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Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [RNA-seq]

ABSTRACT: Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [RNA-seq]

PROVIDER: PRJNA918623 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22986100_1.fastq.gz	Fastqsanger.gz
	SRR22986100_2.fastq.gz	Fastqsanger.gz
	SRR22986101_1.fastq.gz	Fastqsanger.gz
	SRR22986101_2.fastq.gz	Fastqsanger.gz
	SRR22986102_1.fastq.gz	Fastqsanger.gz

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Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [Hi-C]

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Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [ATAC-seq]

Project description:Chemicals or drugs were demonstrated to accumulate within biomolecule condensates formed through phase separation in cells. Here, we employed super-resolution imaging to search for chemicals that induce phase transition of chromatin at the microscale. We found that adriamycin (doxorubicin), a widely-used chemotherapeutic drug against malignancies, is able to induce local condensation and global conformational change of chromatin in cancer and primary cells. Hi-C and ATAC-seq experiments demonstrated that adriamycin-induced chromatin condensation is accompanied by weakened chromatin interaction within topologically-associated domains, compartment A/B switching, lower chromatin accessibility, and corresponding transcriptomic changes. Mechanistically, adriamycin complexes with histone H1 and induces the phase transition of H1, forming fibrous aggregates in vitro. Our results reveal a new action mechanism of an anti-cancer drug discovered for decades, demonstrate the link between the physical properties of chromatin and gene expression, and suggest that interactions between drugs and biomolecules could exert profound effects on cells.

2023-01-11 | GSE222220 | GEO

Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [RNA-seq]

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Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [Hi-C]

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Chemical-induced phase transition and global conformational reorganization of chromatin.

Project description:Chemicals or drugs can accumulate within biomolecular condensates formed through phase separation in cells. Here, we use super-resolution imaging to search for chemicals that induce phase transition within chromatin at the microscale. This microscopic screening approach reveals that adriamycin (doxorubicin) - a widely used anticancer drug that is known to interact with chromatin - specifically induces visible local condensation and global conformational change of chromatin in cancer and primary cells. Hi-C and ATAC-seq experiments systematically and quantitatively demonstrate that adriamycin-induced chromatin condensation is accompanied by weakened chromatin interaction within topologically associated domains, compartment A/B switching, lower chromatin accessibility, and corresponding transcriptomic changes. Mechanistically, adriamycin complexes with histone H1 and induces phase transition of H1, forming fibrous aggregates in vitro. These results reveal a phase separation-driven mechanism for a chemotherapeutic drug.

| S-EPMC10492836 | biostudies-literature

Juvenility and Vegetative Phase Transition in Tropical/Subtropical Tree Crops.

Project description:In plants, juvenile to adult phase transition is regulated by the sequential activity of two microRNAs: miR156 and miR172. A decline in miR156 and increase in miR172 abundance is associated with phase transition. There is very limited information on phase transition in economically important horticultural tree crops, which have a significantly long vegetative phase affecting fruit bearing. Here we profiled various molecular cues known to be involved in phase transition and flowering, including the microRNAs miR156 and miR172, in three horticultural tree crops avocado (Persea americana), mango (Mangifera indica) and macadamia (Macadamia integrifolia). We observed that miR156 expression decreases as these trees age and can potentially be used as a juvenility marker. Consistent with findings in annual plants, we also observed conserved regulation of the miR156-SPL3/4/5 regulatory module in these genetically distant tree crops, suggesting that this pathway may play a highly conserved role in vegetative identity. Meanwhile, the abundance of miR172 and its target AP2-like genes, as well as the accumulation level of SPL9 transcripts, were not related with plant age in these crops except in avocado where miR172 expression increased steadily. Finally, we demonstrate that various floral genes, including AP1 and SOC1 were upregulated in the reproductive phase and can be used as potential markers for the reproductive phase transition. Overall, this study provides an insight into the molecular associations of juvenility and phase transition in horticultural trees where crop breeding and improvement is encumbered by long juvenile phases.

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Characterization of estrogen and the endocrine-disrupting chemical-induced mouse mammary gland reorganization

Project description:Characterization of estrogen and the endocrine-disrupting chemical-induced mouse mammary gland reorganization

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Project description:This study is based on two microarray datasets, in one hand a phase transition comparison using the expression profiles of 630E strain after 4h and 10h of growth. In other hand a comparison at 10h of growth between a mutant of the sigH gene and the WT strains. This experimental procedure was designed to investigate the effect of sigH in the growth phase transition of Clostridium difficile. This SuperSeries is composed of the SubSeries listed below.

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