New Hi-C technologies have revealed that chromosomes have a complex network of spatial contacts in the cell nucleus of higher organisms, whose organisation is only partially understood. Here, we ...investigate the structure of such a network in human GM12878 cells, to derive a large scale picture of nuclear architecture. We find that the intensity of intra-chromosomal interactions is power-law distributed. Inter-chromosomal interactions are two orders of magnitude weaker and exponentially distributed, yet they are not randomly arranged along the genomic sequence. Intra-chromosomal contacts broadly occur between epigenomically homologous regions, whereas inter-chromosomal contacts are especially associated with regions rich in highly expressed genes. Overall, genomic contacts in the nucleus appear to be structured as a network of networks where a set of strongly individual chromosomal units, as envisaged in the 'chromosomal territory' scenario derived from microscopy, interact with each other via on average weaker, yet far from random and functionally important interactions.
•Methods on the implementation of polymer models describing chromatin folding are reviewed.•The related Molecular Dynamics simulations are discussed.•The SBS model is discussed in details as a case ...study.•Successful applications to chromatin folding are summarized.•The case study of the Sox9 locus is reviewed in details.
In recent years interest has grown on the applications of polymer physics to model chromatin folding in order to try to make sense of the complexity of experimental data emerging from new technologies such as Hi-C or GAM, in a principled way. Here we review the methods employed to efficiently implement Molecular Dynamics computer simulations of polymer models, focusing in particular on the String&Binders Switch (SBS) model. The constant improvement of such methods and computer power is returning increasingly more accurate insights on the structure and molecular mechanisms underlying the spatial organization of chromosomes in the cell nucleus. We aim to provide an account of the state of the art of computational techniques employed in this type of investigations and to review recent applications of such methods to the description of real genomic loci, such as the Sox9 locus in mESC.
Cooks syndrome (CS) is an ultrarare limb malformation due to
in tandem
microduplications involving
KCNJ2
and extending to the 5′ regulatory element of
SOX9
. To date, six CS families were resolved at ...the molecular level. Subsequent studies explored the evolutionary and pathological complexities of the
SOX9-KCNJ2/Sox9-Kcnj2
locus, and suggested a key role for the formation of novel topologically associating domain (TAD) by inter-TAD duplications in causing CS. Here, we report a unique case of CS associated with a de novo 1;17 translocation affecting the
KCNJ2
locus. On chromosome 17, the breakpoint mapped between
KCNJ16
and
KCNJ2
, and combined with a ~ 5 kb deletion in the 5′ of
KCNJ2
. Based on available capture Hi-C data, the breakpoint on chromosome 17 separated
KCNJ2
from a putative enhancer. Gene expression analysis demonstrated downregulation of
KCNJ2
in both patient’s blood cells and cultured skin fibroblasts. Our findings suggest that a complex rearrangement falling in the 5′ of
KCNJ2
may mimic the developmental consequences of
in tandem
duplications affecting the
SOX9-KCNJ2/Sox9-Kcnj2
locus. This finding adds weight to the notion of an intricate role of gene regulatory regions and, presumably, the related three-dimensional chromatin structure in normal and abnormal human morphology.
We investigate the three-dimensional (3D) conformations of the α-globin locus at the single-allele level in murine embryonic stem cells (ESCs) and erythroid cells, combining polymer physics models ...and high-resolution Capture-C data. Model predictions are validated against independent fluorescence in situ hybridization (FISH) data measuring pairwise distances, and Tri-C data identifying three-way contacts. The architecture is rearranged during the transition from ESCs to erythroid cells, associated with the activation of the globin genes. We find that in ESCs, the spatial organization conforms to a highly intermingled 3D structure involving non-specific contacts, whereas in erythroid cells the α-globin genes and their enhancers form a self-contained domain, arranged in a folded hairpin conformation, separated from intermingling flanking regions by a thermodynamic mechanism of micro-phase separation. The flanking regions are rich in convergent CTCF sites, which only marginally participate in the erythroid-specific gene-enhancer contacts, suggesting that beyond the interaction of CTCF sites, multiple molecular mechanisms cooperate to form an interacting domain.
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•The structure of the mouse α-globin locus is investigated with polymer physics models•The conformation is highly intermingled when the globin genes are inactive in ESCs•The locus is folded in a hairpin-shaped conformation when active in erythroid cells•The model accurately predicts three-way contacts, as confirmed by TriC experimental data
Chiariello et al. use polymer physics models to infer the 3D conformations of the murine α-globin locus. In the transition from ESCs to erythroid cells, the locus rearranges from an inactive highly intermingled conformation to an active, hairpin-shaped structure, marked by cell-specific three-way contacts accurately predicted by the models.
The high-mobility group Hmga family of proteins are non-histone chromatin-interacting proteins which have been associated with a number of nuclear functions, including heterochromatin formation, ...replication, recombination, DNA repair, transcription, and formation of enhanceosomes. Due to its role based on dynamic interaction with chromatin, Hmga2 has a pathogenic role in diverse tumors and has been mainly studied in a cancer context; however, whether Hmga2 has similar physiological functions in normal cells remains less explored. Hmga2 was additionally shown to be required during the exit of embryonic stem cells (ESCs) from the ground state of pluripotency, to allow their transition into epiblast-like cells (EpiLCs), and here, we use that system to gain further understanding of normal Hmga2 function. We demonstrated that Hmga2 KO pluripotent stem cells fail to develop into EpiLCs. By using this experimental system, we studied the chromatin changes that take place upon the induction of EpiLCs and we observed that the loss of Hmga2 affects the histone mark H3K27me3, whose levels are higher in Hmga2 KO cells. Accordingly, a sustained expression of polycomb repressive complex 2 (PRC2), responsible for H3K27me3 deposition, was observed in KO cells. However, gene expression differences between differentiating wt vs Hmga2 KO cells did not show any significant enrichments of PRC2 targets. Similarly, endogenous Hmga2 association to chromatin in epiblast stem cells did not show any clear relationships with gene expression modification observed in Hmga2 KO. Hmga2 ChIP-seq confirmed that this protein preferentially binds to the chromatin regions associated with nuclear lamina. Starting from this observation, we demonstrated that nuclear lamina underwent severe alterations when Hmga2 KO or KD cells were induced to exit from the naïve state and this phenomenon is accompanied by a mislocalization of the heterochromatin mark H3K9me3 within the nucleus. As nuclear lamina (NL) is involved in the organization of 3D chromatin structure, we explored the possible effects of Hmga2 loss on this phenomenon. The analysis of Hi-C data in wt and Hmga2 KO cells allowed us to observe that inter-TAD (topologically associated domains) interactions in Hmga2 KO cells are different from those observed in wt cells. These differences clearly show a peculiar compartmentalization of inter-TAD interactions in chromatin regions associated or not to nuclear lamina. Overall, our results indicate that Hmga2 interacts with heterochromatic lamin-associated domains, and highlight a role for Hmga2 in the crosstalk between chromatin and nuclear lamina, affecting the establishment of inter-TAD interactions.
Models of chromosome structure Nicodemi, Mario; Pombo, Ana
Current opinion in cell biology,
06/2014, Letnik:
28
Journal Article
Recenzirano
Odprti dostop
Understanding the mechanisms that control chromosome folding in the nucleus of eukaryotes and their contribution to gene regulation is a key open issue in molecular biology. Microscopy and ...chromatin-capture techniques have shown that chromatin has a complex organization, which dynamically changes across organisms and cell types. The need to make sense of such a fascinating complexity has prompted the development of quantitative models from physics, to find the principles of chromosome folding, its origin and function. Here, we concisely review recent advances in chromosome modeling, focusing on a recently proposed framework, the Strings & Binders Switch (SBS) model, which recapitulates key features of chromosome organization in space and time.
The X-linked gene encoding aristaless-related homeobox (
) is a bi-functional transcription factor capable of activating or repressing gene transcription, whose mutations have been found in a wide ...spectrum of neurodevelopmental disorders (NDDs); these include cortical malformations, paediatric epilepsy, intellectual disability (ID) and autism. In addition to point mutations, duplications of the
locus have been detected in male patients with ID. These rearrangements include telencephalon ultraconserved enhancers, whose structural alterations can interfere with the control of
expression in the developing brain. Here, we review the structural features of 15 gain copy-number variants (CNVs) of the
locus found in patients presenting wide-ranging phenotypic variations including ID, speech delay, hypotonia and psychiatric abnormalities. We also report on a further novel Xp21.3 duplication detected in a male patient with moderate ID and carrying a fully duplicated copy of the
locus and the ultraconserved enhancers. As consequences of this rearrangement, the patient-derived lymphoblastoid cell line shows abnormal activity of the ARX-KDM5C-SYN1 regulatory axis. Moreover, the three-dimensional (3D) structure of the
locus, both in mouse embryonic stem cells and cortical neurons, provides new insight for the functional consequences of
duplications. Finally, by comparing the clinical features of the 16 CNVs affecting the
locus, we conclude that-depending on the involvement of tissue-specific enhancers-the
duplications are ID-associated risk CNVs with variable expressivity and penetrance.
Recent super-resolution imaging technologies enable tracing chromatin conformation with nanometer-scale precision at the single-cell level. They revealed, for example, that human chromosomes fold ...into a complex three-dimensional structure within the cell nucleus that is essential to establish biological activities, such as the regulation of the genes. Yet, to decode from imaging data the molecular mechanisms that shape the structure of the genome, quantitative methods are required. In this review, we consider models of polymer physics of chromosome folding that we benchmark against multiplexed FISH data available in human loci in IMR90 fibroblast cells. By combining polymer theory, numerical simulations and machine learning strategies, the predictions of the models are validated at the single-cell level, showing that chromosome structure is controlled by the interplay of distinct physical processes, such as active loop-extrusion and thermodynamic phase-separation.
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