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Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (RNA-seq)

ABSTRACT: Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (RNA-seq)

PROVIDER: PRJNA1302837 | ENA |

REPOSITORIES: ENA

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Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space.

Project description:Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space.

| PRJNA1302778 | ENA

Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (TSA-seq)

Project description:Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (TSA-seq)

| PRJNA1298163 | ENA

Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (RNA-seq)

Project description:A subset of highly active chromosomal "hot zones" reproducibly positions adjacent to nuclear speckles (NS). Genes within these regions amplify their expression with NS proximity. However, gene expression changes inversely correlate with changes in NS distance genome-wide. We hypothesized the existence of additional gene expression "niches" away from but spatially correlated with NS. Here we report the identification of two dynamic perispeckle patterns of protein concentrations extending outwards from nuclear speckles and persisting even after NS are eliminated. Highly active chromosome regions which weakly associate with NS instead show close, NS-independent association with these perispeckle patterns. Additionally, transcripts from model intron-containing versus intronless genes associate differentially with these two patterns. While genes within speckle-associated genomic regions predominately are downregulated upon nuclear speckle depletion, genes associated with perispeckle patterns are biased towards upregulation. We suggest the interchromatin space (ICS) is partitioned into additional gene expression “niches”- surrounding and extending from nuclear speckles- that may be involved in mRNA and gene dynamics.

2025-08-27 | GSE304817 | GEO

Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space (TSA-seq)

2025-08-27 | GSE303871 | GEO

Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space.

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

2025-08-27 | GSE304818 | GEO

Regions of very low H3K27me3 partition the Drosophila genome into topological domains

Project description:Regions of very low H3K27me3 partition the Drosophila genome into topological domains

| PRJNA338669 | ENA

Bacillus subtilis spores, PROTECT experiment, Space-exposed and Mars-exposed vs. Earth-control

Project description:Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars. Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.

2012-05-31 | E-GEOD-37124 | biostudies-arrayexpress

Distinct Stress Response to Mitochondrial Inter-membrane Space and Matrix Proteotoxic Stress are Preferentially Modulated by TOM complex and Vms1, respectively

Project description:Double-membrane-bound architecture of mitochondria is essential for its ATP synthesis function; simultaneously such structure sub-divides the organelle into inter-membrane space (IMS) and matrix. IMS and matrix are inherently different in protein folding milieu due to their contrasting oxido-reductive environments and distinctly different protein quality control (PQC) machineries. By inducing proteotoxic stress limited to IMS or matrix using varied stressor proteins, we decipher distinct cellular response to IMS and matrix stress. IMS stress leads to specific upregulation of IMS-resident chaperones and TOM complex components. In contrast, matrix stress leads to specific upregulation of matrix- chaperones and cytosolic PQC components. We report that cells respond to mitochondrial stress by an adaptive mechanism by adjourning mitochondrial respiration while upregulating glycolysis as a compensatory pathway. By systematic genetic interaction, we show that TOM complex components act as specific modulators of IMS-stress response while Vms1 preferentially modulates the matrix stress response

2024-07-09 | PXD027216 | Pride

Rhodospirillum rubrum S1H Space Flight Experiments

Project description:This SuperSeries is composed of the following subset Series: GSE14239: MESSAGE 2 space experiment with Rhodospirillum rubrum S1H GSE14241: BASE-A space experiment with Rhodospirillum rubrum S1H Refer to individual Series

2010-05-16 | E-GEOD-14265 | biostudies-arrayexpress

BASE-A space experiment with Rhodospirillum rubrum S1H

Project description:R. rubrum S1H inoculated on solid minimal media was sent to the ISS in September 2006 (BASE-A experiment). After 10 days flight, R. rubrum cultures returned back to Earth. These cultures were then subjected to both transcriptomic and proteomic analysis and compared with the corresponding ground control. Whole-genome oligonucleotide microarray and high throughput proteomics, which offer the possibility to survey respectively the global transcriptional and translational response of an organism, were used to test the effect of space flight. Moreover, in an effort to identify a specific stress response of R. rubrum to space flight, ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations, which lead to a more solid dissection of the different factors contribution acting in space flight conditions. Total RNA was extracted from R. rubrum S1H grown after 10 days in space flight or after 10 days in simulated ionizing radiation or simulated microgravity. Each microarray slide contained 3 technical repeats.

2010-05-16 | E-GEOD-14241 | biostudies-arrayexpress

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