Tag: Cas13d

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…

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…

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….

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…

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…

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…

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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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,…

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 …

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…

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…

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…

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…

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…

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….

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…

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…

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…

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….

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…

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…

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,…

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…

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…

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…

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…

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…

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…

(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…

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…

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…

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  …

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 …

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…

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…

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…

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)…

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….