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Aminoacyl-tRNA synthetases in cell signaling.

Authors:
Peng Yao Paul L Fox

Enzymes 2020 12;48:243-275. Epub 2020 Jun 12.

Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States. Electronic address:

Aminoacyl-tRNA synthetases (ARSs) are a family of essential "housekeeping" enzymes ubiquitous in the three major domains of life. ARSs uniquely connect the essential minimal units of both major oligomer classes-the 3-nucleotide codons of oligonucleotides and the amino acids of proteins. They catalyze the esterification of amino acids to the 3'-end of cognate transfer RNAs (tRNAs) bearing the correct anticodon triplet to ensure accurate transfer of information from mRNA to protein according to the genetic code. Read More

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ATP13A2 Regulates Cellular α-Synuclein Multimerization, Membrane Association, and Externalization.

Int J Mol Sci 2021 Mar 7;22(5). Epub 2021 Mar 7.

Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, Bus 1023, 3000 Leuven, Belgium.

ATP13A2, a late endo-/lysosomal polyamine transporter, is implicated in a variety of neurodegenerative diseases, including Parkinson's disease and Kufor-Rakeb syndrome, an early-onset atypical form of parkinsonism. Loss-of-function mutations in ATP13A2 result in lysosomal deficiency as a consequence of impaired lysosomal export of the polyamines spermine/spermidine. Furthermore, accumulating evidence suggests the involvement of ATP13A2 in regulating the fate of α-synuclein, such as cytoplasmic accumulation and external release. Read More

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A cyclin D-CDK6 dimer helps to reshuffle cyclin-dependent kinase inhibitors (CKI) to overcome TGF-beta-mediated arrest and maintain CDK2 activity.

Cell Cycle 2021 Apr 2:1-11. Epub 2021 Apr 2.

Program in Molecular and Cellular Biology, School of Graduate Studies, SUNY Downstate Medical Center, Brooklyn, New York.

The cyclin D-CDK4/6 complex has two distinct functions. Its kinase-dependent role involves its ability to act as serine/threonine kinase, responsible for phosphorylation of substrates required for cell cycle transitions, while its kinase-independent function involves its ability to act as a reservoir for p27. This association sequesters p27 from cyclin E-CDK2 complexes, allowing them to remain active. Read More

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Inhibitor Mimetic Mutations in the PqsE Enzyme Reveal a Protein-Protein Interaction with the Quorum-Sensing Receptor RhlR That Is Vital for Virulence Factor Production.

ACS Chem Biol 2021 Apr 1. Epub 2021 Apr 1.

Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States.

is an opportunistic human pathogen that causes fatal infections. There exists an urgent need for new antimicrobial agents to combat . We conducted a screen for molecules that bind the virulence-controlling protein PqsE and characterized hit compounds for inhibition of PqsE enzymatic activity. Read More

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Structural insights into the function of the catalytically active human Taspase1.

Structure 2021 Mar 25. Epub 2021 Mar 25.

Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", Spanish National Research Council (CSIC), Madrid 28006, Spain. Electronic address:

Taspase1 is an Ntn-hydrolase overexpressed in primary human cancers, coordinating cancer cell proliferation, invasion, and metastasis. Loss of Taspase1 activity disrupts proliferation of human cancer cells in vitro and in mouse models of glioblastoma. Taspase1 is synthesized as an inactive proenzyme, becoming active upon intramolecular cleavage. Read More

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The activity and stability of a cold-active acylaminoacyl peptidase rely on its dimerization by domain swapping.

Int J Biol Macromol 2021 Mar 26;181:263-274. Epub 2021 Mar 26.

Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy. Electronic address:

The study of enzymes from extremophiles arouses interest in Protein Science because of the amazing solutions these proteins adopt to cope with extreme conditions. Recently solved, the structure of the psychrophilic acyl aminoacyl peptidase from Sporosarcina psychrophila (SpAAP) pinpoints a mechanism of dimerization unusual for this class of enzymes. The quaternary structure of SpAAP relies on a domain-swapping mechanism involving the N-terminal A1 helix. Read More

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The RAC1 activator Tiam1 regulates centriole duplication through controlling PLK4 levels.

J Cell Sci 2021 Mar 23. Epub 2021 Mar 23.

Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK

Centriole duplication is tightly controlled to maintain correct centriole number through the cell cycle. Key to this is the regulated degradation of PLK4, the master regulator of centriole duplication. Here we show that the Rac1 guanine nucleotide exchange factor (GEF) Tiam1 localises to centrosomes during S-phase, where it is required for maintenance of normal centriole number. Read More

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GMPPA defects cause a neuromuscular disorder with α-dystroglycan hyperglycosylation.

J Clin Invest 2021 Mar 23. Epub 2021 Mar 23.

Institute of Human Genetics, University Hospital Jena, Jena, Germany.

GDP-mannose-pyrophosphorylase-B (GMPPB) facilitates the generation of GDP-mannose, a sugar donor required for glycosylation. GMPPB defects cause muscle disease due to hypoglycosylation of α-dystroglycan (α-DG). Alpha-DG is part of a protein complex, which links the extracellular matrix with the cytoskeleton thus stabilizing myofibers. Read More

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Efficient flavinylation of glycosomal fumarate reductase by its own ApbE domain in Trypanosoma brucei.

FEBS J 2021 Mar 23. Epub 2021 Mar 23.

Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany.

A subset of flavoproteins has a covalently attached flavin prosthetic group enzymatically attached via phosphoester bonding. In prokaryotes, this is catalysed by alternative pyrimidine biosynthesis E (ApbE) flavin transferases. ApbE-like domains are present in few eukaryotic taxa, for example the N-terminal domain of fumarate reductase (FRD) of Trypanosoma, a parasitic protist known as a tropical pathogen causing African sleeping sickness. Read More

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Expression of PRIP, a phosphatidylinositol 4,5-bisphosphate binding protein, attenuates PI3K/AKT signaling and suppresses tumor growth in a xenograft mouse model.

Biochem Biophys Res Commun 2021 May 18;552:106-113. Epub 2021 Mar 18.

Department of Cellular and Molecular Pharmacology, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553, Japan; Department of Cell Biology and Pharmacology, Faculty of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan. Electronic address:

Cancer is characterized by uncontrolled proliferation resulting from aberrant cell cycle progression. The activation of phosphatidylinositol 3-kinase (PI3K)/AKT signaling, a regulatory pathway for the cell cycle, stabilizes cyclin D1 in the G1 phase by inhibiting the activity of glycogen synthase kinase 3β (GSK3β) via phosphorylation. We previously reported that phospholipase C-related catalytically inactive protein (PRIP), a phosphatidylinositol 4,5-bisphosphate [PI(4,5)P] binding protein, regulates PI3K/AKT signaling by competitively inhibiting substrate recognition by PI3K. Read More

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Neutral Sphingomyelinase 2 Heightens Anti-Melanoma Immune Responses and Anti-PD-1 Therapy Efficacy.

Cancer Immunol Res 2021 Mar 16. Epub 2021 Mar 16.

INSERM UMR 1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.

Dysregulation of lipid metabolism affects the behavior of cancer cells, but how this happens is not completely understood. Neutral sphingomyelinase 2 (nSMase2), encoded by , catalyzes the breakdown of sphingomyelin to produce the anti-oncometabolite ceramide. We found that this enzyme was often downregulated in human metastatic melanoma, likely contributing to immune escape. Read More

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Enantioselective Conjugate Addition of Catalytically Generated Zinc Homoenolate.

J Am Chem Soc 2021 Mar 16;143(12):4775-4781. Epub 2021 Mar 16.

Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.

We report herein an enantioselective conjugate addition reaction of a zinc homoenolate, catalytically generated via ring opening of a cyclopropanol, to an α,β-unsaturated ketone. The reaction is promoted by a zinc aminoalkoxide catalyst generated from EtZn and a chiral β-amino alcohol to afford 1,6-diketones, which undergo, upon heating, intramolecular aldol condensation to furnish highly substituted cyclopentene derivatives with good to high enantioselectivities. The reaction has proved applicable to various 1-substituted cyclopropanols as well as chalcones and related enones. Read More

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A Cas12a-based gene editing system for Phytophthora infestans reveals monoallelic expression of an elicitor.

Mol Plant Pathol 2021 Mar 16. Epub 2021 Mar 16.

Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA.

Phytophthora infestans is a destructive pathogen of potato and a model for investigations of oomycete biology. The successful application of a CRISPR gene editing system to P. infestans is so far unreported. Read More

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Telomerase reverse transcriptase (TERT) activates transcription of miR500A to inhibit Hedgehog signaling and promote cell invasiveness.

Mol Oncol 2021 Mar 13. Epub 2021 Mar 13.

Telomerase, Cancer and Aging Group, Research Unit, Department of Surgery, University Hospital 'Virgen de la Arrixaca', 30120, Murcia, Spain.

Telomerase reverse transcriptase (TERT) maintains telomere homeostasis, thus ensuring chromosome stability and cell proliferation. In addition, several telomere-independent functions of human TERT have been described. In this study, we report that TERT binds directly to the TCF binding elements (TBE) located upstream of the oncomiR miR500A, and induces its transcription. Read More

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Oligomeric assembly regulating mitochondrial HtrA2 function as examined by methyl-TROSY NMR.

Proc Natl Acad Sci U S A 2021 Mar;118(11)

Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;

Human High temperature requirement A2 (HtrA2) is a mitochondrial protease chaperone that plays an important role in cellular proteostasis and in regulating cell-signaling events, with aberrant HtrA2 function leading to neurodegeneration and parkinsonian phenotypes. Structural studies of the enzyme have established a trimeric architecture, comprising three identical protomers in which the active sites of each protease domain are sequestered to form a catalytically inactive complex. The mechanism by which enzyme function is regulated is not well understood. Read More

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CRISPR/dCas system as the modulator of gene expression.

Prog Mol Biol Transl Sci 2021 18;178:99-122. Epub 2021 Jan 18.

Department of Botany, Visva-Bharati, Santiniketan, West Bengal, India. Electronic address:

CRISPR/Cas has been a very exciting field of research because of its multifaceted applications in biological science for editing genome. This tool can be programmed to target any region of DNA of choice by designing gRNA. The potential of gRNA to recruit a CRISPR-associated protein at a specific genomic site allowed scientists to engineer genome of diverse species for research and development. Read More

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January 2021

A New Generation of Functional Tagged Proteins for HIV Fluorescence Imaging.

Viruses 2021 02 28;13(3). Epub 2021 Feb 28.

Department of Cell and Developmental Biology, Northwestern University, Chicago, IL 60611, USA.

During the last decade, there was a marked increase in the development of tools and techniques to study the molecular mechanisms of the HIV replication cycle by using fluorescence microscopy. Researchers often apply the fusion of tags and fluorophores to viral proteins, surrogate proteins, or dyes to follow individual virus particles while they progress throughout infection. The inclusion of such fusion motifs or surrogates frequently disrupts viral infectivity or results in a change of the wild-type phenotype. Read More

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February 2021

Impact of DJ-1 and Helix 8 on the Proteome and Degradome of Neuron-Like Cells.

Cells 2021 Feb 16;10(2). Epub 2021 Feb 16.

Institute of Surgical Pathology, Medical Center, University of Freiburg, Breisacher Straße 115a, D-79106 Freiburg, Germany.

DJ-1 is an abundant and ubiquitous component of cellular proteomes. DJ-1 supposedly exerts a wide variety of molecular functions, ranging from enzymatic activities as a deglycase, protease, and esterase to chaperone functions. However, a consensus perspective on its molecular function in the cellular context has not yet been reached. Read More

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February 2021

Novel bisubstrate uridine-peptide analogues bearing a pyrophosphate bioisostere as inhibitors of human O-GlcNAc transferase.

Bioorg Chem 2021 Feb 13;110:104738. Epub 2021 Feb 13.

Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia; School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia; School of Chemistry, The University of Sydney, NSW 2006, Australia. Electronic address:

Protein O-linked β-D-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), an essential post-translational as well as cotranslational modification, is the attachment of β-D-N-acetylglucosamine to serine and threonine residues of nucleocytoplasmic proteins. An aberrant O-GlcNAc profile on certain proteins has been implicated in metabolic diseases such as diabetes and cancer. Inhibitors of O-GlcNAc transferase (OGT) are valuable tools to study the cell biology of protein O-GlcNAc modification. Read More

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February 2021

Biosynthesis of 6-Hydroxymellein Requires a Collaborating Polyketide Synthase-like Enzyme.

Angew Chem Int Ed Engl 2021 Mar 4. Epub 2021 Mar 4.

Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany.

The polyketide synthase (PKS)-like protein TerB, consisting of inactive dehydratase, inactive C-methyltransferase, and functional ketoreductase domains collaborates with the iterative non reducing PKS TerA to produce 6-hydroxymellein, a key pathway intermediate during the biosynthesis of various fungal natural products. The catalytically inactive dehydratase domain of TerB appears to mediate productive interactions with TerA, demonstrating a new mode of trans-interaction between iterative PKS components. Read More

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Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer.

Sci Rep 2021 Feb 25;11(1):4518. Epub 2021 Feb 25.

Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257, Vilnius, Lithuania.

Argonaute (Ago) proteins are found in all three domains of life. The best-characterized group is eukaryotic Argonautes (eAgos), which are the core of RNA interference. The best understood prokaryotic Ago (pAgo) proteins are full-length pAgos. Read More

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February 2021

Implementation of dCas9-mediated CRISPRi in the fission yeast Schizosaccharomyces pombe.

G3 (Bethesda) 2021 Feb 22. Epub 2021 Feb 22.

Department of Cell Biology, Institute of Life Science, Kurume University, Asahi-machi 67, Kurume, Fukuoka 830-0011, Japan.

Controllable and reversible transcriptional repression is an essential method to study gene functions. A systematic knock-down method using catalytically inactive Cas9 (dCas9) was originally established in bacteria. dCas9 forms a ribonucleoprotein with a small guide RNA and uses it to recognize a specific DNA sequence via Watson-Crick base-pairing. Read More

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February 2021

Shared and distinct roles of Esc2 and Mms21 in suppressing genome rearrangements and regulating intracellular sumoylation.

PLoS One 2021 18;16(2):e0247132. Epub 2021 Feb 18.

Department of Cellular and Molecular Medicine, University of California School of Medicine, San Diego, La Jolla, California, United States of America.

Protein sumoylation, especially when catalyzed by the Mms21 SUMO E3 ligase, plays a major role in suppressing duplication-mediated gross chromosomal rearrangements (dGCRs). How Mms21 targets its substrates in the cell is insufficiently understood. Here, we demonstrate that Esc2, a protein with SUMO-like domains (SLDs), recruits the Ubc9 SUMO conjugating enzyme to specifically facilitate Mms21-dependent sumoylation and suppress dGCRs. Read More

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February 2021

Cezanne is a critical regulator of pathological arterial remodelling by targeting β-catenin signalling.

Cardiovasc Res 2021 Feb 18. Epub 2021 Feb 18.

Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.

Aim: Pathological arterial remodelling including neointimal hyperplasia and atherosclerosis is the main underlying cause for occluding arterial diseases. Cezanne is a novel deubiquitinating enzyme, functioning as a NF-кB negative regulator, and plays a key role in renal inflammatory response and kidney injury induced by ischemia. Here we attempted to examine its pathological role in vascular smooth muscle cell (VSMC) pathology and arterial remodelling. Read More

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February 2021

Structure of the Complete Dimeric Human GDAP1 Core Domain Provides Insights into Ligand Binding and Clustering of Disease Mutations.

Front Mol Biosci 2020 27;7:631232. Epub 2021 Jan 27.

Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.

Charcot-Marie-Tooth disease (CMT) is one of the most common inherited neurological disorders. Despite the common involvement of ganglioside-induced differentiation-associated protein 1 (GDAP1) in CMT, the protein structure and function, as well as the pathogenic mechanisms, remain unclear. We determined the crystal structure of the complete human GDAP1 core domain, which shows a novel mode of dimerization within the glutathione S-transferase (GST) family. Read More

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January 2021

A Cellular Stress Response Induced by the CRISPR-dCas9 Activation System Is Not Heritable Through Cell Divisions.

CRISPR J 2020 06;3(3):188-197

Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.

The CRISPR-Cas9 system can be modified to perform "epigenetic editing" by utilizing the catalytically inactive (dead) Cas9 (dCas9) to recruit regulatory proteins to specific genomic locations. In prior studies, epigenetic editing with multimers of the transactivator VP16 and guide RNAs (gRNAs) was found to cause adverse cellular responses. These side effects may confound studies inducing new cellular properties, especially if the cellular responses are maintained through cell divisions-an epigenetic regulatory property. Read More

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A multiplex CRISPR interference tool for virulence gene interrogation in Legionella pneumophila.

Commun Biol 2021 Feb 4;4(1):157. Epub 2021 Feb 4.

Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.

Catalytically inactive dCas9 imposes transcriptional gene repression by sterically precluding RNA polymerase activity at a given gene to which it was directed by CRISPR (cr)RNAs. This gene silencing technology, known as CRISPR interference (CRISPRi), has been employed in various bacterial species to interrogate genes, mostly individually or in pairs. Here, we developed a multiplex CRISPRi platform in the pathogen Legionella pneumophila capable of silencing up to ten genes simultaneously. Read More

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February 2021

The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold.

PLoS Pathog 2021 Feb 3;17(2):e1009223. Epub 2021 Feb 3.

Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

Nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) in plants can detect avirulence (AVR) effectors of pathogenic microbes. The Mildew locus a (Mla) NLR gene has been shown to confer resistance against diverse fungal pathogens in cereal crops. In barley, Mla has undergone allelic diversification in the host population and confers isolate-specific immunity against the powdery mildew-causing fungal pathogen Blumeria graminis forma specialis hordei (Bgh). Read More

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February 2021

Role of oculocerebrorenal syndrome of Lowe (OCRL) protein in megakaryocyte maturation, platelet production and functions: a study in patients with Lowe syndrome.

Br J Haematol 2021 Mar 2;192(5):909-921. Epub 2021 Feb 2.

Université de Paris, Innovations Thérapeutiques en Hémostase, Paris, INSERM U1140, France.

Lowe syndrome (LS) is an oculocerebrorenal syndrome of Lowe (OCRL1) genetic disorder resulting in a defect of the OCRL protein, a phosphatidylinositol-4,5-bisphosphate 5-phosphatase containing various domains including a Rho GTPase-activating protein (RhoGAP) homology domain catalytically inactive. We previously reported surgery-associated bleeding in patients with LS, suggestive of platelet dysfunction, accompanied with a mild thrombocytopenia in several patients. To decipher the role of OCRL in platelet functions and in megakaryocyte (MK) maturation, we conducted a case-control study on 15 patients with LS (NCT01314560). Read More

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A CRISPR-Cas9-Based Near-Infrared Upconversion-Activated DNA Methylation Editing System.

ACS Appl Mater Interfaces 2021 Feb 1;13(5):6043-6052. Epub 2021 Feb 1.

Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, Oncology Key Laboratory of Cancer Prevention and Therapy, National Clinical, Research Center of Cancer, 300060Tianjin, China.

DNA methylation is a kind of a crucial epigenetic marker orchestrating gene expression, molecular function, and cellular phenotype. However, manipulating the methylation status of specific genes remains challenging. Here, a clustered regularly interspaced palindromic repeats-Cas9-based near-infrared upconversion-activated DNA methylation editing system (CNAMS) was designed for the optogenetic editing of DNA methylation. Read More

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February 2021