Publications de Giovanna Ambrosini

Publications associées (38)

Integrating distribution kinetics and toxicodynamics to assess repeat dose neurotoxicity in vitro using human BrainSpheres: a case study on amiodarone

For ethical, economical, and scientific reasons, animal experimentation, used to evaluate the potential neurotoxicity of chemicals before their release in the market, needs to be replaced by new approach methodologies. To illustrate the use of new approach ...

FRONTIERS MEDIA SA2023

Nuclear Factor I genomic binding associates with chromatin boundaries

Giovanni Dietler, Philipp Bucher, Giovanna Ambrosini, Nicolas Mermod, Petar Pjanic

Background: The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipitation and high throughput sequenci ...

BioMed Central2013

A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing

Didier Trono, Philipp Bucher, Jacques Rougemont, Giovanna Ambrosini, Nadine Fournier, Adamantia Kapopoulou, Anna Claire Groner, Annamaria Kauzlaric

BACKGROUND: KRAB-ZFPs (Kruppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, KAP1, which recruits effectors respo ...

BioMed Central2011

Common genetic variants associated with Parkinson's disease display widespread signature of epigenetic plasticity

Philipp Bucher, Giovanna Ambrosini

Parkinson disease (PD) is characterized by a pivotal progressive loss of substantia nigra dopaminergic neurons and aggregation of alpha-synuclein protein encoded by the SNCA gene. Genome-wide association studies identified almost 100 sequence variants link ...

Springer Nature2019

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Philipp Bucher, Giovanna Ambrosini, René Dreos, Romain Fernand Pietro Groux

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

2020

SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity

Philipp Bucher, Giovanna Ambrosini

SNP2TFBS is a computational resource intended to support researchers investigating the molecular mechanisms underlying regulatory variation in the human genome. The database essentially consists of a collection of text files providing specific annotations ...

Oxford University Press2016

KRAB-Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

Didier Trono, Philipp Bucher, Giovanna Ambrosini, Nadine Fournier, Anna Claire Groner, Nicolas Dénervaud

Krüppel-associated box domain-zinc finger proteins (KRAB-ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic rep ...

Public Library of Science2010

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux

BackgroundPositional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological application ...

2020

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Giovanna Ambrosini, Nicolas Jean Philippe Guex, Christian Iseli

Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpre ...

BMC2024

Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing

Giovanna Ambrosini, Nicolas Jean Philippe Guex, Christian Iseli

Crop genomes accumulate deleterious mutations—a phenomenon known as the cost of domestication. Precision genome editing has been proposed to eliminate such potentially harmful mutations; however, experimental demonstration is lacking. Here we identified a ...

2025

The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche

Philipp Bucher, Cathrin Brisken, Giovanna Ambrosini, Rachel Marcone, Céline Berthe Constantin, Dalya Ataca, Marie Shamseddin, Csaba Ferenc László, Marian Caikovski, Patrik Aouad

Estrogens and progesterone control breast development and carcinogenesis via their cognate receptors expressed in a subset of luminal cells in the mammary epithelium. How they control the extracellular matrix, important to breast physiology and tumorigenes ...

Nature Research2020

Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING

Daniel Constam, Giovanna Ambrosini, Nicolas Jean Philippe Guex, Christian Iseli, Katarina Pinjusic, Olga Egorova

The transforming growth factor-beta (TGF-beta) family member activin A (hereafter Activin-A) is overexpressed in many cancer types, often correlating with cancer-associated cachexia and poor prognosis. Activin-A secretion by melanoma cells indirectly imped ...

Frontiers Media Sa2024

Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site

Philipp Bucher, Giovanna Ambrosini

Nucleosome depletion at transcription start sites (TSS) has been documented genome-wide in multiple eukaryotic organisms. However, the mechanisms that mediate this nucleosome depletion and its functional impact on transcription remain largely unknown. We h ...

Oxford University Press2009

biogrowleR: Enhancing Longitudinal Data Analysis

Cathrin Brisken, Giovanna Ambrosini, Andrea Agnoletto, Carlos Henrique Venturi Ronchi, Daria Matvienko, Hazel Margaret Quinn

Time course measurements are used for many applications in biomedical research, ranging from growth curves to drug efficacy testing and high-throughput screening. Statistical methods used to analyze the resulting longitudinal data, such as t-tests or repea ...

Springer Science and Business Media LLC2025

DNA methylation by CcrM contributes to genome maintenance in the Agrobacterium tumefaciens plant pathogen

Giovanna Ambrosini, Nicolas Jean Philippe Guex, Christian Iseli

The cell cycle-regulated DNA methyltransferase CcrM is conserved in most Alphaproteobacteria, but its role in bacteria with complex or multicentric genomes remains unexplored. Here, we compare the methylome, the transcriptome and the phenotypes of wild-typ ...

OXFORD UNIV PRESS2024

Contraceptive progestins with androgenic properties stimulate breast epithelial cell proliferation

Philipp Bucher, Cathrin Brisken, Giovanna Ambrosini, Valentina Scabia, Laura Battista, Fabio De Martino, Céline Berthe Constantin, Marie Shamseddin, Csaba Ferenc László

Hormonal contraception exposes women to synthetic progesterone receptor (PR) agonists, progestins, and transiently increases breast cancer risk. How progesterone and progestins affect the breast epithelium is poorly understood because we lack adequate mode ...

2021

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-r ...

Oxford University Press2018

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

Philipp Bucher, Giovanna Ambrosini, Christian Iseli

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

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

Philipp Bucher, Giovanna Ambrosini, René Dreos, Rouayda Cavin Perier, Romain Fernand Pietro Groux

We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next gene ...

2017

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1

Philipp Bucher, Cathrin Brisken, Giovanna Ambrosini, Georgios Sflomos, Valentina Scabia, Patrik Aouad, Laura Battista, Fabio De Martino, Ayyakkannu Ayyanan

Invasive lobular carcinoma (ILC) is the most frequent special histological subtype of breast cancer, typically characterized by loss of E‐cadherin. It has clinical features distinct from other estrogen receptor‐positive (ER+) breast cancers but the molecul ...

2021