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Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [SuperSeries]

ABSTRACT: Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [SuperSeries]

PROVIDER: PRJNA1169930 | ENA |

REPOSITORIES: ENA

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Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [SuperSeries]

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-07-10 | GSE279021 | GEO

Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [RNA-seq]

Project description:To date, most studies explored changes in 3D-genome organization between different tissues or during differentiation, which involve massive reprogramming of transcriptional programs. Much fewer studies examined alterations in genome organization in response to cellular stress, which involves less pervasive transcriptional modulation. Here, we examined associations between spatial chromatin organization and gene expression in two different biological contexts: transcriptional programs determining cell identity and transcriptional responses to stress, using p53 activation as a model. We selected 10 cell lines of diverse tissues, and in each performed micro-C, RNA-seq, and p53 ChIP-seq, before and after p53 induction. In the comparison between cell types, we delineated marked correlations between gene expression and spatial genome organization and identified hundreds of active enhancer–promoter loops associated with the expression of cell-type marker genes. In contrast, within each cell type, no such links were observed for expression changes induced by p53 activation, even for enhancers and promoters activated by p53 binding. Our analysis points to a fundamental difference between chromatin interactions that define cell identity and those that are established in response to cellular stress. Our results on p53-induced transcriptional responses support the recently proposed TF activity gradient model, which speculated a contact-independent mechanism for enhancer–promoter communication.

2025-07-10 | GSE278979 | GEO

Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [Micro-C]

Project description:To date, most studies explored changes in 3D-genome organization between different tissues or during differentiation, which involve massive reprogramming of transcriptional programs. Much fewer studies examined alterations in genome organization in response to cellular stress, which involves less pervasive transcriptional modulation. Here, we examined associations between spatial chromatin organization and gene expression in two different biological contexts: transcriptional programs determining cell identity and transcriptional responses to stress, using p53 activation as a model. We selected 10 cell lines of diverse tissues, and in each performed micro-C, RNA-seq, and p53 ChIP-seq, before and after p53 induction. In the comparison between cell types, we delineated marked correlations between gene expression and spatial genome organization and identified hundreds of active enhancer-promoter loops associated with the expression of cell-type marker genes. In contrast, within each cell type, no such links were observed for expression changes induced by p53 activation, even for enhancers and promoters activated by p53 binding. Our analysis points to a fundamental difference between chromatin interactions that define cell identity and those that are established in response to cellular stress. Our results on p53-induced transcriptional responses support the recently proposed TF activity gradient model, which speculated a contact-independent mechanism for enhancer-promoter communication.

2025-07-10 | GSE278978 | GEO

Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [ChIP-seq]

Project description:To date, most studies explored changes in 3D-genome organization between different tissues or during differentiation, which involve massive reprogramming of transcriptional programs. Much fewer studies examined alterations in genome organization in response to cellular stress, which involves less pervasive transcriptional modulation. Here, we examined associations between spatial chromatin organization and gene expression in two different biological contexts: transcriptional programs determining cell identity and transcriptional responses to stress, using p53 activation as a model. We selected 10 cell lines of diverse tissues, and in each performed micro-C, RNA-seq, and p53 ChIP-seq, before and after p53 induction. In the comparison between cell types, we delineated marked correlations between gene expression and spatial genome organization and identified hundreds of active enhancer-promoter loops associated with the expression of cell-type marker genes. In contrast, within each cell type, no such links were observed for expression changes induced by p53 activation, even for enhancers and promoters activated by p53 binding. Our analysis points to a fundamental difference between chromatin interactions that define cell identity and those that are established in response to cellular stress. Our results on p53-induced transcriptional responses support the recently proposed TF activity gradient model, which speculated a contact-independent mechanism for enhancer-promoter communication.

2025-07-10 | GSE278977 | GEO

Neonatal Heart Maturation (NHM) SuperSeries GSE85728

Project description:Neonatal Heart Maturation (NHM) SuperSeries GSE85728

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Dkk4 and Eda regulate distinctive developmental mechanisms for subtypes of mouse hair

Project description:This SuperSeries is composed of the following subset Series: GSE19309: Dkk4 and Eda regulate distinctive developmental mechanisms for subtypes of mouse hair-1 GSE19312: Dkk4 and Eda regulate distinctive developmental mechanisms for subtypes of mouse hair-2 Refer to individual Series

2010-09-03 | E-GEOD-19364 | biostudies-arrayexpress

STAG proteins mediate heterochromatin organization to support translation and cell identity [UMI-4C]

Project description:STAG proteins mediate heterochromatin organization to support translation and cell identity [UMI-4C]

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STAG proteins mediate heterochromatin organization to support translation and cell identity [Iso-Seq]

Project description:STAG proteins mediate heterochromatin organization to support translation and cell identity [Iso-Seq]

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STAG proteins mediate heterochromatin organization to support translation and cell identity [RNA-Seq]

Project description:STAG proteins mediate heterochromatin organization to support translation and cell identity [RNA-Seq]

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Distinctive features of the central synaptic organization of <i>Drosophila</i> larval proprioceptors.

Project description:Proprioceptive feedback is critically needed for locomotor control, but how this information is incorporated into central proprioceptive processing circuits remains poorly understood. Circuit organization emerges from the spatial distribution of synaptic connections between neurons. This distribution is difficult to discern in model systems where only a few cells can be probed simultaneously. Therefore, we turned to a relatively simple and accessible nervous system to ask: how are proprioceptors' input and output synapses organized in space, and what principles underlie this organization? Using the Drosophila larval connectome, we generated a map of the input and output synapses of 34 proprioceptors in several adjacent body segments (5-6 left-right pairs per segment). We characterized the spatial organization of these synapses, and compared this organization to that of other somatosensory neurons' synapses. We found three distinguishing features of larval proprioceptor synapses: (1) Generally, individual proprioceptor types display segmental somatotopy. (2) Proprioceptor output synapses both converge and diverge in space; they are organized into six spatial domains, each containing a unique set of one or more proprioceptors. Proprioceptors form output synapses along the proximal axonal entry pathway into the neuropil. (3) Proprioceptors receive few inhibitory input synapses. Further, we find that these three features do not apply to other larval somatosensory neurons. Thus, we have generated the most comprehensive map to date of how proprioceptor synapses are centrally organized. This map documents previously undescribed features of proprioceptors, raises questions about underlying developmental mechanisms, and has implications for downstream proprioceptive processing circuits.

| S-EPMC10410283 | biostudies-literature

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