Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.1
3.5
Journals
Genes
Special Issues
CRISPR-Based Nucleic Acid Detection and Genome Editing in Animals
share announcement

CRISPR-Based Nucleic Acid Detection and Genome Editing in Animals

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

Deadline for manuscript submissions: closed (20 October 2023) | Viewed by 8000

Special Issue Editors

Prof. Dr. Shengsong Xie

E-Mail Website
Guest Editor
College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
Interests: gene editing breeding; CRISPR-based diagnostic; bioinformatics; functional genomics; pig
Prof. Dr. Jun Song

E-Mail Website
Guest Editor
College of Life Science, Northeast Agricultural University, Harbin 150030, China
Interests: gene editing; animal model; rabbit; immunodeficiency; humanization; embryo
Dr. Jinxue Ruan

E-Mail Website
Guest Editor
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
Interests: gene editing; CRISPR/Cas9; pig; animal model
Dr. Changzhi Zhao

E-Mail Website
Guest Editor
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
Interests: genome editing breeding; CRISPR-based diagnostic; CRISPR screen; epigenome editing; pig

Special Issue Information

Dear Colleagues,

Genome editing methods have resulted in profound changes in the field of molecular biology science. Beyond their widespread application as genome-editing and regulatory tools, CRISPR/Cas systems also play a critical role in nucleic acid detection due to their high sensitivity and specificity.

The basic aim of this Special Issue is to provide a platform for researchers, innovators, scholars and students worldwide to share their research with us. The scope of the Special Issue covers all areas of CRISPR-based nucleic acid detection and genome editing in animals, including, but not limited to: 

  1. New genome-editing tools and resources;
  2. Genome editing in animals;
  3. Novel nucleic acid detection strategies based on CRISPR/Cas;
  4. Functional Genomics via CRISPR/Cas;
  5. CRISPR-based enrichment strategies for targeted sequencing;
  6. Bioinformatic tools for CRISPR/Cas.

Cutting-edge research includes CRISPR-based diagnostics and genome editing in animals
In addition to primary research articles, we welcome the submission of review and opinion articles regarding recent advancements in research and issues of interest to the broad readership in this cutting-edge field.

Prof. Dr. Shengsong Xie
Prof. Dr. Jun Song
Dr. Jinxue Ruan
Dr. Changzhi Zhao
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

  • CRISPR-based diagnostics
  • genome editing
  • functional genomics
  • animals
  • CRISPR/Cas

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

13 pages, 2957 KiB  
Article
Highly Efficient A-to-G Editing in PFFs via Multiple ABEs
by Qiqi Jing, Weiwei Liu, Haoyun Jiang, Yaya Liao, Qiang Yang and Yuyun Xing
Genes 2023, 14(4), 908; https://doi.org/10.3390/genes14040908 - 13 Apr 2023
Cited by 1 | Viewed by 1233
Abstract
Cytosine base editors (CBEs) and adenine base editors (ABEs) are recently developed CRISPR-mediated genome-editing tools that do not introduce double-strand breaks. In this study, five ABEs, ABE7.10, ABEmax, NG-ABEmax, ABE8e and NG-ABE8e, were used to generate A-to-G (T-to-C) conversions in five genome loci [...] Read more.
Cytosine base editors (CBEs) and adenine base editors (ABEs) are recently developed CRISPR-mediated genome-editing tools that do not introduce double-strand breaks. In this study, five ABEs, ABE7.10, ABEmax, NG-ABEmax, ABE8e and NG-ABE8e, were used to generate A-to-G (T-to-C) conversions in five genome loci in porcine fetal fibroblasts (PFFs). Variable yet appreciable editing efficiencies and variable activity windows were observed in these targeting regions via these five editors. The strategy of two sgRNAs in one vector exhibited superior editing efficiency to that of using two separate sgRNA expression vectors. ABE-mediated start-codon mutation in APOE silenced its expression of protein and, unexpectedly, eliminated the vast majority of its mRNA. No off-target DNA site was detected for these editors. Substantial off-target RNA events were present in the ABE-edited cells, but no KEGG pathway was found to be significantly enriched. Our study supports that ABEs are powerful tools for A-to-G (T-to-C) point-mutation modification in porcine cells. Full article
(This article belongs to the Special Issue CRISPR-Based Nucleic Acid Detection and Genome Editing in Animals)
►▼ Show Figures

Figure 1

11 pages, 1559 KiB  
Article
Detecting Melanocortin 1 Receptor Gene’s SNPs by CRISPR/enAsCas12a
by Wei Yang, Dagang Tao, Bingrong Xu, Yueting Zheng and Shuhong Zhao
Genes 2023, 14(2), 394; https://doi.org/10.3390/genes14020394 - 02 Feb 2023
Viewed by 1575
Abstract
Beyond its powerful genome-editing capabilities, the CRISPR/Cas system has opened up a new era of molecular diagnostics due to its highly specific base recognition and trans-cleavage activity. However, most CRISPR/Cas detection systems are mainly used to detect nucleic acids of bacteria or viruses, [...] Read more.
Beyond its powerful genome-editing capabilities, the CRISPR/Cas system has opened up a new era of molecular diagnostics due to its highly specific base recognition and trans-cleavage activity. However, most CRISPR/Cas detection systems are mainly used to detect nucleic acids of bacteria or viruses, while the application of single nucleotide polymorphism (SNP) detection is limited. The MC1R SNPs were investigated by CRISPR/enAsCas12a and are not limited to the protospacer adjacent motif (PAM) sequence in vitro. Specifically, we optimized the reaction conditions, which proved that the enAsCas12a has a preference for divalent magnesium ion (Mg2+) and can effectively distinguish the genes with a single base difference in the presence of Mg2+, and the Melanocortin l receptor (MC1R) gene with three kinds of SNP sites (T305C, T363C, and G727A) was quantitatively detected. Since the enAsCas12a is not limited by PAM sequence in vitro, the method shown here can extend this extraordinary CRISPR/enAsCas12a detection system to other SNP targets, thus providing a general SNP detection toolbox. Full article
(This article belongs to the Special Issue CRISPR-Based Nucleic Acid Detection and Genome Editing in Animals)
►▼ Show Figures

Figure 1

11 pages, 888 KiB  
Article
CCR4-NOT Complex 2—A Cofactor in Host Cell for Porcine Epidemic Diarrhea Virus Infection
by Jieru Wang, Hailong Liu, Dongdong Yin, Mei Zhou, Lei Yin, Yuqing Yang, Zishi Guo, Xuehuai Shen, Yin Dai, Shaohua Shi, Shengsong Xie, Ruihong Zhao, Xueli Zhou, Xiaomiao Hu, Hongyan Hou, Chonglong Wang and Xiaocheng Pan
Genes 2022, 13(9), 1504; https://doi.org/10.3390/genes13091504 - 23 Aug 2022
Cited by 2 | Viewed by 1643
Abstract
The porcine epidemic diarrhea virus (PEDV) has catastrophic impacts on the global pig industry. However, there is no consensus on the primary receptor associated with the PEDV invasion of host cells. An increasing number of studies have reported that PEDV invading host cells [...] Read more.
The porcine epidemic diarrhea virus (PEDV) has catastrophic impacts on the global pig industry. However, there is no consensus on the primary receptor associated with the PEDV invasion of host cells. An increasing number of studies have reported that PEDV invading host cells may require collaboration between multiple receptors and to better understand the virus-host interaction during PEDV entry, surface plasmon resonance (SPR) assays are performed to investigate relevant host factors interacting with PEDV spike-1 protein (S1) in Vero and IPEC-J2 cell membranes. Subsequently, the rabbit anti-PEDV S1 polyclonal antibody is used as bait to recognize the complexes of IPEC-J2 membrane proteins with or without PEDV infection, followed by detection using liquid chromatography with tandem mass spectrometry (LC-MS-MS). Our results show that 13 and 10 proteins interacting between the S1 protein and plasma membrane protein of Vero or IPEC-J2 can be identified. More specifically, a total of 11 differentially expressed interacting proteins were identified in IPEC-J2 membrane proteins after PEDV infection, compared to the uninfected group. Furthermore, we found that the differentially interacting protein CCR4-NOT complex 2 (CNOT2), identified in PEDV S1 with plasma membrane proteins of Vero cells, is involved in viral infection. The results show that the knockout of CNOT2 significantly inhibits PEDV replication in vitro. These data provide novel insights into the entry mechanism of PEDV. Full article
(This article belongs to the Special Issue CRISPR-Based Nucleic Acid Detection and Genome Editing in Animals)
►▼ Show Figures

Figure 1

Review

Jump to: Research

25 pages, 973 KiB  
Review
Development of CRISPR-Mediated Nucleic Acid Detection Technologies and Their Applications in the Livestock Industry
by Xuying Zhang
Genes 2022, 13(11), 2007; https://doi.org/10.3390/genes13112007 - 02 Nov 2022
Cited by 4 | Viewed by 2978
Abstract
The rapid rate of virus transmission and pathogen mutation and evolution highlight the necessity for innovative approaches to the diagnosis and prevention of infectious diseases. Traditional technologies for pathogen detection, mostly PCR-based, involve costly/advanced equipment and skilled personnel and are therefore not feasible [...] Read more.
The rapid rate of virus transmission and pathogen mutation and evolution highlight the necessity for innovative approaches to the diagnosis and prevention of infectious diseases. Traditional technologies for pathogen detection, mostly PCR-based, involve costly/advanced equipment and skilled personnel and are therefore not feasible in resource-limited areas. Over the years, many promising methods based on clustered regularly interspaced short palindromic repeats and the associated protein systems (CRISPR/Cas), i.e., orthologues of Cas9, Cas12, Cas13 and Cas14, have been reported for nucleic acid detection. CRISPR/Cas effectors can provide one-tube reaction systems, amplification-free strategies, simultaneous multiplex pathogen detection, visual colorimetric detection, and quantitative identification as alternatives to quantitative PCR (qPCR). This review summarizes the current development of CRISPR/Cas-mediated molecular diagnostics, as well as their design software and readout methods, highlighting technical improvements for integrating CRISPR/Cas technologies into on-site applications. It further highlights recent applications of CRISPR/Cas-based nucleic acid detection in livestock industry, including emerging infectious diseases, authenticity and composition of meat/milk products, as well as sex determination of early embryos. Full article
(This article belongs to the Special Issue CRISPR-Based Nucleic Acid Detection and Genome Editing in Animals)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop