Mariano Barbieri

Complexity of chromatin folding is captured by the strings and binders switch model

Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been detected by single-cell imaging and chromosome conformation capture-based approaches. However, a unified quantitative framework describing spatial chromatin organization is still lacking. Here, we explore the “strings and binders switch” model to explain the origin and variety of chromatin behaviors that coexist and dynamically change within living cells. This simple polymer model recapitulates the scaling properties of chromatin folding reported experimentally in different cellular systems, the fractal state of chromatin, the processes of domain formation, and looping out. Additionally, the strings and binders switch model reproduces the recently proposed “fractal–globule” model, but only as one of many possible transient conformations.

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

Mammalian chromosomes fold into arrays of megabase‐sized topologically associating domains (TADs), which are arranged into compartments spanning multiple megabases of genomic DNA. TADs have internal substructures that are often cell type specific, but their higher‐order organization remains elusive. Here, we investigate TAD higher‐order interactions with Hi‐C through neuronal differentiation and show that they form a hierarchy of domains‐within‐domains (metaTADs) extending across genomic scales up to the range of entire chromosomes. We find that TAD interactions are well captured by tree‐like, hierarchical structures irrespective of cell type. metaTAD tree structures correlate with genetic, epigenomic and expression features, and structural tree rearrangements during differentiation are linked to transcriptional state changes. Using polymer modelling, we demonstrate that hierarchical folding promotes efficient chromatin packaging without the loss of contact specificity, highlighting a role far beyond the simple need for packing efficiency.

Complex multi-enhancer contacts captured by genome architecture mapping

The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. Here we report a genome-wide method, genome architecture mapping (GAM), for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large genomic distances using a mathematical model termed SLICE (statistical inference of co-segregation). GAM also reveals an abundance of three-way contacts across the genome, especially between regions that are highly transcribed or contain super-enhancers, providing a level of insight into genome architecture that, owing to the technical limitations of current technologies, has previously remained unattainable. Furthermore, GAM highlights a role for gene-expression-specific contacts in organizing the genome in mammalian nuclei.

Conformation regulation of the X chromosome inactivation center: a model.

X-Chromosome Inactivation (XCI) is the process whereby one, randomly chosen X becomes transcriptionally silenced in female cells. XCI is governed by the Xic, a locus on the X encompassing an array of genes which interact with each other and with key molecular factors. The mechanism, though, establishing the fate of the Xs, and the corresponding alternative modifications of the Xic architecture, is still mysterious. In this study, by use of computer simulations, we explore the scenario where chromatin conformations emerge from its interaction with diffusing molecular factors. Our aim is to understand the physical mechanisms whereby stable, non-random conformations are established on the Xics, how complex architectural changes are reliably regulated, and how they lead to opposite structures on the two alleles. In particular, comparison against current experimental data indicates that a few key cis-regulatory regions orchestrate the organization of the Xic, and that two major molecular regulators are involved.

A polymer model explains the complexity of large-scale chromatin folding

The underlying global organization of chromatin within the cell nucleus has been the focus of intense recent research. Hi-C methods have allowed for the detection of genome-wide chromatin interactions, revealing a complex large-scale organization where chromosomes tend to partition into megabase-sized “topological domains” of local chromatin interactions and intra-chromosomal contacts extends over much longer scales, in a cell-type and chromosome specific manner. Until recently, the distinct chromatin folding properties observed experimentally have been difficult to explain in a single conceptual framework. We reported that a simple polymer-physics model of chromatin, the strings and binders switch (SBS) model, succeeds in describing the full range of chromatin configurations observed in vivo. The SBS model simulates the interactions between randomly diffusing binding molecules and binding sites on a polymer chain. It explains how polymer architectural patterns can be established, how different stable conformations can be produced and how conformational changes can be reliably regulated by simple strategies, such as protein upregulation or epigenetic modifications, via fundamental thermodynamics mechanisms.

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

Gene expression states influence the 3D conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a gene-dense genomic region containing closely spaced genes with distinct activation states in mouse embryonic stem (ES) cells. To predict possible folding scenarios, we performed computer simulations of polymer models informed with different chromatin occupancy features that define promoter activation states or binding sites for the transcription factor CTCF. Single-cell imaging of the locus folding was performed to test model predictions. While CTCF occupancy alone fails to predict the in vivo folding at genomic length scale of 10 kb, we found that homotypic interactions between active and Polycomb-repressed promoters co-occurring in the same DNA fiber fully explain the HoxB folding patterns imaged in single cells. We identify state-dependent promoter interactions as major drivers of chromatin folding in gene-dense regions.

A model of the large-scale organization of chromatin.

In the cell nucleus, chromosomes have a complex spatial organization, spanning several length scales, which serves vital functional purposes. It is unknown, however, how their three-dimensional architecture is orchestrated. In the present article, we review the application of a model based on classical polymer physics, the strings and binders switch model, to explain the molecular mechanisms of chromatin self-organization. We explore the scenario where chromatin architecture is shaped and regulated by the interactions of chromosomes with diffusing DNA-binding factors via thermodynamics mechanisms and compare it with available experimental data.

Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus

We review some of the recent progresses made by the application of polymer physics to the understanding of the spatial organization of chromosomes in the cell nucleus. In particular, we focus on some scaling properties of the contact probability of pairs of sites, discovered by recent genome-wide experiments exploiting new technologies such as Hi-C methods.

Polymer models of chromatin organization

The exploration of the spatial organiza-tion of chromosomes in the cell nucleushas been greatly enhanced by genome-scale technologies such as Hi-C methods.Polymermodels arehelpingto understandthe new emerging complex scenarios andhere we review some recent developments.In the cell nucleus of eukaryotes, chro-mosomes have a complex spatial organi-zation serving vital functional purposes,with structural disruptions being linkedto disease (Fraser and Bickmore, 2007;Lanctot et al., 2007; Misteli, 2007; Pomboand Branco, 2007). The development oftechnologies such as Hi-C ( Lieberman-Aiden et al., 2009) has opened the wayto mapping chromatin interactions ata genomic scale. It is emerging thatchromosomes tend to form 1Mb sizeddomains with increased levels of intra-interactions (known, e.g., as TopologicalDomains, TDs) (Dixon et al., 2012; Noraet al., 2012), but contacts extend acrossentire chromosomes (Branco and Pombo,2006; Shopland et al., 2006; Fraser andBickmore, 2007; Kalhor et al., 2011;Sexton et al., 2012), as highlighted bythe average contact probability of twosites,

Polymer models of the organization of chromosomes in the nucleus of cells

Understanding the mechanisms that control the organization of chromosomes in the space of the nucleus of cells, and its contribution to gene regulation, is a key open issue in molecular biology. New technologies have shown that chromosomes have a complex 3D organization, which dynamically changes across organisms and cell types. To understand such complex behaviors, quantitative models from polymer physics have been developed, to find the principles of chromosome folding, their origin and function. Here, we provide a short review of recent progress in such an important research field where Physical and Life Sciences meet.