Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of HMGN variants on cellular transcription profile

ABSTRACT: HMGN (high mobility group N) is a family of intrinsically disordered nuclear proteins that binds to nucleosomes, alters the structure of chromatin and affects transcription. A major unresolved question is the extent of functional specificity, or redundancy, between the various members of the HMGN protein family. Here we analyze the transcriptional profile of cells in which the expression of various HMGN proteins has been either deleted or doubled. The results reveal an HMGN-variant specific effect on the fidelity of the cellular transcription profile, indicating that functionally, the various HMGN subtypes are not fully redundant.

ORGANISM(S): Mus musculus

PROVIDER: GSE27546 | GEO | 2011/02/28

SECONDARY ACCESSION(S): PRJNA137095

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Effects of HMGN variants on cellular transcription profile

Project description:HMGN (high mobility group N) is a family of intrinsically disordered nuclear proteins that binds to nucleosomes, alters the structure of chromatin and affects transcription. A major unresolved question is the extent of functional specificity, or redundancy, between the various members of the HMGN protein family. Here we analyze the transcriptional profile of cells in which the expression of various HMGN proteins has been either deleted or doubled. The results reveal an HMGN-variant specific effect on the fidelity of the cellular transcription profile, indicating that functionally, the various HMGN subtypes are not fully redundant. RNA was collected from either primary knock-out MEFs or SV40-transformed MEFs and MIN6 cells over expressing various HMGN proteins and mutants and hybridized to Affymetrix arrays. We obtained a double ammount of HMGN proteins in MEFs and MIN6 cells by retroviral infection and subsequent selection procedure. We collected all infected cells (pools, not clones) in order to eliminate the effect of viral integration in the genome.

2011-02-28 | E-GEOD-27546 | biostudies-arrayexpress

Expression data from AtT20 mouse pituitary gland cells following overexpression or down regulation of NSBP1

2009-06-13 | GSE16564 | GEO

Transcription profiling of mouse AtT20 pituitary gland cells following overexpression or down regulation of NSBP1

Project description:Chromatin architectural protein NSBP1/HMGN5 belongs to the family of HMGN proteins which specifically interact with nucleosomes via Nucleosome Binding Domain, unfold chromatin and affect transcription. Mouse NSBP1 is a new and uncharacterized member of HMGN protein family. NSBP1 is a nuclear protein which is localized to euchromatin, binds to linker histone H1 and unfolds chromatin. We analyzed the effect of altered expression levels of mouse NSBP1 protein on global gene expression profile in AtT20 pituitary cells. We found that NSBP1 modulates the fidelity of cellular transcription in the nucleosome binding-dependent manner. Experiment Overall Design: Stable clones overexpressing wild type mouse NSBP1 protein or mutated NSBP1SE protein which does not bind to nucleosomes were generated by retroviral infection of AtT20 cells. siRNA treatment was applied to down regulate NSBP1 in the cells. Total RNA was collected from biological triplicates and analyzed by Affymetrix expression arrays.

2009-06-23 | E-GEOD-16564 | biostudies-arrayexpress

Proteomic Profile of Daphnia pulex using Data-Independent Acquisition Mass Spectrometry and Ion Mobility Separation

Project description:In this study, various sample preparation and mass spectrometry acquisition methods were performed for the purpose of improving Daphnia pulex proteome exploration. We observed benefits for employing both in-gel and in-solution methods of trypsin digestion. Furthermore, data independent acquisition methods employing ion-mobility separation greatly increased peptide identification and more than doubled our proteome coverage.

2018-07-11 | PXD008455 | Pride

Structural dynamics of the chicken TRPV4 N-terminal domain

Project description:Intrinsically disordered regions (IDRs) are essential for membrane receptor regulation but often remain unresolved in structural studies. TRPV4, a member of the TRP vanilloid channel family involved in thermo- and osmosensation, has a large N-terminal IDR of approximately 150 amino acids. With an integrated structural biology approach, we analyze the structural ensemble of the TRPV4 IDR and identify a network of regulatory elements that modulate channel activity in a hierarchical lipid-dependent manner through transient long-range interactions. A highly conserved autoinhibitory patch acts as a master regulator by competing with PIP2 binding to attenuate channel activity. Molecular dynamics simulations show that loss of the interaction between PIP2-binding site and the membrane reduces the force exerted by the IDR on the structured core of TRPV4. This work demonstrates that IDR structural dynamics are coupled to TRPV4 activity and highlights the importance of IDRs for TRP channel function and regulation.

2023-10-24 | PXD041067 | Pride

Saccharomyces cerevisiae BY4741

Project description:Intrinsically disordered regions direct transcription factor in-vivo binding specificity

| PRJNA573518 | ENA

SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ChIP-Seq Dataset 3]

Project description:The transition from pluripotent to somatic states marks a critical checkpoint in mammalian development. How this is regulated remains largely unresolved. Here we report the identification of SS18 by whole genome CRISPR screen as a checkpoint regulator. SS18 regulates pluripotent to somatic transition or PST by relocating from pluripotent loci to somatic ones accompanied by corresponding chromatin closing-opening and remodeling of SS18-centric protein complexes. Mechanistically, SS18 forms phase separation granules (PSG) with an intrinsically disordered region (IDR) rich in tyrosine (Y), which, once mutated, no longer form PSG nor rescue SS18-/- defect in PST. These results reveal that rapid cell fate decision can be achieved by massive redistribution of chromatin remodeling37 complexes through phase separation.

2021-05-31 | GSE175818 | GEO

SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ChIP-Seq Dataset 2]

2021-05-18 | GSE152175 | GEO

SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [RNA-Seq]

2021-05-18 | GSE135397 | GEO

SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [ATAC-Seq]

2021-05-18 | GSE135395 | GEO