Metaphase-Chromosome-Organization
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR351511_1.fastq.gz | Fastqsanger.gz | |||
| ERR351511_2.fastq.gz | Fastqsanger.gz | |||
| ERR351512_1.fastq.gz | Fastqsanger.gz | |||
| ERR351512_2.fastq.gz | Fastqsanger.gz | |||
| ERR351513_1.fastq.gz | Fastqsanger.gz |
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Project description:Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved. We applied chromosome conformation capture methods, 5C and Hi-C, across the cell cycle and revealed two alternative three-dimensional folding states of the human genome. We show that the highly compartmentalized and cell-type-specific organization described previously for non-synchronous cells is restricted to interphase. In metaphase, we identify a homogenous folding state, which is locus-independent, common to all chromosomes, and consistent among cell types, suggesting a general principle of metaphase chromosome organization. Using polymer simulations, we find that metaphase Hi-C data is inconsistent with classic hierarchical models, and is instead best described by a linearly-organized longitudinally compressed array of consecutive chromatin loops.
2013-11-05 | E-MTAB-1948 | biostudies-arrayexpress
Project description:Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.
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Project description:Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.
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Project description:Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.
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Project description:Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.
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Project description:Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.
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Project description:Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.
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