Aliaksandr A Halavatyi

• PhD
• Scientific Officer at European Molecular Biology Laboratory

How cells establish the interphase genome organization after mitosis is incompletely understood. Using quantitative and super-resolution microscopy, we show that the transition from a Condensin to a Cohesin-based genome organization occurs dynamically over 2 h. While a significant fraction of Condensins remains chromatin-bound until early G1, Cohes...

Excessive deposition of fibrillar collagen in the interstitial extracellular matrix (ECM) of human lung tissue causes fibrosis, which can ultimately lead to organ failure. Despite our understanding of the molecular mechanisms underlying the disease, no cure for pulmonary fibrosis has yet been found. We screened a drug library and found that dextrom...

Mitotic spindles are dynamically intertwined with the cytoplasm they assemble in. How the physicochemical properties of the cytoplasm affect spindle architecture and size remains largely unknown. Using quantitative biochemistry in combination with adaptive feedback microscopy, we investigated mitotic cell and spindle morphology during neural differ...

How cells establish the interphase genome organization after mitosis is incompletely understood. Using quantitative and super-resolution microscopy, we show that the transition from a Condensin to a Cohesin-based genome organization occurs dynamically over two hours. While a significant fraction of Condensins remains chromatin-bound until early G1,...

Subnuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome in distinct physical and biochemical environments. During X chromosome inactivation (XCI), the noncoding Xist RNA coats the X chromosome, triggers gene silencing and forms a dense body of heterochroma...

Excessive deposition of fibrillar collagen in the interstitial extracellular matrix (ECM) of human lung tissue causes fibrosis, which can ultimately lead to organ failure. Despite our understanding of the molecular mechanisms underlying the disease, a cure for pulmonary fibrosis has not yet been found. In this study, we screened an FDA-approved dru...

The Golgi is a dynamic organelle with a unique morphology that has implications on its function. How the structural integrity of the Golgi is maintained despite its dynamic nature has been a long-standing question. Several siRNA-based screens have addressed this question and have identified a number of key players required for Golgi integrity. Inte...

Proteins that enter the secretory pathway are transported from their place of synthesis in the endoplasmic reticulum to the Golgi complex by COPII-coated carriers. The networks of proteins that regulate these components in response to extracellular cues have remained largely elusive. Using high-throughput microscopy, we comprehensively screened 378...

Development of multicellular organisms requires the generation of gene expression patterns that determines cell fate and organ shape. Groups of genetic interactions known as Gene Regulatory Networks (GRNs) play a key role in the generation of such patterns. However, how the topology and parameters of GRNs determine patterning in vivo remains unclea...

Chronic obstructive pulmonary disease (COPD) is one of the major causes of disability and death worldwide and a significant risk factor for respiratory infections. Rhinoviral infections are the most common trigger of COPD exacerbations which lead to a worsening of disease symptoms, decline in lung function and increased mortality. The lack of suita...

Mechanosensitive nuclear pores The nucleus of eukaryotic cells is enclosed by the nuclear envelope, a double membrane punctuated with nuclear pore complexes (NPCs). These giant channels in the nuclear envelope mediate nucleocytoplasmic exchange. Zimmerli et al . show that the mechanical status of the nuclear membranes controls their nuclear pore di...

Complex traits are characterized by multiple genes and variants acting simultaneously on a phenotype. However, studying the contribution of individual pairs of genes to complex traits has been challenging since human genetics necessitates very large population sizes, while findings from model systems do not always translate to humans. Here, we comb...

A significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in wh...

Sub-nuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome in distinct physical and biochemical environments, where transcription and epigenetic factors are either concentrated or depleted. The inactive X chromosome offers a paradigm for studying sub-nuclear...

Gene regulatory networks (GRNs) regulate the generation of diverse gene expression patterns, which in turn determine cell fate during the development of multicellular organisms. However, how the topology and parameters of GRNs determine this patterning remain largely unknown due to the complexity of most experimental systems. To address this, we us...

Proteins that enter the secretory pathway are transported from their place of synthesis in the Endoplasmic Reticulum (ER) to the Golgi apparatus by COPII coated carriers. The components of the COPII transport machinery have been well characterized, but the network of proteins that regulate these components have remained largely elusive. The discove...

Fibrosis can affect any organ resulting in the loss of tissue architecture and function with often life-threatening consequences. Pathologically, fibrosis is characterised by expansion of connective tissue due to excessive deposition of extracellular matrix proteins (ECM), including the fibrillar forms of collagen. A significant limitation for disc...

Changes in gene regulation underlie much of phenotypic evolution¹. However, our understanding of the potential for regulatory evolution is biased, because most evidence comes from either natural variation or limited experimental perturbations². Using an automated robotics pipeline, we surveyed an unbiased mutation library for a developmental enhanc...

Genetic interactions (GIs), the joint impact of different genes or variants on a phenotype, are foundational to the genetic architecture of complex traits. However, identifying GIs through human genetics is challenging since it necessitates very large population sizes, while findings from model systems not always translate to humans. Here, we combi...

Gene regulatory changes underlie much of phenotypic evolution. However, the evolutionary potential of regulatory evolution is unknown, because most evidence comes from either natural variation or limited experimental perturbations. Surveying an unbiased mutation library for a developmental enhancer in Drosophila melanogaster using an automated robo...

Fibrosis can affect any organ resulting in the loss of tissue architecture and function with often life-threatening consequences. Pathologically, fibrosis is characterised by expansion of connective tissue due to excessive deposition of extracellular matrix proteins (ECM), including the fibrillar forms of collagen. A significant hurdle for discover...

Abstract Arrayed CRISPR‐based screens emerge as a powerful alternative to pooled screens making it possible to investigate a wide range of cellular phenotypes that are typically not amenable to pooled screens. Here, we describe a solid‐phase transfection platform that enables CRISPR‐based genetic screens in arrayed format with flexible readouts. We...

This chapter investigates molecular interactions between molecules of interest, measuring physiological parameters in living samples via sensors based on Förster Resonance Energy Transfer (FRET) and in specialised cases to measure distances on molecular scales using single molecules. It focuses on two FRET acquisition and processing techniques that...

This chapter discusses the issues of Fluorescence recovery after photobleaching (FRAP) model selection and their applications for estimating parameter values. It highlights the important details to be considered to achieve a solid experimental basis for FRAP analysis. The chapter aims to explain the general workflow for analysing FRAP recovery curv...

Focal adhesions are integrin-based structures that link the actin cytoskeleton and the extracellular matrix. They play an important role in various cellular functions such as cell signaling, cell motility and cell shape. To ensure and fine tune these different cellular functions, adhesions are regulated by a large number of proteins. The LIM domain...

Newly synthesized proteins are sorted into COPII-coated transport carriers at the endoplasmic reticulum (ER). Assembly of the COPII coat complex, which occurs at ER exit sites (ERES), is initiated by membrane association and GTP loading of SAR1, followed by the recruitment of the SEC23/24 and SEC13/31 sub-complexes. Both of these two sub-complexes...

The majority of human cancer deaths are caused by metastasis. The metastatic dissemination is initiated by the breakdown of epithelial cell homeostasis. During this phenomenon, referred to as epithelial to mesenchymal transition (EMT), cells change their genetic and trancriptomic program leading to phenotypic and functional alterations. The challen...

Primers used for detection of miRNAs and mRNAs (primer sequences (5′ – 3′)) (Genecust). (TIF)

Expression data of miRNAs differentially expressed at an established EMT state. Microarrays were performed at 72 h and 96 h of SNAI1 induction in our EMT cell model. Averaged expression values for each time point were calculated taking into account only replicates which have moduli of log-ratios≥0.5 and t-test p-values≤0.01. (XLS)

Large-scale analysis of miRNA expressions combining our SNAI1-induced EMT study with epithelial/mesenchymal signatures. The large-scale analysis combines our microarray analysis results and signatures from four published miRNA microarray analyses of the NCI60 cancer cell line panel. For each analysis, a table provides a list of miRNAs with correspo...

Correlation analysis of miRNA expression levels. Expression matrices of four published NCI60 studies were processed with the M@IA environment [38], by merging replicates with the average method on the miRNA_id provided in each study (miRBase). Correlation matrices were calculated with the R environment (http://www.r-project.org), with the Pearson m...

Continuous dynamic model generation and perturbation. (DOC)

Proliferation curves of and percentage of early apoptotic events in HTB129-ctrl and HTB129-miR203 cells. A) Representative proliferation curves of HTB129-ctrl and HTB129-miR203 cells. Cell proliferation was assayed over 96 h and quantified using the MTT assay. B) Percentage of early apoptotic HTB129-ctrl and HTB129-miR203 cells, as determined by fl...

Expression profiles of miR-200b cluster members upon SNAI1-induction in the MCF7-SNAI1 EMT cell model. MiR-200b (A), miR-200a (B), miR-429 (C) expression levels were determined by qRT-PCR and normalized to U44 expression and expression levels in non-induced MCF7-SNAI1 cells. (TIF)

Ectopic miR-203 expression levels in stably transfected HTB129 cells. Mir-203 expression levels were determined by qRT-PCR and normalized to U44 expression and expression levels in HTB129-ctrl cells. (TIF)

Initially detected in leukocytes and cancer cells derived from solid tissues, L-plastin/fimbrin belongs to a large family of actin crosslinkers and is considered as a marker for many cancers. Phosphorylation of L-plastin on residue Ser5 increases its F-actin binding activity and is required for L-plastin-mediated cell invasion. To study the kinetic...

A novel mathematical model of the actin dynamics in living cells under steady-state conditions has been developed for fluorescence recovery after photobleaching (FRAP) experiments. As opposed to other FRAP fitting models, which use the average lifetime of actins in filaments and the actin turnover rate as fitting parameters, our model operates with...

We report on an advanced universal Monte Carlo simulation model of actin polymerization processes offering a broad application panel. The model integrates major actin-related reactions, such as assembly of actin nuclei, association/dissociation of monomers to filament ends, ATP-hydrolysis via ADP-Pi formation and ADP-ATP exchange, filament branchin...