Long-distance association of topological boundaries through nuclear condensates
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA801249 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Chromatin is partitioned into distinct topological domains in an activity-dependent manner, with topological boundaries limiting the interaction between adjacent domains. Recent studies support the concept that several well-established nuclear compartments are assembled as ribonucleoprotein condensates. Here we ask whether the physical processes driving the assembly of the nuclear condensates play any role in three-dimensional chromatin architecture. We report that the insulation of approximately 20% of topological boundaries in human embryonic stem cells is substantially weakened following brief treatment with 1,6-hexanediol, a chemical known to disrupt several nuclear condensates. The disrupted boundaries are characterized by a high level of transcription, striking spatial clustering, and the augmented presence of transcription units widely expressed in diverse cell types. These topological boundary regions tend to be spatially associated, even inter-chromosomally, and segregate with nuclear speckles. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring widely-expressed transcription units and associated transcriptional condensates.
2022-06-15 | GSE195563 | GEO
Project description:Chromatin is partitioned into distinct topological domains in an activity-dependent manner, with topological boundaries limiting the interaction between adjacent domains. Recent studies support the concept that several well-established nuclear compartments are assembled as ribonucleoprotein condensates. Here we ask whether the physical processes driving the assembly of the nuclear condensates play any role in three-dimensional chromatin architecture. We report that the insulation of approximately 20% of topological boundaries in human embryonic stem cells is substantially weakened following brief treatment with 1,6-hexanediol, a chemical known to disrupt several nuclear condensates. The disrupted boundaries are characterized by a high level of transcription, striking spatial clustering, and the augmented presence of transcription units widely expressed in diverse cell types. These topological boundary regions tend to be spatially associated, even inter-chromosomally, and segregate with nuclear speckles. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring widely-expressed transcription units and associated transcriptional condensates.
2022-06-15 | GSE195562 | GEO
Project description:Chromatin is partitioned into distinct topological domains in an activity-dependent manner, with topological boundaries limiting the interaction between adjacent domains. Recent studies support the concept that several well-established nuclear compartments are assembled as ribonucleoprotein condensates. Here we ask whether the physical processes driving the assembly of the nuclear condensates play any role in three-dimensional chromatin architecture. We report that the insulation of approximately 20% of topological boundaries in human embryonic stem cells is substantially weakened following brief treatment with 1,6-hexanediol, a chemical known to disrupt several nuclear condensates. The disrupted boundaries are characterized by a high level of transcription, striking spatial clustering, and the augmented presence of transcription units widely expressed in diverse cell types. These topological boundary regions tend to be spatially associated, even inter-chromosomally, and segregate with nuclear speckles. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring widely-expressed transcription units and associated transcriptional condensates.
2022-06-15 | GSE195561 | GEO
Project description:Chromatin is partitioned into distinct topological domains in an activity-dependent manner, with topological boundaries limiting the interaction between adjacent domains. Recent studies support the concept that several well-established nuclear compartments are assembled as ribonucleoprotein condensates. Here we ask whether the physical processes driving the assembly of the nuclear condensates play any role in three-dimensional chromatin architecture. We report that the insulation of approximately 20% of topological boundaries in human embryonic stem cells is substantially weakened following brief treatment with 1,6-hexanediol, a chemical known to disrupt several nuclear condensates. The disrupted boundaries are characterized by a high level of transcription, striking spatial clustering, and the augmented presence of transcription units widely expressed in diverse cell types. These topological boundary regions tend to be spatially associated, even inter-chromosomally, and segregate with nuclear speckles. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring widely-expressed transcription units and associated transcriptional condensates.
2022-06-15 | GSE195565 | GEO
Project description:Long-distance association of topological boundaries through nuclear condensates (GRO-Seq)
| PRJNA801254 | ENA
Project description:Long-distance association of topological boundaries through nuclear condensates (ChIP-Seq)
| PRJNA801255 | ENA
Project description:Long-distance association of topological boundaries through nuclear condensates (Hi-C)
| PRJNA801256 | ENA
Project description:Long-distance association of topological boundaries through nuclear condensates (PRO-Seq)
| PRJNA801257 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-06-13 | GSE195566 | GEO
Project description:The nucleus contains diverse phase-separated condensates that compartmentalize and concentrate biomolecules with distinct physicochemical properties. Here we consider whether condensates concentrate small molecule cancer therapeutics such that their pharmacodynamic properties are altered. We found that antineoplastic drugs become concentrated in specific protein condensates in vitro and that this occurs through physicochemical properties independent of the drug target. This behavior was also observed in tumor cells, where drug partitioning influenced drug activity. Altering the properties of the condensate was found to impact the concentration and activity of drugs. These results suggest that selective partitioning and concentration of small molecules within condensates contributes to drug pharmacodynamics and that further understanding of this phenomenon may facilitate advances in disease therapy.
2020-04-27 | GSE149085 | GEO