3D structures of individual mammalian genomes reveal principles of nuclear organization
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE80280 | GEO | 2017/03/07
SECONDARY ACCESSION(S): PRJNA318485
REPOSITORIES: GEO
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Project description:Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. elegans genome. By systematically and acutely inactivating each SMC complex, we observe that in contrast to other studied systems, cohesin creates small loops, while condensin I has a major role in genome folding: its inactivation causes genome-wide decompaction, chromosome mixing, loss of loops and TAD structures and reinforcement of fine-scale epigenomic compartments. Counter-intuitively, removal of condensin I and its X-specific variant condensin IDC from the X chromosomes led to the formation of a loop compartment coinciding with a subset of previously characterized loading sites for condensin IDC and bound by the X-targeting complex SDC. While transcriptional changes were limited for all autosomes upon cohesin and condensin II inactivation, removal of condensin I/IDC from the X chromosome led to transcriptional up-regulation of X-linked genes demonstrating that a sustained role for condensin IDC in gene regulation. Finally, while condensin I inactivation leads to reduced lifespan, we show that this reduction is due to X-specific gene upregulation rather than global genome decompaction.
2024-04-18 | GSE199721 | GEO
Project description:Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. elegans genome. By systematically and acutely inactivating each SMC complex, we observe that in contrast to other studied systems, cohesin creates small loops, while condensin I has a major role in genome folding: its inactivation causes genome-wide decompaction, chromosome mixing, loss of loops and TAD structures and reinforcement of fine-scale epigenomic compartments. Counter-intuitively, removal of condensin I and its X-specific variant condensin IDC from the X chromosomes led to the formation of a loop compartment coinciding with a subset of previously characterized loading sites for condensin IDC and bound by the X-targeting complex SDC. While transcriptional changes were limited for all autosomes upon cohesin and condensin II inactivation, removal of condensin I/IDC from the X chromosome led to transcriptional up-regulation of X-linked genes demonstrating that a sustained role for condensin IDC in gene regulation. Finally, while condensin I inactivation leads to reduced lifespan, we show that this reduction is due to X-specific gene upregulation rather than global genome decompaction.
2024-04-18 | GSE199719 | GEO
Project description:Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. elegans genome. By systematically and acutely inactivating each SMC complex, we observe that in contrast to other studied systems, cohesin creates small loops, while condensin I has a major role in genome folding: its inactivation causes genome-wide decompaction, chromosome mixing, loss of loops and TAD structures and reinforcement of fine-scale epigenomic compartments. Counter-intuitively, removal of condensin I and its X-specific variant condensin IDC from the X chromosomes led to the formation of a loop compartment coinciding with a subset of previously characterized loading sites for condensin IDC and bound by the X-targeting complex SDC. While transcriptional changes were limited for all autosomes upon cohesin and condensin II inactivation, removal of condensin I/IDC from the X chromosome led to transcriptional up-regulation of X-linked genes demonstrating that a sustained role for condensin IDC in gene regulation. Finally, while condensin I inactivation leads to reduced lifespan, we show that this reduction is due to X-specific gene upregulation rather than global genome decompaction.
2024-04-18 | GSE199717 | GEO
Project description:For a eukaryotic genome to properly function, its chromatin must be precisely organized, as genome topology impacts transcriptional regulation, cell division, DNA replication, and DNA repair, among other essential processes. Disruption of human genome topology can lead to disease states, such as cancer. The advent of chromosome conformation capture with high-throughput sequencing (Hi-C) technologies to assess genome organization has revolutionized our understanding of the arrangement of chromosomes within the nuclear genome. Critical developments include chromosomal territories, active/silent chromatin compartments, Topologically Associated Domains (TADs), and chromatin loops. However, to fully elucidate folding principles at the gene level, Hi-C datasets at an extremely high resolution are required: while low resolution (e.g., 40 kb bin) heatmaps can provide important insights into chromosomal level contacts, lower resolution datasets cannot provide information about individual gene or promoter contacts. Thus, high-resolution Hi-C datasets can elucidate principles of folding, including those of model organisms whose chromosome conformation can elucidate the folding of the human genome. Here, we have examined the high-resolution genome topology of the model fungal organism Neurospora crassa: our composite Hi-C dataset, generated using two restriction enzymes to monitor euchromatin (DpnII) and heterochromatin (MseI), provides exquisite detail for both larger chromosomal structures and individual gene contacts, including how repressed euchromatic genes associate with constitutive heterochromatic regions. Our high-resolution Neurospora Hi-C datasets should be an outstanding resource to the fungal community and provide valuable insights to the folding of higher organism genomes.
2022-03-01 | GSE173593 | GEO
Project description:Mammalian chromosomes are folded into intricate hierarchies of interaction domains, within which topologically associating domains (TADs) and CTCF-associated loops partition the physical interactions between regulatory sequences. Current understanding of chromosome folding largely relies on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after crosslinking of chromatin. To measure chromosome structure in vivo, quantitatively and without relying on crosslinking and ligation, we have implemented a modified version of damID named damC. DamC combines DNA-methylation based detection of chromosomal interactions with next-generation sequencing and a biophysical model of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of TADs and CTCF loops and confirms 3C-based measurements of the scaling of contact probabilities. Combining damC with transposon-mediated genomic engineering shows that new loops can be formed between ectopically introduced and endogenous CTCF sites, which alters the partitioning of physical interactions within TADs. This orthogonal approach to 3C provides the first crosslinking- and ligation-free validation of the existence of key structural features of mammalian chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.
2019-06-03 | PXD013507 | Pride
Project description:Eukaryotic genomes are folded into a hierarchy of three-dimensional structures that impact nuclear functions, including transcription, replication, and repair1-3. Studies in Drosophila and mammals have revealed megabase-sized topologically associated domains (TADs) within chromosomes, which in turn are spatially restricted within the nucleus4-8. However, little is known about local physical constraints that drive higher-order folding of chromosomes. Here we performed Hi-C analysis of the fission yeast Schizosaccharomyces pombe to explore genome organization at high resolution. S. pombe comprises a small genome ideal for examining structural features of chromatin folding, and contains fundamental components present in higher eukaryotes. Large domains of heterochromatin coat centromeres and telomeres and recruit cohesin, a ring-like protein complex that binds sister chromatids and mediates long range looping of interphase chromosomes. Our analyses reveal a highly ordered chromosome organization, consistent with a Rabl configuration, which is dependent on constraints imposed at centromeres and telomeres. We find that local chromatin compaction and cohesin recruitment to centromeres mediated by heterochromatin is required for maintaining global genome territorial restraint. In addition to larger complex domains, we also observed locally interacting regions of chromatin ~50 kilobases long, which organize chromosome arms into structures referred to as “globules”. Globule boundaries are enriched in cohesin and convergent gene orientation. The role of cohesin in maintaining globule domains is independent of its role in sister chromatid cohesion, as globule domains are also a feature of G1 chromosome architecture. Defect in cohesin disrupts globule domains and results in an altered chromosome organization at larger scales, including the loss of chromosome territories. Disruption of globules also affects functional annotation of the genome, leading to impairment of borders between neighboring transcriptional units. Our analyses reveal key features of chromatin organization and folding and show that distinct mechanisms uniquely impact the hierarchy of genome organization to protect genome integrity and to coordinate nuclear functions. Comparison of HiC contact maps under various conditions reveal fundamental principles of genome organization
2014-10-22 | E-GEOD-57316 | biostudies-arrayexpress
Project description:Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates’ secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. Our results suggest that cotranscriptional RNA folding in vivo is a mixture of cooperative folding events, in which local RNA secondary structure elements are formed as they get transcribed, and non-cooperative events, in which 5΄-halves of long-range helices get sequestered into transient non-native interactions until their 3΄ counterparts have been transcribed. Together our work provides the first transcriptome-scale overview of RNA cotranscriptional folding in a living organism.
2017-07-19 | GSE95567 | GEO
Project description:Background: The packaging of long chromatin fibres in the nucleus poses a major challenge, as it must fulfil both physical and functional requirements. Until recently, insight into the chromosomal architecture of plants was mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalised description of nuclear organization. Results: Employing circular chromosome conformation capture (4C), this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organisation of chromosomes is reflected in the genome-wide interactome. In addition, we studied the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 (hk4s) maintained a pericentromere-like interaction profile and interactome despite its euchromatic surrounding. Conclusion: Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: (i) heterochromatin and euchromatin represent two distinct interactomes, (ii) interactions between chromosomes correlates with the linear position on the chromosome arm, and (iii) distal chromosome regions have a higher potential to interact with other chromosomes.
2013-11-01 | GSE50181 | GEO
Project description:Background: The packaging of long chromatin fibres in the nucleus poses a major challenge, as it must fulfil both physical and functional requirements. Until recently, insight into the chromosomal architecture of plants was mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalised description of nuclear organization. Results: Employing circular chromosome conformation capture (4C), this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organisation of chromosomes is reflected in the genome-wide interactome. In addition, we studied the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 (hk4s) maintained a pericentromere-like interaction profile and interactome despite its euchromatic surrounding. Conclusion: Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: (i) heterochromatin and euchromatin represent two distinct interactomes, (ii) interactions between chromosomes correlates with the linear position on the chromosome arm, and (iii) distal chromosome regions have a higher potential to interact with other chromosomes. This study includes circular chromosome conformation capture (4C) sequencing information of 13 samples, present in two batches, each present in duplicates (A and B). The individual 4C sequencing information can be retrieved by the 4C primer sequence, given in the 4C primer information file.
2013-11-01 | E-GEOD-50181 | biostudies-arrayexpress
Project description: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 understanding of chromosome folding largely relies on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after crosslinking of chromatin. To measure chromosome structure in vivo, quantitatively and without relying on crosslinking and ligation, we have implemented a new method named damC. DamC combines DNA-methylation based detection of chromosomal interactions with next-generation sequencing and a biophysical model of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of TADs and CTCF loops, confirms 3C-based measurements of the scaling of contact probabilities within TADs, and provides evidence that mammalian chromatin in vivo is essentially rigid below 5 kilobases. Combining damC with transposon-mediated genomic engineering shows that new loops can be formed between ectopically introduced and endogenous CTCF sites, which alters the partitioning of physical interactions within TADs. This establishes damC as a crosslinking- and ligation-free framework to measure and modify chromosome interactions combined with a solid theoretical background for rigorous data interpretation. This orthogonal approach to 3C validates the existence of key structural features of mammalian chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.
2019-05-16 | GSE128014 | GEO