Luca Giorgetti
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View article: Loop extrusion creates rare, long-lived encounters underlying enhancer-promoter communication
Loop extrusion creates rare, long-lived encounters underlying enhancer-promoter communication Open
Enhancers regulate transcription from distal genomic positions, but how their spatial encounters with promoters drive activation remains unclear. Using polymer simulations and high-resolution live-cell microscopy, we identify rare but long…
View article: From raw data to research-ready: A FHIR-based transformation pipeline in a real-world oncology setting
From raw data to research-ready: A FHIR-based transformation pipeline in a real-world oncology setting Open
The exponential growth of healthcare data, driven by advancements in medical research and digital health technologies, has underscored the critical need for interoperability and standardization. However, the heterogeneous nature of real-wo…
View article: Single-molecule chromosome tracing reveals a diversity of megabase heterochromatin domains
Single-molecule chromosome tracing reveals a diversity of megabase heterochromatin domains Open
Chromosomes fold into distinct domains that regulate transcription, replication, and repair. Beyond well-characterized TADs and compartments, the diversity of heterochromatin domains remains poorly defined at the sequence level. Using sing…
View article: Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruption
Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruption Open
Genome folding is not static, but emerges from dynamic processes that control transcription, replication, recombination, and repair. DNA loop extrusion by cohesin is central to genome organization, yet it remains unclear how cells can tune…
View article: Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis
Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis Open
The three-dimensional folding of chromosomes is essential for nuclear functions such as DNA replication and gene regulation. The emergence of chromatin architecture is thus an important process during embryogenesis. To shed light on the mo…
View article: Genome-wide absolute quantification of chromatin looping
Genome-wide absolute quantification of chromatin looping Open
3D genomics methods such as Hi-C and Micro-C have uncovered chromatin loops across the genome and linked these loops to gene regulation. However, these methods only measure 3D interaction probabilities on a relative scale. Here, we overcom…
View article: Author Correction: Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF
Author Correction: Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF Open
View article: Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF
Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF Open
View article: Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis
Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis Open
The three-dimensional folding of chromosomes is essential for nuclear functions such as DNA replication and gene regulation. The emergence of chromatin architecture is thus an important process during embryogenesis. To shed light on the mo…
View article: Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes
Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes Open
View article: Integrative approaches to study enhancer–promoter communication
Integrative approaches to study enhancer–promoter communication Open
View article: Cohesin and CTCF control the dynamics of chromosome folding
Cohesin and CTCF control the dynamics of chromosome folding Open
In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, how long they last and how they dep…
View article: Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication
Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication Open
The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors (e.g. CTCF) underlying topologically associating domains (TADs) leads to modest alterati…
View article: VisuStatR: visualizing motility and morphology statistics on images in R
VisuStatR: visualizing motility and morphology statistics on images in R Open
Motivation Live-cell microscopy has become an essential tool for analyzing dynamic processes in various biological applications. Thereby, high-throughput and automated tracking analyses allow the simultaneous evaluation of large numbers of…
View article: Nonlinear control of transcription through enhancer–promoter interactions
Nonlinear control of transcription through enhancer–promoter interactions Open
Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs) 1–4 . Howev…
View article: Live-cell imaging and physical modeling reveal control of chromosome folding dynamics by cohesin and CTCF
Live-cell imaging and physical modeling reveal control of chromosome folding dynamics by cohesin and CTCF Open
Physical proximity between genomic sequences in mammalian chromosomes controls key biological processes such as transcriptional regulation and DNA repair. Yet it is currently unknown if chromosomal contacts are rare and stable or instead f…
View article: Inversion of a topological domain leads to restricted changes in its gene expression and affects inter-domain communication
Inversion of a topological domain leads to restricted changes in its gene expression and affects inter-domain communication Open
The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors underlying genome topology, such as CTCF and cohesin, leads to modest alterations in gen…
View article: deepBlink: threshold-independent detection and localization of diffraction-limited spots
deepBlink: threshold-independent detection and localization of diffraction-limited spots Open
Detection of diffraction-limited spots in single-molecule microscopy images is traditionally performed with mathematical operators designed for idealized spots. This process requires manual tuning of parameters that is time-consuming and n…
View article: Nonlinear control of transcription through enhancer-promoter interactions
Nonlinear control of transcription through enhancer-promoter interactions Open
Chromosome structure in mammals is thought to regulate transcription by modulating the three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated interactions and topologically associating domains (TADs) …
View article: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
HP1 drives de novo 3D genome reorganization in early Drosophila embryos Open
View article: deepBlink: Threshold-independent detection and localization of diffraction-limited spots
deepBlink: Threshold-independent detection and localization of diffraction-limited spots Open
Detection of diffraction-limited spots is traditionally performed with mathematical operators designed for idealized spots. This process requires manual tuning of parameters that is time-consuming and not always reliable. We have developed…
View article: Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function
Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function Open
View article: A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary
A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary Open
View article: DamC reveals principles of chromatin folding in vivo without crosslinking and ligation
DamC reveals principles of chromatin folding in vivo without crosslinking and ligation Open
View article: A symmetric toggle switch explains the onset of random X inactivation in different mammals
A symmetric toggle switch explains the onset of random X inactivation in different mammals Open
View article: Challenges and guidelines toward 4D nucleome data and model standards
Challenges and guidelines toward 4D nucleome data and model standards Open
View article: Modeling of DNA methylation in cis reveals principles of chromatin folding <i>in vivo</i> in the absence of crosslinking and ligation
Modeling of DNA methylation in cis reveals principles of chromatin folding <i>in vivo</i> in the absence of crosslinking and ligation Open
Mammalian chromosomes are folded into an intricate hierarchy of structural domains, within which topologically associating domains (TADs) and CTCF-associated loops partition the physical interactions between regulatory sequences. Current u…
View article: Integrating experiment, theory and simulation to determine the structure and dynamics of mammalian chromosomes
Integrating experiment, theory and simulation to determine the structure and dynamics of mammalian chromosomes Open
View article: The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells
The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells Open
View article: Two coupled feedback loops explain random mono-allelic Xist upregulation at the onset of X-chromosome inactivation
Two coupled feedback loops explain random mono-allelic Xist upregulation at the onset of X-chromosome inactivation Open
In female mammal s, dosage compensation for X-linked genes is ensured through random X-chromosome inactivation, which is initiated by mono-allelic up-regulation of Xist . We use mathematical modeling to identify the regulatory principles r…