Publications related to Transcription activator-like effector nuclease

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

EPFL2023

Multivalent Virucidal Antivirals: Synthesis, Mechanisms of Action, and Immune-stimulating Effects

Yong Zhu

Viruses initiate invasion by binding to cell surface glycoproteins. Materials mimicking the carbohydrate motifs of these glycoproteins, such as heparan sulfate (HS) and sialic acid (SA) can block viral attachment and inhibit the infection. Multivalent disp ...

EPFL2023

Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Julius Valten Upmeier Zu Belzen

Optogenetic control of CRISPR-Cas9 systems has significantly improved our ability to perform genome perturbations in living cells with high precision in time and space. As new Cas orthologues with advantageous properties are rapidly being discovered and en ...

2021

Constraint-based metabolic control analysis for rational strain engineering

Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

2021

Variants in USP48 encoding ubiquitin hydrolase are associated with autosomal dominant non-syndromic hereditary hearing loss

Nicolas Jean Philippe Guex

Non-Syndromic Hereditary Hearing Loss (NSHHL) is a genetically heterogeneous sensory disorder with about 120 genes already associated. Through exome sequencing (ES) and data aggregation, we identified a family with six affected individuals and one unrelate ...

Oxford University Press2021

Computational design of anti-CRISPR proteins with improved inhibition potency

Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Andreas Scheck, Wei Sun, Stéphane Rosset, Zander Harteveld, Julius Valten Upmeier Zu Belzen, Yujia Wang

Anti-CRISPR (Acr) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. Here, we applied structure-based design on AcrIIC1, a broad-spectrum CRISPR-Cas9 inhibitor, ...

NATURE PUBLISHING GROUP2020

Efficient viral transduction in mouse inner ear hair cells with utricle injection and AAV9-PHP.B

Bernard Schneider, Paola Andrea Solanes Vega

Viral delivery of exogenous coding sequences into the inner ear has the potential for therapeutic benefit for patients suffering genetic or acquired hearing loss. To devise improved strategies for viral delivery, we investigated two injection techniques, r ...

2020

Human shelterin protein POT1 prevents severe telomere instability induced by homology-directed DNA repair

Joachim Lingner, Galina Glousker, Anna-Sophia Briod

The evolutionarily conserved POT1 protein binds single-stranded G-rich telomeric DNA and has been implicated in contributing to telomeric DNA maintenance and the suppression of DNA damage checkpoint signaling. Here, we explore human POT1 function through g ...

WILEY2020

Establishing a Ternary System for Optical Monitoring of DNA-Protein Interactions with Single-Walled Carbon Nanotubes

Shang-Jung Wu

DNA-protein interactions lie at the crux of life's essential processes. As such, various technologies have been developed to characterize these interactions. The distinct advantages of these technologies can be leveraged to study different facets of these ...

EPFL2020

Optimized antiangiogenic reprogramming of the tumor microenvironment potentiates CD40 immunotherapy

Michele De Palma, Nicolo Rigamonti, Alan Nicolas Thierry Guichard, Daniela Pais Ferreira

Cancer immunotherapies are increasingly combined with targeted therapies to improve therapeutic outcomes. We show that combination of agonistic anti-CD40 with antiangiogenic antibodies targeting 2 proangiogenic factors, vascular endothelial growth factor A ...

2020

Phosphorylation of the VAR2CSA extracellular region is associated with enhanced adhesive properties to the placental receptor CSA

Romain Hamelin, Florence Armand, Marc Moniatte

Plasmodium falciparum is the main cause of disease and death from malaria. P. falciparum virulence resides in the ability of infected erythrocytes (IEs) to sequester in various tissues through the interaction between members of the polymorphic P. falciparu ...

2019

A selective ER‐phagy exerts procollagen quality control via a Calnexin‐FAM134B complex

Maurizio Molinari

Autophagy is a cytosolic quality control process that recognizessubstrates through receptor-mediated mechanisms. Procollagens,the most abundant gene products in Metazoa, are synthesized inthe endoplasmic reticulum (ER), and a fraction that fails to attaint ...

2018

Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld

Anti-CRISPR proteins are powerful tools for CRISPR-Cas9 regulation; the ability to precisely modulate their activity could facilitate spatiotemporally confined genome perturbations and uncover fundamental aspects of CRISPR biology. We engineered optogeneti ...

NATURE PUBLISHING GROUP2018

Efficient cleavage of aryl ether C–O linkages by Rh–Ni and Ru–Ni nanoscale catalysts operating in water

Paul Joseph Dyson, Vassily Hatzimanikatis, Duncan Thomas Lindsay Alexander, Antoine Philippe Van Muyden, Ning Yan, Georgios Savoglidis, Sviatlana Siankevich, Safak Bulut

Bimetallic Ru–Ni and Rh–Ni nanocatalysts coated with a phase transfer agent efficiently cleave aryl ether C–O linkages in water in the presence of hydrogen. For dimeric substrates with weaker C–O linkages, i.e. α-O-4 and β-O-4 bonds, low loadings of the pr ...

2018

TAL Effectors Specificity Stems from Negative Discrimination

Matteo Dal Peraro, Marco Stenta, Basile Isidore Martin Wicky

Transcription Activator-Like (TAL) effectors are DNA-binding proteins secreted by phytopathogenic bacteria that interfere with native cellular functions by binding to plant DNA promoters. The key element of their architecture is a domain of tandem-repeats ...

Public Library of Science2013

UV radiation induces genome-mediated, site-specific cleavage in viral protein

Tamar Kohn, Yury Tsybin, Laure Menin, Hisham Ben Hamidane, Krista Rule Wigginton, Anne Thérèse Sigstam, Michele Cascella

Much research has been dedicated to understanding the molecular basis of UV damage to biomolecules, yet many questions remain regarding the specific pathways involved. Here we describe a genome-mediated mechanism that causes sitespecific virus protein clea ...

2012

ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites

Giovanna Ambrosini, Christian Iseli, Philipp Bucher

Background: Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specificity is not a ...

BioMed Central2011