scholarly journals Mutations in a β-group of solute carrier gene are responsible for egg and eye coloration of the brown egg 4 (b-4) mutant in the silkworm, Bombyx mori

2021 ◽  
Author(s):  
Kenta Tomihara ◽  
Katsuya Satta ◽  
Shohei Matsuzaki ◽  
Kazutoshi Yoshitake ◽  
Kimiko Yamamoto ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Gene Knockout ◽  
Exon Skipping ◽  
Mutant Gene ◽  
Compound Eyes ◽  
Reading Frame ◽  
Eye Color ◽  
Solute Carrier ◽  
Reddish Brown Color ◽  
Brown Color

The brown egg 4 (b-4) is a recessive mutant in the silkworm (Bombyx mori), whose egg and adult compound eyes exhibit a reddish-brown color instead of normal purple and black, respectively. By double digest restriction-site associated DNA sequencing (ddRAD-seq) analysis, we narrowed down a region linked to the b-4 phenotype to approximately 1.1 Mb that contains 69 predicted gene models. RNA-seq analysis in a b-4 strain indicated that one of the candidate genes had a different transcription start site, which generates a short open reading frame. We also found that exon skipping was induced in the same gene due to an insertion of a transposable element in other two b-4 mutant strains. This gene encoded a putative amino acid transporter that belongs to the β-group of solute carrier (SLC) family and is orthologous to Drosophila eye color mutant gene, mahogany (mah). Accordingly, we named this gene Bmmah. We performed CRISPR/Cas9-mediated gene knockout targeting Bmmah. Several adult moths in generation 0 (G0) had totally or partially reddish-brown compound eyes. We also established three Bmmah knockout strains, all of which exhibit reddish-brown eggs and adult compound eyes. Furthermore, eggs from complementation crosses between the b-4 mutants and the Bmmah knockout mutants also exhibited reddish-brown color, which was similar to the b-4 mutant eggs, indicating that Bmmah is responsible for the b-4 phenotypes.

scholarly journals Evaluating the potential of novel genetic approaches for the treatment of Duchenne muscular dystrophy

2021 ◽  
Author(s):  
Vratko Himič ◽  
Kay E. Davies
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Structural Integrity ◽  
Viral Vector ◽  
Exon Skipping ◽  
Dystrophin Gene ◽  
Pharmacological Treatments ◽  
Genetic Sequencing ◽  
Reading Frame ◽  
Target Effects

AbstractDuchenne muscular dystrophy (DMD) is an X-linked progressive muscle-wasting disorder that is caused by a lack of functional dystrophin, a cytoplasmic protein necessary for the structural integrity of muscle. As variants in the dystrophin gene lead to a disruption of the reading frame, pharmacological treatments have only limited efficacy; there is currently no effective therapy and consequently, a significant unmet clinical need for DMD. Recently, novel genetic approaches have shown real promise in treating DMD, with advancements in the efficacy and tropism of exon skipping and surrogate gene therapy. CRISPR-Cas9 has the potential to be a ‘one-hit’ curative treatment in the coming decade. The current limitations of gene editing, such as off-target effects and immunogenicity, are in fact partly constraints of the delivery method itself, and thus research focus has shifted to improving the viral vector. In order to halt the loss of ambulation, early diagnosis and treatment will be pivotal. In an era where genetic sequencing is increasingly utilised in the clinic, genetic therapies will play a progressively central role in DMD therapy. This review delineates the relative merits of cutting-edge genetic approaches, as well as the challenges that still need to be overcome before they become clinically viable.

scholarly journals Polypurine Reverse-Hoogsteen Hairpins as a Tool for Exon Skipping at the Genomic Level in Mammalian Cells

2021 ◽  
Vol 22 (7) ◽  
pp. 3784
Author(s):  
Véronique Noé ◽  
Carlos J. Ciudad
Keyword(s):  
Dna Sequencing ◽  
Rare Diseases ◽  
Mammalian Cells ◽  
Mrna Level ◽  
Exon Skipping ◽  
Selective Medium ◽  
Rt Pcr ◽  
Exon 2 ◽  
Reading Frame ◽  
Additional Exon

Therapeutic strategies for rare diseases based on exon skipping are aimed at mediating the elimination of mutated exons and restoring the reading frame of the affected protein. We explored the capability of polypurine reverse-Hoogsteen hairpins (PPRHs) to cause exon skipping in NB6 cells carrying a duplication of exon 2 of the DHFR gene that causes a frameshift abolishing DHFR activity. Methods: Different editing PPRHs were designed and transfected in NB6 cells followed by incubation in a DHFR-selective medium lacking hypoxanthine and thymidine. Surviving colonies were analyzed by DNA sequencing, RT-PCR, Western blotting and DHFR enzymatic activity. Results: Transfection of editing PPRHs originated colonies in the DHFR-selective medium. DNA sequencing results proved that the DHFR sequence in all these colonies corresponded to the wildtype sequence with just one copy of exon 2. In the edited colonies, the skipping of the additional exon was confirmed at the mRNA level, the DHFR protein was restored, and it showed high levels of DHFR activity. Conclusions: Editing-PPRHs are able to cause exon skipping at the DNA level and could be applied as a possible therapeutic tool for rare diseases.

scholarly journals Personalized Development of Antisense Oligonucleotides for Exon Skipping Restores Type XVII Collagen Expression in Junctional Epidermolysis Bullosa

2021 ◽  
Vol 22 (7) ◽  
pp. 3326
Author(s):  
Michael Ablinger ◽  
Thomas Lettner ◽  
Nicole Friedl ◽  
Hannah Potocki ◽  
Theresa Palmetzhofer ◽  
...  
Keyword(s):  
Epidermolysis Bullosa ◽  
Antisense Oligonucleotides ◽  
Exon Skipping ◽  
Junctional Epidermolysis Bullosa ◽  
Reading Frame ◽  
Collagen Expression ◽  
Promising Tool ◽  
Mucous Membranes ◽  
Personalized Approach ◽  
Xvii Collagen

Intermediate junctional epidermolysis bullosa caused by mutations in the COL17A1 gene is characterized by the frequent development of blisters and erosions on the skin and mucous membranes. The rarity of the disease and the heterogeneity of the underlying mutations renders therapy developments challenging. However, the high number of short in-frame exons facilitates the use of antisense oligonucleotides (AON) to restore collagen 17 (C17) expression by inducing exon skipping. In a personalized approach, we designed and tested three AONs in combination with a cationic liposomal carrier for their ability to induce skipping of COL17A1 exon 7 in 2D culture and in 3D skin equivalents. We show that AON-induced exon skipping excludes the targeted exon from pre-mRNA processing, which restores the reading frame, leading to the expression of a slightly truncated protein. Furthermore, the expression and correct deposition of C17 at the dermal–epidermal junction indicates its functionality. Thus, we assume AON-mediated exon skipping to be a promising tool for the treatment of junctional epidermolysis bullosa, particularly applicable in a personalized manner for rare genotypes.

Characterization of the open reading frame 7a from Bombyx mori nucleopolyhedrovirus

2012 ◽  
Vol 40 (2) ◽  
pp. 865-873
Author(s):  
Yong Liu ◽  
Feng Yu ◽  
Huiling Wu ◽  
Qing Cao ◽  
Yu Wu ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Open Reading Frame ◽  
Bombyx Mori Nucleopolyhedrovirus ◽  
Reading Frame

Mutations in a β-group of solute carrier gene are responsible for egg and eye coloration of the brown egg 4 (b-4) mutant in the silkworm, Bombyx mori

2021 ◽  
pp. 103624
Author(s):  
Kenta Tomihara ◽  
Katsuya Satta ◽  
Shohei Matsuzaki ◽  
Kazutoshi Yoshitake ◽  
Kimiko Yamamoto ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Solute Carrier ◽  
Silkworm Bombyx Mori

scholarly journals Bombyx mori β-1,3-Glucan Recognition Protein 4 (BmβGRP4) Could Inhibit the Proliferation of B. mori Nucleopolyhedrovirus through Promoting Apoptosis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 743
Author(s):  
Jie Wang ◽  
Lin-Bao Zhu ◽  
Yan Ma ◽  
Ying-Xue Liu ◽  
Hui-Hua Cao ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Protein Gene ◽  
Phosphatase And Tensin Homolog ◽  
Reading Frame ◽  
Larval Stages ◽  
Tensin Homolog ◽  
Transcriptome Database ◽  
Recognition Protein ◽  
Apoptosis Gene ◽  
Bmn Cells

β-1,3-glucan recognition proteins (βGRPs) as pattern recognition receptors (PRRs) play an important role in recognizing various pathogens and trigger complicated signaling pathways in insects. In this study, we identified a Bombyx mori β-1,3-glucan recognition protein gene named BmβGRP4, which showed differential expression, from a previous transcriptome database. The full-length cDNA sequence was 1244 bp, containing an open reading frame (ORF) of 1128 bp encoding 375 amino acids. BmβGRP4 was strongly expressed in the larval stages and highly expressed in the midgut of B. mori larvae in particular. After BmNPV infection, the expression of BmβGRP4 was reduced significantly in the midgut. Furthermore, a significant increase in the copy number of BmNPV was observed after the knockdown of BmβGRP4 in 5th instar larvae, while the overexpression of BmβGRP4 suppressed the proliferation of BmNPV in BmN cells. Subsequently, the expression analysis of several apoptosis-related genes and observation of the apoptosis morphology demonstrated that overexpression of BmβGRP4 facilitated apoptosis induced by BmNPV in BmN cells. Moreover, BmβGRP4 positively regulated the phosphatase and tensin homolog gene (BmPTEN), while expression of the inhibitor of apoptosis gene (BmIAP) was negatively regulated by BmβGRP4. Hence, we hypothesize that BmNPV infection might suppress BmPTEN and facilitate BmIAP to inhibit cell apoptosis by downregulating the expression of BmβGRP4 to escape host antiviral defense. Taken together, these results show that BmβGRP4 may play a role in B. mori response to BmNPV infection and lay a foundation for studying its functions.

scholarly journals Combination Antisense Treatment for Destructive Exon Skipping of Myostatin and Open Reading Frame Rescue of Dystrophin in Neonatal mdx Mice

2015 ◽  
Vol 23 (8) ◽  
pp. 1341-1348 ◽  
Author(s):  
Ngoc B Lu-Nguyen ◽  
Susan A Jarmin ◽  
Amer F Saleh ◽  
Linda Popplewell ◽  
Michael J Gait ◽  
...  
Keyword(s):  
Exon Skipping ◽  
Open Reading Frame ◽  
Mdx Mice ◽  
Reading Frame

Open reading frame 60 of the Bombyx mori nucleopolyhedrovirus plays a role in budded virus production

2010 ◽  
Vol 151 (2) ◽  
pp. 185-191 ◽  
Author(s):  
Zhong-Jian Guo ◽  
Li-Hua Qiu ◽  
Shi-Heng An ◽  
Qin Yao ◽  
Enoch Y. Park ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Virus Production ◽  
Open Reading Frame ◽  
Bombyx Mori Nucleopolyhedrovirus ◽  
Reading Frame ◽  
Budded Virus

scholarly journals ExonSkipDB: functional annotation of exon skipping event in human

2019 ◽  
Author(s):  
Pora Kim ◽  
Mengyuan Yang ◽  
Ke Yiya ◽  
Weiling Zhao ◽  
Xiaobo Zhou
Keyword(s):  
Functional Annotation ◽  
Exon Skipping ◽  
Tissue Expression ◽  
The Cancer Genome Atlas ◽  
Multiple Cancer ◽  
Annotation Database ◽  
Reading Frame ◽  
Normal Tissues ◽  
Cancer Genome Atlas ◽  
Functional Features

AbstractExon skipping (ES) is reported to be the most common alternative splicing event due to loss of functional domains/sites or shifting of the open reading frame (ORF), leading to a variety of human diseases and considered therapeutic targets. To date, systematic and intensive annotations of ES events based on the skipped exon units in cancer and normal tissues are not available. Here, we built ExonSkipDB, the ES annotation database available at https://ccsm.uth.edu/ExonSkipDB/, aiming to provide a resource and reference for functional annotation of ES events in multiple cancer and tissues to identify therapeutically targetable genes in individual exon units. We collected 14 272 genes that have 90 616 and 89 845 ES events across 33 cancer types and 31 normal tissues from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). For the ES events, we performed multiple functional annotations. These include ORF assignment of exon skipped transcript, studies of lost protein functional features due to ES events, and studies of exon skipping events associated with mutations and methylations based on multi-omics evidence. ExonSkipDB will be a unique resource for cancer and drug research communities to identify therapeutically targetable exon skipping events.

scholarly journals Nucleotide sequences of segments 1, 3 and 4 of the genome of Bombyx mori cypovirus 1 encoding putative capsid proteins VP1, VP3 and VP4, respectively

2002 ◽  
Vol 83 (6) ◽  
pp. 1477-1482 ◽  
Author(s):  
Kyoji Hagiwara ◽  
Shujing Rao ◽  
Simon W. Scott ◽  
Gerald R. Carner
Keyword(s):  
Amino Acids ◽  
Bombyx Mori ◽  
Nucleotide Sequences ◽  
Open Reading Frame ◽  
Capsid Proteins ◽  
Structural Proteins ◽  
Reading Frame ◽  
The Family ◽  
Molecular Masses ◽  
Rice Ragged Stunt Virus

The complete nucleotide sequences of genomic segments S1, S3 and S4 from Bombyx mori cypovirus 1 (BmCPV-1) have been determined. The segments consisted of 4190, 3846 and 3262 nucleotides encoding putative proteins of 1333, 1239 and 1058 amino acids with molecular masses of approximately 148, 140 and 120 kDa (p148, p140 and p120, respectively). All segments possess a single open reading frame. Homology searches showed that all three proteins have homologies to proteins of Rice ragged stunt virus, a member of the genus Oryzavirus within the family Reoviridae. Partial homologies of p140 to structural proteins in other viruses were also found. The predicted molecular masses and the homologies with structural proteins in other viruses lead us to suggest that S1, S3 and S4 encode the capsid proteins VP1, VP3, and VP4, respectively, of BmCPV-1.

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