Publications by Giovanna Ambrosini

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Giovanna Ambrosini

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

Nuclear Factor I genomic binding associates with chromatin boundaries

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

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

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

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

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

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

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

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

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

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

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

biogrowleR: Enhancing Longitudinal Data Analysis

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

Contraceptive progestins with androgenic properties stimulate breast epithelial cell proliferation

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

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

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

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