Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Special Issue "RNA-Targeting CRISPR Systems"

Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (20 August 2023) | Viewed by 5716

Share This Special Issue

Special Issue Editor

Dr. Giancarlo Russo

E-Mail Website
Guest Editor

EMBL Partner Institute for Gene Editing, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
Interests: CRISPR-Cas; microbiology; next-generation sequencing; bioinformatics data analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (Cas) systems are mechanisms of acquired defense in prokaryotes. CRISPR arrays are DNA stretches in the prokaryote genomic that store short genomic sequences (spacers) of bacteriophages from past attacks. Upon a new phage challenge, these spacers are spliced and the resulting RNA acts as a guide to binding to the complementary sequence in the attacking phage; the associated Cas effector then cleaves the phage DNA and the viral threat is neutralized.

Since their discovery, CRISPR-Cas systems have been engineered into the most promising genome editing tool: a programmable effector deliverable anywhere in a genomic sequence to modify a nucleotide sequence.

Initially, it seemed that CRISPR-Cas systems were capable of targeting exclusively DNA. Later it has been discovered that they can also cleave RNA. The main advantage of RNA-targeting CRISPR-Cas is that they act on a transient entity, therefore allowing modifications that might otherwise be deleterious or lethal if applied to the genome.

This Special Issue will focus on the growing number of applications of RNA-targeting CRISPR-Cas-based editing, such as transcriptional repression, RNA editing, guided isoform splicing, nucleic acid detection, expression regulation, and viral resistance. Additional suggested topics include RNA-targeting CRISPR systems structures and mechanisms of action, off-target activity in CRISPR-mediated RNA cleavage, and in silico methods for the discovery of new systems.

Dr. Giancarlo Russo
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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-Cas
Cas13
Cmr
Csm
RNA editing
RNA knockdown
CRISPRi
off-target effects

Published Papers (4 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review, Other

Open AccessArticle

Site-Specific RNA Editing of Stop Mutations in the CFTR mRNA of Human Bronchial Cultured Cells

and

Int. J. Mol. Sci. 2023, 24(13), 10940; https://doi.org/10.3390/ijms241310940 - 30 Jun 2023

Viewed by 625

Abstract

It is reported that about 10% of cystic fibrosis (CF) patients worldwide have nonsense (stop) mutations in the CFTR gene, which cause the premature termination of CFTR protein synthesis, leading to a truncated and non-functional protein. To address this issue, we investigated the possibility of rescuing the CFTR nonsense mutation (UGA) by sequence-specific RNA editing in CFTR mutant CFF-16HBEge, W1282X, and G542X human bronchial cells. We used two different base editor tools that take advantage of ADAR enzymes (adenosine deaminase acting on RNA) to edit adenosine to inosine (A-to-I) within the mRNA: the REPAIRv2 (RNA Editing for Programmable A to I Replacement, version 2) and the minixABE (A to I Base Editor). Immunofluorescence experiments show that both approaches were able to recover the CFTR protein in the CFTR mutant cells. In addition, RT-qPCR confirmed the rescue of the CFTR full transcript. These findings suggest that site-specific RNA editing may efficiently correct the UGA premature stop codon in the CFTR transcript in CFF-16HBEge, W1282X, and G542X cells. Thus, this approach, which is safer than acting directly on the mutated DNA, opens up new therapeutic possibilities for CF patients with nonsense mutations. Full article

(This article belongs to the Special Issue RNA-Targeting CRISPR Systems)

► Show Figures

Figure 1

Open AccessArticle

Harnessing the LdCsm RNA Detection Platform for Efficient microRNA Detection

Zhenxiao Yu

Jianan Xu

and

Qunxin She

Int. J. Mol. Sci. 2023, 24(3), 2857; https://doi.org/10.3390/ijms24032857 - 02 Feb 2023

Viewed by 1124

Abstract

In cancer diagnosis, diverse microRNAs (miRNAs) are used as biomarkers for carcinogenesis of distinctive human cancers. Thus, the detection of these miRNAs and their quantification are very important in prevention of cancer diseases in human beings. However, efficient RNA detection often requires RT-PCR, which is very complex for miRNAs. Recently, the development of CRISPR-based nucleic acid detection tools has brought new promises to efficient miRNA detection. Three CRISPR systems can be explored for miRNA detection, including type III, V, and VI, among which type III (CRISPR-Cas10) systems have a unique property as they recognize RNA directly and cleave DNA collaterally. In particular, a unique type III-A Csm system encoded by Lactobacillus delbrueckii subsp. bulgaricus (LdCsm) exhibits robust target RNA-activated DNase activity, which makes it a promising candidate for developing efficient miRNA diagnostic tools. Herein, LdCsm was tested for RNA detection using fluorescence-quenched DNA reporters. We found that the system is capable of specific detection of miR-155, a microRNA implicated in the carcinogenesis of human breast cancer. The RNA detection system was then improved by various approaches including assay conditions and modification of the 5′-repeat tag of LdCsm crRNAs. Due to its robustness, the resulting LdCsm detection platform has the potential to be further developed as a better point-of-care miRNA diagnostics relative to other CRISPR-based RNA detection tools. Full article

(This article belongs to the Special Issue RNA-Targeting CRISPR Systems)

► Show Figures

Figure 1

Review

Jump to: Research, Other

Open AccessReview

RNA-Dependent RNA Targeting by CRISPR-Cas Systems: Characterizations and Applications

and

Int. J. Mol. Sci. 2023, 24(8), 6894; https://doi.org/10.3390/ijms24086894 - 07 Apr 2023

Cited by 1 | Viewed by 1331

Abstract

Genome editing technologies that are currently available and described have a fundamental impact on the development of molecular biology and medicine, industrial and agricultural biotechnology and other fields. However, genome editing based on detection and manipulation of the targeted RNA is a promising alternative to control the gene expression at the spatiotemporal transcriptomic level without complete elimination. The innovative CRISPR-Cas RNA-targeting systems changed the conception of biosensing systems and also allowed the RNA effectors to be used in various applications; for example, genomic editing, effective virus diagnostic tools, biomarkers, transcription regulations. In this review, we discussed the current state-of-the-art of specific CRISPR-Cas systems known to bind and cleave RNA substrates and summarized potential applications of the versatile RNA-targeting systems. Full article

(This article belongs to the Special Issue RNA-Targeting CRISPR Systems)

► Show Figures

Figure 1

Other

Jump to: Research, Review

Open AccessPerspective

Current Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects

Muhammad Naeem

and

Omer S. Alkhnbashi

Int. J. Mol. Sci. 2023, 24(7), 6261; https://doi.org/10.3390/ijms24076261 - 27 Mar 2023

Cited by 2 | Viewed by 2136

Abstract

The CRISPR-Cas system has evolved into a cutting-edge technology that has transformed the field of biological sciences through precise genetic manipulation. CRISPR/Cas9 nuclease is evolving into a revolutionizing method to edit any gene of any species with desirable outcomes. The swift advancement of CRISPR-Cas technology is reflected in an ever-expanding ecosystem of bioinformatics tools designed to make CRISPR/Cas9 experiments easier. To assist researchers with efficient guide RNA designs with fewer off-target effects, nuclease target site selection, and experimental validation, bioinformaticians have built and developed a comprehensive set of tools. In this article, we will review the various computational tools available for the assessment of off-target effects, as well as the quantification of nuclease activity and specificity, including web-based search tools and experimental methods, and we will describe how these tools can be optimized for gene knock-out (KO) and gene knock-in (KI) for model organisms. We also discuss future directions in precision genome editing and its applications, as well as challenges in target selection, particularly in predicting off-target effects. Full article

(This article belongs to the Special Issue RNA-Targeting CRISPR Systems)

► Show Figures

Journal Menu

Journal Browser

Special Issue "RNA-Targeting CRISPR Systems"

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Published Papers (4 papers)

Research

Review

Other

Further Information

Guidelines

MDPI Initiatives

Follow MDPI