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Genes
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Screens, Genes, and Phenotypes
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Screens, Genes, and Phenotypes

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (1 October 2022) | Viewed by 8332

Special Issue Editors

Dr. Shawn Burgess

E-Mail Website
Guest Editor
Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892-8004, USA
Interests: zebrafish; regeneration; genomics; hearing
Dr. Gaurav K. Varshney

E-Mail Website
Guest Editor
Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
Interests: deafness; zebrafish; gene editing; human disease

Special Issue Information

Dear Colleagues,

We are launching a Special Issue for the journal Genes titled “Screens, Genes, and Phenotypes”. The purpose of this issue is to provide an information outlet for researchers who have generated collections of knockouts, unpublished phenotypes, targeting approaches, or other forms of genetic screening, both conventional and unconventional. Often in the process of generating data, there is important information gathered on gene knockouts, efficacy of sgRNA guides, observed gene redundancies, or other data that never make it to publication because they do not tell a “complete” story, but such information would be very useful to disseminate for other researchers. Topics may include the description of and general results for a genetic screen, a confirmed set of gene knockouts, validated CRISPR guides for F0 screening, obvious phenotypes resulting from gene knockouts, a streamlined protocol for specific phenotyping, etc. The collection is open to both “traditional” model organisms as well as contributions from “emerging” models.

Dr. Shawn Burgess
Dr. Gaurav K. Varshney
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetic screen
  • phenotype
  • gene editing
  • resources

Published Papers (3 papers)

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Research

11 pages, 2544 KiB  
Article
A Mouse Model with Ablated Asparaginase and Isoaspartyl Peptidase 1 (Asrgl1) Develops Early Onset Retinal Degeneration (RD) Recapitulating the Human Phenotype
by Pooja Biswas, Anne Marie Berry, Qais Zawaydeh, Dirk-Uwe G. Bartsch, Pongali B. Raghavendra, J. Fielding Hejtmancik, Naheed W. Khan, S. Amer Riazuddin and Radha Ayyagari
Genes 2022, 13(8), 1461; https://doi.org/10.3390/genes13081461 - 17 Aug 2022
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Abstract
We previously identified a homozygous G178R mutation in human ASRGL1 (hASRGL1) through whole-exome analysis responsible for early onset retinal degeneration (RD) in patients with cone–rod dystrophy. The mutant G178R ASRGL1 expressed in Cos-7 cells showed altered localization, while the mutant ASRGL1 [...] Read more.
We previously identified a homozygous G178R mutation in human ASRGL1 (hASRGL1) through whole-exome analysis responsible for early onset retinal degeneration (RD) in patients with cone–rod dystrophy. The mutant G178R ASRGL1 expressed in Cos-7 cells showed altered localization, while the mutant ASRGL1 in E. coli lacked the autocatalytic activity needed to generate the active protein. To evaluate the effect of impaired ASRGL1 function on the retina in vivo, we generated a mouse model with c.578_579insAGAAA (NM_001083926.2) mutation (Asrgl1mut/mut) through the CRISPR/Cas9 methodology. The expression of ASGRL1 and its asparaginase activity were undetectable in the retina of Asrgl1mut/mut mice. The ophthalmic evaluation of Asrgl1mut/mut mice showed a significant and progressive decrease in scotopic electroretinographic (ERG) response observed at an early age of 3 months followed by a decrease in photopic response around 5 months compared with age-matched wildtype mice. Immunostaining and RT-PCR analyses with rod and cone cell markers revealed a loss of cone outer segments and a significant decrease in the expression of Rhodopsin, Opn1sw, and Opn1mw at 3 months in Asrgl1mut/mut mice compared with age-matched wildtype mice. Importantly, the retinal phenotype of Asrgl1mut/mut mice is consistent with the phenotype observed in patients harboring the G178R mutation in ASRGL1 confirming a critical role of ASRGL1 in the retina and the contribution of ASRGL1 mutations in retinal degeneration. Full article
(This article belongs to the Special Issue Screens, Genes, and Phenotypes)
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18 pages, 11215 KiB  
Article
PHEXL222P Mutation Increases Phex Expression in a New ENU Mouse Model for XLH Disease
by Carole El Hakam, Alexis Parenté, Fabienne Baraige, Laetitia Magnol, Lionel Forestier, Florent Di Meo and Véronique Blanquet
Genes 2022, 13(8), 1356; https://doi.org/10.3390/genes13081356 - 28 Jul 2022
Cited by 2 | Viewed by 2231
Abstract
PhexL222P mouse is a new ENU mouse model for XLH disease due to Leu to Pro amino acid modification at position 222. PhexL222P mouse is characterized by growth retardation, hypophosphatemia, hypocalcemia, reduced body bone length, and increased epiphyseal growth plate thickness [...] Read more.
PhexL222P mouse is a new ENU mouse model for XLH disease due to Leu to Pro amino acid modification at position 222. PhexL222P mouse is characterized by growth retardation, hypophosphatemia, hypocalcemia, reduced body bone length, and increased epiphyseal growth plate thickness and femur diameter despite the increase in PHEXL222P expression. Actually, PhexL222P mice show an increase in Fgf23, Dmp1, and Mepe and Slc34a1 (Na-Pi IIa cotransporter) mRNA expression similar to those observed in Hyp mice. Femoral osteocalcin and sclerostin and Slc34a1 do not show any significant variation in PhexL222P mice. Molecular dynamics simulations support the experimental data. P222 might locally break the E217-Q224 β-sheet, which in turn might disrupt inter-β-sheet interactions. We can thus expect local protein misfolding, which might be responsible for the experimentally observed PHEXL222P loss of function. This model could be a valuable addition to the existing XLH model for further comprehension of the disease occurrence and testing of new therapies. Full article
(This article belongs to the Special Issue Screens, Genes, and Phenotypes)
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24 pages, 2742 KiB  
Article
A Primer Genetic Toolkit for Exploring Mitochondrial Biology and Disease Using Zebrafish
by Ankit Sabharwal, Jarryd M. Campbell, Tanya L. Schwab, Zachary WareJoncas, Mark D. Wishman, Hirotaka Ata, Wiebin Liu, Noriko Ichino, Danielle E. Hunter, Jake D. Bergren, Mark D. Urban, Rhianna M. Urban, Shannon R. Holmberg, Bibekananda Kar, Alex Cook, Yonghe Ding, Xiaolei Xu, Karl J. Clark and Stephen C. Ekker
Genes 2022, 13(8), 1317; https://doi.org/10.3390/genes13081317 - 23 Jul 2022
Cited by 3 | Viewed by 3203
Abstract
Mitochondria are a dynamic eukaryotic innovation that play diverse roles in biology and disease. The mitochondrial genome is remarkably conserved in all vertebrates, encoding the same 37-gene set and overall genomic structure, ranging from 16,596 base pairs (bp) in the teleost zebrafish ( [...] Read more.
Mitochondria are a dynamic eukaryotic innovation that play diverse roles in biology and disease. The mitochondrial genome is remarkably conserved in all vertebrates, encoding the same 37-gene set and overall genomic structure, ranging from 16,596 base pairs (bp) in the teleost zebrafish (Danio rerio) to 16,569 bp in humans. Mitochondrial disorders are amongst the most prevalent inherited diseases, affecting roughly 1 in every 5000 individuals. Currently, few effective treatments exist for those with mitochondrial ailments, representing a major unmet patient need. Mitochondrial dysfunction is also a common component of a wide variety of other human illnesses, ranging from neurodegenerative disorders such as Huntington’s disease and Parkinson’s disease to autoimmune illnesses such as multiple sclerosis and rheumatoid arthritis. The electron transport chain (ETC) component of mitochondria is critical for mitochondrial biology and defects can lead to many mitochondrial disease symptoms. Here, we present a publicly available collection of genetic mutants created in highly conserved, nuclear-encoded mitochondrial genes in Danio rerio. The zebrafish system represents a potentially powerful new opportunity for the study of mitochondrial biology and disease due to the large number of orthologous genes shared with humans and the many advanced features of this model system, from genetics to imaging. This collection includes 15 mutant lines in 13 different genes created through locus-specific gene editing to induce frameshift or splice acceptor mutations, leading to predicted protein truncation during translation. Additionally, included are 11 lines created by the random insertion of the gene-breaking transposon (GBT) protein trap cassette. All these targeted mutant alleles truncate conserved domains of genes critical to the proper function of the ETC or genes that have been implicated in human mitochondrial disease. This collection is designed to accelerate the use of zebrafish to study many different aspects of mitochondrial function to widen our understanding of their role in biology and human disease. Full article
(This article belongs to the Special Issue Screens, Genes, and Phenotypes)
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