Tag: Cas13d

CRISPR-Cas13d screens identify KILR a breast cancer risk-associated lncRNA that regulates DNA replication and repair.

Abstract Long noncoding RNAs (lncRNAs) have surpassed the number of protein-coding genes, yet the majority have no known function. We previously discovered >800 lncRNAs at regions identified by breast cancer genome-wide association studies (GWAS). Here, we performed a pooled CRISPR-Cas13d RNA knockdown screen to identify which of these lncRNAs altered…

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Cas13’s Intrinsic Targeting of Host RNA Limits Its Utility

Cas13 is capable of intrinsically targeting host RNA in mammalian cells through mechanisms that were not previously understood. Through transcript-specific mechanisms that are independent of the CRISPR RNA sequence and dynamically dependent on the conformational state of Cas13, Cas13 can also cleave host RNA. This effect is demonstrated by a…

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Intrinsic targeting of host RNA by Cas13 constrains its utility

Abudayyeh, O. O. et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353, aaf5573 (2016). Article  PubMed  PubMed Central  Google Scholar  Terns, M. P. CRISPR-based technologies: impact of RNA-targeting systems. Mol. Cell 72, 404–412 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Abudayyeh, O. O. et al….

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Mitigating a TDP-43 proteinopathy by concentrating on ataxin-2 utilizing

Concentrating on ataxin-2 with RfxCas13d Due to its potential to affect TDP-43-associated toxicity20,25,26, ataxin-2 has emerged as a doubtlessly broadly relevant goal for ALS-FTD, as TDP-43 pathology is noticed in ~97% of ALS instances1,4,5 and ~45% FTD occurrences1,2,4. Given this, we sought to find out if RNA-targeting CRISPR effector proteins…

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Locanabio Announces Participation in Chardan’s 7th Annual Genetic Medicines Conference

Locanabio, Inc. SAN DIEGO, Sept. 25, 2023 (GLOBE NEWSWIRE) — Locanabio, Inc., a genetic medicines company developing RNA-targeted therapeutics for patients with rare genetic neuromuscular and neurodegenerative diseases, today announced that Jim Burns, Ph.D., Locanabio’s chief executive officer, will provide a corporate overview at 5:30 pm. ET on Monday, October…

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Precision RNA base editing with engineered and endogenous effectors

Gray, M. W. Evolutionary origin of RNA editing. Biochemistry 51, 5235–5242 (2012). Article  CAS  PubMed  Google Scholar  Covello, P. & Gray, M. On the evolution of RNA editing. Trends Genet. 9, 265–268 (1993). Article  CAS  PubMed  Google Scholar  Yablonovitch, A. L., Deng, P., Jacobson, D. & Li, J. B. The…

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Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox

Abstract Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental…

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Novel epigenetic molecular therapies for imprinting disorders

Surani MA, Barton SC, Norris ML. Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature. 1984;308:548–50. Article  CAS  PubMed  Google Scholar  McGrath J, Solter D. Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell. 1984;37:179–83. Article  CAS  PubMed  Google Scholar  Barlow DP, Stoger…

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Cas13d-mediated multiplex RNA targeting confers a broad-spectrum resistance against RNA viruses in potato

Boualem, A., Dogimont, C. & Bendahmane, A. The battle for survival between viruses and their host plants. Curr. Opin. Virol. 17, 32–38 (2016). Article  CAS  PubMed  Google Scholar  Rashid, M. O., Wang, Y. & Han, C. G. Molecular detection of potato viruses in Bangladesh and their phylogenetic analysis. Plants 9,…

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Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells

Bourque, G. et al. Ten things you should know about transposable elements. Genome Biol. 19, 199 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18, 71–86 (2017). Article  CAS …

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RNA Editing Tool Predicts Target Performance With Pooled Screening, Machine Learning

In a paper appearing in Nature Biotechnology, a team from New York Genome Center, New York University, and Columbia University outline a deep learning and CRISPR-Cas13d-based RNA editing strategy for gauging the on-target gene expression effects of transcriptome engineering in human cells. With an approach dubbed “targeted inhibition of gene…

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AI Predicts Activity of RNA-Targeting CRISPR Tools

Researchers at New York University (NYU), Columbia University, and the New York Genome Center have developed an artificial intelligence (AI) platform that can predict on- and off-target activity of CRISPR tools that target RNA instead of DNA. The team paired a deep learning model with CRISPR screens to control the…

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Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing

Background: The CRISPR/Cas12a and CRISPR/Cas13d systems are widely used for fundamental research and hold great potential for future clinical applications. However, the short half-life of guide RNAs (gRNAs), particularly free gRNAs without Cas nuclease binding, limits their editing efficiency and durability. Results: Here, we engineer circular free gRNAs (cgRNAs) to…

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Sometimes Experiments Don’t Go As Expected (and That’s Not Bad)

The COVID-19 pandemic that emerged in early 2020 has affected all of us in many ways. Also for a group of people who are dedicated to research. Many of us have been wondering what we can do to help solve this tremendous global health problem, which has been progressing uncontrollably…

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Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing,Genome Biology

Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing Genome Biology ( IF 17.906 ) Pub Date : 2023-06-23 , DOI: 10.1186/s13059-023-02992-z Xin Zhang, Xinlong…

Continue Reading Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing,Genome Biology

Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing | Genome Biology

Plasmid construction For U6+27 gRNA-expressing constructs, the DNA sequences including the hU6+27 promoter, a gRNA scaffold, and a gRNA insert site were synthesized and cloned into the pBluSKM vector. For Pre gRNA-expressing constructs, a second gRNA scaffold was inserted downstream of the gRNA insert site in the U6+27 gRNA-expressing constructs….

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Locanabio experimental therapy shows promise for C9ORF72 ALS

Locanabio‘s investigational therapy significantly reduced the buildup of toxic RNA molecules in amyotrophic lateral sclerosis (ALS) patient cells and mouse models associated with C9ORF72 mutations, according to new data. These RNA products — intermediate molecules that are produced from DNA as a template for protein production — are associated with…

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Locanabio Presents Preclinical Data from its Vectorized snRNA Exon Skipping Program for DMD and Cas13d Multi-targeting Program for C9orf72 ALS at the American Society of Gene and Cell Therapy (ASGCT) 26th Annual Meeting

Locanabio, Inc. LBIO-115 demonstrates robust exon 51 skipping resulting in high levels of dystrophin restoration in patient-derived muscle cells and an in vivo DMD disease model Cas13d Multi-targeting efficiently knocks down both sense and antisense toxic RNAs and decreases dipeptide repeats in C9orf72 ALS patient fibroblasts and an in vivo…

Continue Reading Locanabio Presents Preclinical Data from its Vectorized snRNA Exon Skipping Program for DMD and Cas13d Multi-targeting Program for C9orf72 ALS at the American Society of Gene and Cell Therapy (ASGCT) 26th Annual Meeting

Targeted knock-ins with pseudovirus for the stable expression of large transgenes

Integrase-deficient lentivirus (IDLV) enables reverse transcription of an encoded payload from an RNA molecule into a DNA template, which creates a useful yet low-efficiency donor for HDR. We engineered the IDLV genome to include CRISPR ‘cut sites’ that match the intended genomic cut site (Fig. 1). Cas9 ribonucleoprotein electroporated into…

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CRISPR/Cas13d-Mediated Mutant Huntingtin Elimination

Huntington’s disease (HD) is a late-onset, fatal neurodegenerative disorder with no cure; currently available treatments merely provide modest relief of symptoms. HD is caused by a gain-of-function mutation: a trinucleotide repeat hyperexpansion in the first intron of the HTT gene, which codes for the Huntingtin protein. Spearheaded by collaborators Dr….

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Locanabio Announces Presentations at the American Society of Gene and Cell Therapy (ASGCT) 26th Annual Meeting

Locanabio, Inc. Locanabio to report preclinical data from snRNA exon skipping program in DMD and Cas13d-mediated C9orf72 ALS program SAN DIEGO, May 02, 2023 (GLOBE NEWSWIRE) — Locanabio, Inc., a genetic medicines company developing RNA-targeted therapeutics for patients with rare genetic neuromuscular and neurodegenerative diseases, today announced that data from…

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Stable expression of large transgenes via the knock-in of an integrase-deficient lentivirus

CLIP enables high-efficiency knock-in into an essential locus To create CLIP, we leverage integrase-deficient lentiviruses (IDLV) to deliver an HDR donor template as a viral RNA genome to cells25,26. IDLV consists of lentiviral components but with a D64V mutation in the integrase, maintaining this enzyme’s ability to package and nuclear…

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Revolutionizing viral disease vaccination: the promising clinical advancements of non-replicating mRNA vaccines | Virology Journal

To KK-W, Sridhar S, Chiu KH-Y, Hung DL-L, Li X, Hung IF-N, Tam AR, Chung TW-H, Chan JF-W, Zhang AJ-X, et al. Lessons learned 1 year after SARS-CoV-2 emergence leading to COVID-19 pandemic. Emerg Microbes Infect. 2021;10(1):507–35. Article  CAS  PubMed  PubMed Central  Google Scholar  Gao Q, Bao L, Mao H,…

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Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d

ABSTRACT Type VI CRISPR enzymes cleave target RNAs and are widely used for gene regulation, RNA tracking, and diagnostics. However, a systematic understanding of their RNA binding specificity and cleavage activation is lacking. Here, we describe RNA chip-hybridized association-mapping platform (RNA-CHAMP), a massively parallel platform that repurposes next-generation DNA sequencing…

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Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2

Affiliations Expand Affiliations 1 Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands. 2 Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain. Free PMC article Item in…

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Orthogonally Activatable CRISPR-Cas13d Nanoprodrug to Reverse Chemoresistance for Enhanced Chemo-Photodynamic Therapy

Orthogonal therapy that combines CRISPR-based gene editing and prodrug-based chemotherapy is a promising approach to combat multidrug-resistant cancer. However, its potency to precisely regulate different therapeutic modalities in vivo is limited due to the lack of integrated platform with high spatiotemporal resolution. Taking advantage of CRISPR technology, Pt(IV)-based prodrug and…

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Bioconductor – crisprDesign (development version)

DOI: 10.18129/B9.bioc.crisprDesign   This is the development version of crisprDesign; for the stable release version, see crisprDesign. Comprehensive design of CRISPR gRNAs for nucleases and base editors Bioconductor version: Development (3.17) Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and…

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Oz Biosciences Cas13d Genome E | MRNA27-1000 | OZ BIOSCIENCES

Plasmids and viral vectors are traditionally used in CRISPR genome editing to express the required proteins. However, there is a risk to use DNA instead of mRNA: double stranded DNA breaks catalyse insertion of DNA at the cut site. At some substantial frequency, the protein expression vectors can integrate, which…

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Viruses | Free Full-Text | Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2

Figure 1. Replication cycle of SARS-CoV-2 and genome organization. (A) The SARS-CoV-2 replication cycle. Binding of the viral S protein to the ACE-2 receptor triggers SARS-CoV-2 infection and the plus genomic RNA (+gRNA) is translated into polyprotein (pp)1a and pp1ab. These proteins are proteolytically cleaved to generate 16 non-structural proteins…

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Optimized RNA-targeting CRISPR/Cas13d engineering outperforms shRNA inside determining well-designed circRNAs.

(T Endod The year 2010;Thirty six:1056-1060)The set up view that will schizophrenia could have a favorable final result throughout building countries may be not too long ago questioned; nevertheless, systematic research is rare. On this document selleck chemical , many of us illustrate the particular medical upshot of schizophrenia amid…

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News: Researchers at Johns Hopkins and USCD Report Novel CRISPR-Cas13d Therapy for Huntington’s Disease

Dr. Wenzhen Duan (left), Professor of Psychiatry and Behavioural Science at Johns Hopkins University School of Medicine, and Dr. Gene Yeo (right), Professor of Cellular and Molecular Medicine at the University of California San Diego, have created a novel CRISPR-Cas13d based therapy for Huntington’s Disease that depletes mutant Huntingtin transcripts…

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Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches,Nature Communications

A major challenge in the application of the CRISPR-Cas13d system is to accurately predict its guide-dependent on-target and off-target effect. Here, we perform CRISPR-Cas13d proliferation screens and design a deep learning model, named DeepCas13, to predict the on-target activity from guide sequences and secondary structures. DeepCas13 outperforms existing methods to…

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CRISPR-Cas13d effectively targets SARS-CoV-2 variants, including Delta and Omicron, and inhibits viral infection

doi: 10.1002/mco2.208. eCollection 2023 Feb. Zongzhi Liu  1   2   3 , Xiang Gao  4 , Chuanwen Kan  2   5 , Lingyu Li  1   2   3 , Yuan Zhang  6 , Yibo Gao  7 , Shengyuan Zhang  4 , Liangji Zhou  6 , Hui Zhao  6   8   9 , Mingkun Li  2  …

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Cryo-EM structure and protease activity of the type III-E CRISPR-Cas effector

Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between bacteria and their phage foes. Nature 577, 327–336 (2020). Article  CAS  Google Scholar  Makarova, K. S. et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467–477 (2011). Article  CAS  Google Scholar …

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731 Type VI A Cas13a In Cas13a direct repeat region of crRNA is composed of 5 6

7.3.1Type VI-A (Cas13a)In Cas13a, direct repeat region of crRNA is composed of 5–6 bp stem using Watsonand Crick base pairing with an unpaired 2 nt bulge (AA or AC) present at 30end ofstem, while loop region of stem contains 7–9 nt depending upon homologs ofCas13a. In addition, an 8–12 nt…

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Frontiers | A Mutated Nme1Cas9 Is a Functional Alternative RNase to Both LwaCas13a and RfxCas13d in the Yeast S. cerevisiae

Introduction The clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) protein systems naturally exist in prokaryotes. They are RNA-mediated defense mechanisms to protect bacteria and archaea from invading nucleic acids (Barrangou et al., 2007). CRISPR–Cas systems are classified into two classes (1 and 2). Class 2 CRISPR–Cas require a single…

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CRISPR-Cas13d for CHO Cell Engineering and Antibody Production

Abstract Chinese hamster ovary (CHO) cell is the predominant cell factory to produce biopharmaceuticals such as immunoglobulin G (IgG), but in CHO cells lactate accumulation and cell death compromise IgG production while fucosylation mitigates the antibody-dependent cellular cytotoxicity (ADCC) of IgG. To tackle these problems, we harnessed a burgeoning gene…

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New Techniques and Complex Models

CRISPR systems that rely on inactivated Cas enzymes—that is, dead Cas (dCas) enzymes—never looked more alive. They harness the targeting power associated with CRISPR—but not the double-strand cuts. As such, they give researchers new ways to interrogate and manipulate gene function. Possibilities include CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa)…

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Vertex and Arbor Strike a $1.2 Billion Deal for Gene-Editing Programs

With a handful of drugs for cystic fibrosis already approved, Vertex Pharmaceuticals has turned its attention to expanding its pipeline through collaborations and acquisitions the past few years. Today, the California company announced a new agreement with an old partner. Nearly three years ago, Vertex and Arbor Biotechnologies struck a deal….

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