the last 3 years have witnessed the development of a cohort of protocols allowing efficient differentiation of human pluripotent stem cells (hPSCs) towards defined kidney progenitor populations using two-dimensional (2D) culture systems or through generating organoids...
October 7, 2017: Nephron
https://www.readbyqxmd.com/read/28942966/haploinsufficiency-of-the-chromatin-remodeler-bptf-causes-syndromic-developmental-and-speech-delay-postnatal-microcephaly-and-dysmorphic-features
#2
Paweł Stankiewicz, Tahir N Khan, Przemyslaw Szafranski, Leah Slattery, Haley Streff, Francesco Vetrini, Jonathan A Bernstein, Chester W Brown, Jill A Rosenfeld, Surya Rednam, Sarah Scollon, Katie L Bergstrom, Donald W Parsons, Sharon E Plon, Marta W Vieira, Caio R D C Quaio, Wagner A R Baratela, Johanna C Acosta Guio, Ruth Armstrong, Sarju G Mehta, Patrick Rump, Rolph Pfundt, Raymond Lewandowski, Erica M Fernandes, Deepali N Shinde, Sha Tang, Juliane Hoyer, Christiane Zweier, André Reis, Carlos A Bacino, Rui Xiao, Amy M Breman, Janice L Smith, Nicholas Katsanis, Bret Bostwick, Bernt Popp, Erica E Davis, Yaping Yang
Bromodomain PHD finger transcription factor (BPTF) is the largest subunit of nucleosome remodeling factor (NURF), a member of the ISWI chromatin-remodeling complex. However, the clinical consequences of disruption of this complex remain largely uncharacterized. BPTF is required for anterior-posterior axis formation of the mouse embryo and was shown to promote posterior neuroectodermal fate by enhancing Smad2-activated wnt8 expression in zebrafish. Here, we report eight loss-of-function and two missense variants (eight de novo and two of unknown origin) in BPTF on 17q24...
October 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28924386/alkbh4-and-atrn-act-maternally-to-regulate-zebrafish-epiboly
#3
Qingrui Sun, Xingfeng Liu, Bo Gong, Di Wu, Anming Meng, Shunji Jia
During embryonic gastrulation, coordinated cell movements occur to bring cells to their correct position. Among them, epiboly produces the first distinct morphological changes, which is essential for the early development of zebrafish. Despite its fundamental importance, little is known to understand the underlying molecular mechanisms. By generating maternal mutant lines with CRISPR/Cas9 technology and using morpholino knockdown strategy, we showed that maternal Alkbh4 depletion leads to severe epiboly defects in zebrafish...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/28911203/mutations-of-conserved-non-coding-elements-of-pitx2-in-patients-with-ocular-dysgenesis-and-developmental-glaucoma
#4
Meredith E Protas, Eric Weh, Tim Footz, Jay Kasberger, Scott C Baraban, Alex V Levin, L Jay Katz, Robert Ritch, Michael A Walter, Elena V Semina, Douglas B Gould
Mutations in FOXC1 and PITX2 constitute the most common causes of ocular anterior segment dysgenesis (ASD), and confer a high risk for secondary glaucoma. The genetic causes underlying ASD in approximately half of patients remain unknown, despite many of them being screened by whole exome sequencing. Here, we performed whole genome sequencing on DNA from two affected individuals from a family with dominantly inherited ASD and glaucoma to identify a 748-kb deletion in a gene desert that contains conserved putative PITX2 regulatory elements...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28893856/distinct-and-cooperative-roles-of-amh-and%C3%A2-dmrt1-in-self-renewal-and-differentiation-of-male-germ-cells-in-zebrafish
#5
Qiaohong Lin, Jie Mei, Zhi Li, Xuemei Zhang, Li Zhou, Jian-Fang Gui
Spermatogenesis is a fundamental process in male reproductive biology, and depends on precise balance between self-renewal and differentiation of male germ cells. However, the regulative factors for controlling the balance are poorly understood. In this study, we examined the roles of amh and dmrt1 in male germ cell development by generating their mutants with Crispr/Cas9 technology in zebrafish. Amh mutant zebrafish displayed a female-biased sex ratio, and both male and female amh mutants developed hypertrophic gonads due to uncontrolled proliferation and impaired differentiation of germ cells...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28880872/microtubule-actin-crosslinking-factor-1-macf1-domain-function-in-balbiani-body-dissociation-and-nuclear-positioning
#6
Matias Escobar-Aguirre, Hong Zhang, Allison Jamieson-Lucy, Mary C Mullins
Animal-vegetal (AV) polarity of most vertebrate eggs is established during early oogenesis through the formation and disassembly of the Balbiani Body (Bb). The Bb is a structure conserved from insects to humans that appears as a large granule, similar to a mRNP granule composed of mRNA and proteins, that in addition contains mitochondria, ER and Golgi. The components of the Bb, which have amyloid-like properties, include germ cell and axis determinants of the embryo that are anchored to the vegetal cortex upon Bb disassembly...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28859103/myt1l-mutations-cause-intellectual-disability-and-variable-obesity-by-dysregulating-gene-expression-and-development-of-the-neuroendocrine-hypothalamus
#7
Patricia Blanchet, Martina Bebin, Shaam Bruet, Gregory M Cooper, Michelle L Thompson, Benedicte Duban-Bedu, Benedicte Gerard, Amelie Piton, Sylvie Suckno, Charu Deshpande, Virginia Clowes, Julie Vogt, Peter Turnpenny, Michael P Williamson, Yves Alembik, Eric Glasgow, Alisdair McNeill
Deletions at chromosome 2p25.3 are associated with a syndrome consisting of intellectual disability and obesity. The smallest region of overlap for deletions at 2p25.3 contains PXDN and MYT1L. MYT1L is expressed only within the brain in humans. We hypothesized that single nucleotide variants (SNVs) in MYT1L would cause a phenotype resembling deletion at 2p25.3. To examine this we sought MYT1L SNVs in exome sequencing data from 4, 296 parent-child trios. Further variants were identified through a genematcher-facilitated collaboration...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28854362/loss-of-apela-peptide-in-mice-causes-low-penetrance-embryonic-lethality-and-defects-in-early-mesodermal-derivatives
#8
Laina Freyer, Chih-Wei Hsu, Sonja Nowotschin, Andrea Pauli, Junji Ishida, Keiji Kuba, Akiyoshi Fukamizu, Alexander F Schier, Pamela A Hoodless, Mary E Dickinson, Anna-Katerina Hadjantonakis
Apela (also known as Elabela, Ende, and Toddler) is a small signaling peptide that activates the G-protein-coupled receptor Aplnr to stimulate cell migration during zebrafish gastrulation. Here, using CRISPR/Cas9 to generate a null, reporter-expressing allele, we study the role of Apela in the developing mouse embryo. We found that loss of Apela results in low-penetrance cardiovascular defects that manifest after the onset of circulation. Three-dimensional micro-computed tomography revealed a higher penetrance of vascular remodeling defects, from which some mutants recover, and identified extraembryonic anomalies as the earliest morphological distinction in Apela mutant embryos...
August 29, 2017: Cell Reports
https://www.readbyqxmd.com/read/28835569/zebrafish-nephrosin-helps-host-defence-against-escherichia-coli-infection
#9
Qianqian Di, Qing Lin, Zhibin Huang, Yali Chi, Xiaohui Chen, Wenqing Zhang, Yiyue Zhang
Neutrophils play important roles in innate immunity and are mainly dependent on various enzyme-containing granules to kill engulfed microorganisms. Zebrafish nephrosin (npsn) is specifically expressed in neutrophils; however, its function is largely unknown. Here, we generated an npsn mutant (npsn(smu5) ) via CRISPR/Cas9 to investigate the in vivo function of Npsn. The overall development and number of neutrophils remained unchanged in npsn-deficient mutants, whereas neutrophil antibacterial function was defective...
August 2017: Open Biology
https://www.readbyqxmd.com/read/28815495/ligand-controlled-site-specific-recombination-in-zebrafish
#10
Avinash Chekuru, Veronika Kuscha, Stefan Hans, Michael Brand
Cre-mediated site-specific recombination has emerged as an indispensable tool for the precise manipulation of genomes allowing lineage-tracing studies, temporal and spatial misexpressions, and in particular the generation of conditional knockout alleles. Previously, we and others showed that Cre and its ligand-inducible variant CreER(T2) are also highly efficient in the developing and adult zebrafish. The number of Cre driver and effector lines is currently still limited in zebrafish. However, the recent advent of novel genome editing tools such as TALEN and CRISPR/Cas will significantly increase interest in the conditional Cre/lox-technology in this organism...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28805828/mutations-in-keops-complex-genes-cause-nephrotic-syndrome-with-primary-microcephaly
#11
Daniela A Braun, Jia Rao, Geraldine Mollet, David Schapiro, Marie-Claire Daugeron, Weizhen Tan, Olivier Gribouval, Olivia Boyer, Patrick Revy, Tilman Jobst-Schwan, Johanna Magdalena Schmidt, Jennifer A Lawson, Denny Schanze, Shazia Ashraf, Jeremy F P Ullmann, Charlotte A Hoogstraten, Nathalie Boddaert, Bruno Collinet, Gaëlle Martin, Dominique Liger, Svjetlana Lovric, Monica Furlano, I Chiara Guerrera, Oraly Sanchez-Ferras, Jennifer F Hu, Anne-Claire Boschat, Sylvia Sanquer, Björn Menten, Sarah Vergult, Nina De Rocker, Merlin Airik, Tobias Hermle, Shirlee Shril, Eugen Widmeier, Heon Yung Gee, Won-Il Choi, Carolin E Sadowski, Werner L Pabst, Jillian K Warejko, Ankana Daga, Tamara Basta, Verena Matejas, Karin Scharmann, Sandra D Kienast, Babak Behnam, Brendan Beeson, Amber Begtrup, Malcolm Bruce, Gaik-Siew Ch'ng, Shuan-Pei Lin, Jui-Hsing Chang, Chao-Huei Chen, Megan T Cho, Patrick M Gaffney, Patrick E Gipson, Chyong-Hsin Hsu, Jameela A Kari, Yu-Yuan Ke, Cathy Kiraly-Borri, Wai-Ming Lai, Emmanuelle Lemyre, Rebecca Okashah Littlejohn, Amira Masri, Mastaneh Moghtaderi, Kazuyuki Nakamura, Fatih Ozaltin, Marleen Praet, Chitra Prasad, Agnieszka Prytula, Elizabeth R Roeder, Patrick Rump, Rhonda E Schnur, Takashi Shiihara, Manish D Sinha, Neveen A Soliman, Kenza Soulami, David A Sweetser, Wen-Hui Tsai, Jeng-Daw Tsai, Rezan Topaloglu, Udo Vester, David H Viskochil, Nithiwat Vatanavicharn, Jessica L Waxler, Klaas J Wierenga, Matthias T F Wolf, Sik-Nin Wong, Sebastian A Leidel, Gessica Truglio, Peter C Dedon, Annapurna Poduri, Shrikant Mane, Richard P Lifton, Maxime Bouchard, Peter Kannu, David Chitayat, Daniella Magen, Bert Callewaert, Herman van Tilbeurgh, Martin Zenker, Corinne Antignac, Friedhelm Hildebrandt
Galloway-Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR-Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue...
October 2017: Nature Genetics
https://www.readbyqxmd.com/read/28800611/using-local-chromatin-structure-to-improve-crispr-cas9-efficiency-in-zebrafish
#12
Yunru Chen, Shiyang Zeng, Ruikun Hu, Xiangxiu Wang, Weilai Huang, Jiangfang Liu, Luying Wang, Guifen Liu, Ying Cao, Yong Zhang
Although the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gRNAs is especially important for zebrafish mutant construction. Besides the sequence features, local chromatin structures may have effects on CRISPR/Cas9 efficiency, which remain largely unexplored. In the only related study in zebrafish, nucleosome organization was not found to have an effect on CRISPR/Cas9 efficiency, which is inconsistent with recent studies in vitro and in mammalian cell lines...
2017: PloS One
https://www.readbyqxmd.com/read/28795449/zebrafish-models-of-orofacial-clefts
#13
REVIEW
Kaylia M Duncan, Kusumika Mukherjee, Robert A Cornell, Eric C Liao
Zebrafish is a model organism that affords experimental advantages toward investigating the normal function of genes associated with congenital birth defects. Here we summarize zebrafish studies of genes implicated in orofacial cleft (OFC). The most common use of zebrafish in this context has been to explore the normal function an OFC-associated gene product in craniofacial morphogenesis by inhibiting expression of its zebrafish ortholog. The most frequently deployed method has been to inject embryos with antisense morpholino oligonucleotides targeting the desired transcript...
August 10, 2017: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/28767718/zygotic-vinculin-is-not-essential-for-embryonic-development-in-zebrafish
#14
Mitchell K L Han, Gerard N M van der Krogt, Johan de Rooij
The formation of multicellular tissues during development is governed by mechanical forces that drive cell shape and tissue architecture. Protein complexes at sites of adhesion to the extracellular matrix (ECM) and cell neighbors, not only transmit these mechanical forces, but also allow cells to respond to changes in force by inducing biochemical feedback pathways. Such force-induced signaling processes are termed mechanotransduction. Vinculin is a central protein in mechanotransduction that in both integrin-mediated cell-ECM and cadherin-mediated cell-cell adhesions mediates force-induced cytoskeletal remodeling and adhesion strengthening...
2017: PloS One
https://www.readbyqxmd.com/read/28767326/tracking-of-indels-by-decomposition-is-a-simple-and-effective-method-to-assess-efficiency-of-guide-rnas-in-zebrafish
#15
Christelle Etard, Swarnima Joshi, Johannes Stegmaier, Ralf Mikut, Uwe Strähle
A bottleneck in CRISPR/Cas9 genome editing is variable efficiencies of in silico-designed gRNAs. We evaluated the sensitivity of the TIDE method (Tracking of Indels by DEcomposition) introduced by Brinkman et al. in 2014 for assessing the cutting efficiencies of gRNAs in zebrafish. We show that this simple method, which involves bulk polymerase chain reaction amplification and Sanger sequencing, is highly effective in tracking well-performing gRNAs in pools of genomic DNA derived from injected embryos. The method is equally effective for tracing INDELs in heterozygotes...
August 2, 2017: Zebrafish
https://www.readbyqxmd.com/read/28767277/using-zebrafish-to-test-the-genetic-basis-of-human-craniofacial-diseases
#16
REVIEW
R Grecco Machado, B Frank Eames
Genome-wide association studies (GWASs) opened an innovative and productive avenue to investigate the molecular basis of human craniofacial disease. However, GWASs identify candidate genes only; they do not prove that any particular one is the functional villain underlying disease or just an unlucky genomic bystander. Genetic manipulation of animal models is the best approach to reveal which genetic loci identified from human GWASs are functionally related to specific diseases. The purpose of this review is to discuss the potential of zebrafish to resolve which candidate genetic loci are mechanistic drivers of craniofacial diseases...
October 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28751305/dlx3b-4b-is-required-for-early-born-but-not-later-forming-sensory-hair-cells-during-zebrafish-inner-ear-development
#17
Simone Schwarzer, Sandra Spieß, Michael Brand, Stefan Hans
Morpholino-mediated knockdown has shown that the homeodomain transcription factors Dlx3b and Dlx4b are essential for proper induction of the otic-epibranchial progenitor domain (OEPD), as well as subsequent formation of sensory hair cells in the developing zebrafish inner ear. However, increasing use of reverse genetic approaches has revealed poor correlation between morpholino-induced and mutant phenotypes. Using CRISPR/Cas9-mediated mutagenesis, we generated a defined deletion eliminating the entire open reading frames of dlx3b and dlx4b (dlx3b/4b) and investigated a potential phenotypic difference between mutants and morpholino-mediated knockdown...
September 15, 2017: Biology Open
https://www.readbyqxmd.com/read/28747644/active-nuclear-transcriptome-analysis-reveals-inflammasome-dependent-mechanism-for-early-neutrophil-response-to-mycobacterium-marinum
#18
Amy Kenyon, Daria Gavriouchkina, Jernej Zorman, Giorgio Napolitani, Vincenzo Cerundolo, Tatjana Sauka-Spengler
The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28740134/programmable-base-editing-of-zebrafish-genome-using-a-modified-crispr-cas9-system
#19
Yihan Zhang, Wei Qin, Xiaochan Lu, Jason Xu, Haigen Huang, Haipeng Bai, Song Li, Shuo Lin
Precise genetic modifications in model animals are essential for biomedical research. Here, we report a programmable "base editing" system to induce precise base conversion with high efficiency in zebrafish. Using cytidine deaminase fused to Cas9 nickase, up to 28% of site-specific single-base mutations are achieved in multiple gene loci. In addition, an engineered Cas9-VQR variant with 5'-NGA PAM specificities is used to induce base conversion in zebrafish. This shows that Cas9 variants can be used to expand the utility of this technology...
July 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28739660/a-gene-implicated-in-activation-of-retinoic-acid-receptor-targets-is-a-novel-renal-agenesis-gene-in-humans
#20
Patrick D Brophy, Maria Rasmussen, Mrutyunjaya Parida, Greg Bonde, Benjamin W Darbro, Xiaojing Hong, Jason C Clarke, Kevin A Peterson, James Denegre, Michael Schneider, Caroline R Sussman, Lone Sunde, Dorte L Lildballe, Jens Michael Hertz, Robert A Cornell, Stephen A Murray, J Robert Manak
Renal agenesis (RA) is one of the more extreme examples of congenital anomalies of the kidney and urinary tract (CAKUT). Bilateral renal agenesis is almost invariably fatal at birth, and unilateral renal agenesis can lead to future health issues including end-stage renal disease. Genetic investigations have identified several gene variants that cause RA, including EYA1, LHX1, and WT1 However, whereas compound null mutations of genes encoding α and γ retinoic acid receptors (RARs) cause RA in mice, to date there have been no reports of variants in RAR genes causing RA in humans...
September 2017: Genetics
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