Chromosomal Architecture of Arabidopsis and its Implication in Transposon Intergration
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE55960 | GEO | 2014/08/18
SECONDARY ACCESSION(S): PRJNA241437
REPOSITORIES: GEO
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Project description:Efficient storing and readout of genetic information is not only dependent on tight epigenetic regulation but also on the spatial organization and folding of chromosomes. Although the epigenome of the model plant Arabidopsis has been extensively studied, its interplay with chromosomal architecture is less well understood. We show that chromosomal architecture is tightly linked to the epigenetic state and furthermore how physical constraints such as nuclear size influence folding principles of chromatin. In addition to global principles of chromatin organisation, we describe a novel nuclear structure, termed KNOT, in which genomic regions of all five Arabidopsis chromosomes highly interact. These regions are characterized as heterochromatic islands within the euchromatin and likely represent preferred landing sites for transposons, suggesting a novel transposon defence mechanism in the Arabidopsis nucleus. HiC experiments were performed on Arabidopsis thaliana Col-0 wildtype, homozygous crwn1-1, and homozygous crwn4-1 14-day-old seedlings
2014-08-18 | E-GEOD-55960 | biostudies-arrayexpress
Project description:The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and regions associated with nuclear lamina and nucleoli, have been discovered. However, how these structures are arranged in the same cell and how they are correlated with each other in different cell types in mammalian tissue are largely unknown. Here, we developed Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We applied this method in mouse fetal liver, and identified de novo cell-type-specific chromatin architectures associated with gene expression, as well as chromatin organization principles independent of cell type. Polymer simulation showed that both intra-chromosomal self-associating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our experiments and modeling provide a multiscale and multi-faceted picture of chromatin folding and nucleome architectures in mammalian tissue and illustrate physical principles for maintaining chromatin organization. Here we submit our bulk RNA-sequencing data on E14.5 mouse fetal liver, used in the study to validate image-based RNA profiling results.
2020-05-15 | GSE148072 | GEO
Project description:The three-dimensional (3D) folding of the chromosomal fibre in the human interphase nucleus is an important, but poorly understood aspect of gene regulation. Especially basic principles of 3D chromatin and chromosome organisation are still elusive. In this paper, we quantitatively analyse the 3D structure of large parts of chromosomes 1 and 11 in the G1 nucleus of human cells and relate it to the human transcriptome map (HTM). Despite a considerable cell-to-cell variation, our results show that subchromosomal domains, which are highly expressed, are more decondensed, have a more irregular shape and are located in the nuclear interior compared to clusters of low expressed genes. These aspects of chromosome structure are shared by six different cell lines and therefore are independent of cell type specific differences in gene expression within the investigated domains. Systematic measurements show that there is little to no intermingling of chromatin from different parts of the same chromosome, indicating that the chromosomal fibre itself is a compact structure. Together, our results reveal several basic aspects of 3D chromosome architecture, which are related to genome function. Experiment Overall Design: The data sets presented here together with sample GSM153780, accompany the paper: "The 3D structure of human interphase chromosomes is related to the transcriptome mapâ by Goetze et al., (submitted). All cells were grown under standard conditions (see table below) and harvested at 70% confluency. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate transcriptome maps.
2008-06-15 | E-GEOD-6890 | biostudies-arrayexpress
Project description:Chemical cross-linking and high-throughput sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no such interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of chromatin folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. Male Drosophila salivary glands are compared to normally replicated 0-6 hour embryos to determine the differentially underreplicated regions of polytene chromosomes.
2015-11-05 | E-GEOD-72511 | biostudies-arrayexpress
Project description:Chemical cross-linking and high-throughput sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no such interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of chromatin folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-11-05 | E-GEOD-72512 | biostudies-arrayexpress
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: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:The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Further, our data support that CTCF mediates transcriptional insulator function through enhancer-blocking but not direct facultative heterochromatin barrier activity. Beyond defining the functions of CTCF in chromosome folding these results provide new fundamental insights into the rules governing mammalian genome organization.
2017-05-25 | GSE98671 | 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.
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Project description:Chemical cross-linking and high-throughput sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no such interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of chromatin folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. Hi-C experiments where ligation is performed on beads (tethered) on male Drosophila salivary glands from three independent biological replicates. Also one Hi-C experiment where the ligation is performed in solution (conventional).
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