SPH041
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:A non-synonymous HMGA2 variant decreases height in Shetland ponies and other small horses
| PRJEB9269 | ENA
Project description:The mechanism of body growth in mammals is poorly understood. Here, we report the regulatory networks involved in body growth through analyzing transcriptomes of pituitary and epiphyseal tissues of Debao ponies and Mongolian horses at juvenile and adult stages. We found that GHR was expressed little in long bones though GH was highly expressed in Debao ponies compared with Mongolian horses. Moreover, m-RAS and ATF3, involved in the GHR pathway, were found to be significantly downregulated in juvenile ponies, which slowed the proliferation of bone osteocytes. However, WNT2 and PLCβ2 were obviously upregulated in juvenile Debao ponies, which led to premature mineralization of bone extracellular matrix. Furthermore, we found that the WNT/Ca2+ pathway may be responsible for the regulation of body growth. We then demonstrated that GHR was lacking in long bones of Debao ponies using RT-qPCR and Western blot. Treatment with WNT antagonist 1 decreased expression of the WNT pathway (P≤0.05) in vitro. The transduction of ATDC5 cells with GHR-RNAi lentivirus decreased expression of the GHR pathway (P≤0.05). Additionally, detection of plasma hormone concentrations showed that the ponies had higher levels of IGF-1 as juveniles and GH in adulthood than Mongolian horses, indicating that the hormone regulation in Debao ponies differs from that in Mongolian horses. Our work provides an insight into the genetic regulation for dwarf growth in mammals and a reference for therapeutic strategy for dwarfism
2021-01-27 | GSE146145 | GEO
Project description:Small RNA isolated from synovial fluid of the metacarpophalangeal joints of horses. Horses either had minimal signs of osteoarthritis based on macroscopic and microscopic joint scoring or early (mild) osteoarthritis. Differential expression of small non-coding RNAs was undertaken.
2020-06-30 | E-MTAB-8409 | biostudies-arrayexpress
Project description:Identification of the locus causing skeletal atavism in Shetland ponies
| PRJNA303134 | ENA
Project description:The eukaryotic genome is organized into chromatins, the physiological template for DNA-dependent processes including replication, recombination, repair, and transcription. Chromatin-mediated transcription regulation involves DNA methylation, chromatin remodeling, and histone modifications. However, chromatin also contains non-histone chromatin-associated proteins, of which the high-mobility group (HMG) proteins are the most abundant. Although it is known that HMG proteins induce structural changes of chromatin, the processes underlying transcription regulation by HMG proteins are poorly understood. Here we decipher the molecular mechanism of transcription regulation mediated by the HMG AT-hook 2 protein (HMGA2). We combined proteomic, ChIP-seq, and transcriptome data to show that HMGA2-induced transcription requires phosphorylation of the histone variant H2AX at S139 (H2AXS139ph; γ-H2AX) mediated by the protein kinase ataxia telangiectasia mutated (ATM). Furthermore, we demonstrate the biological relevance of this mechanism within the context of TGFβ1 signaling. The interplay between HMGA2, ATM, and H2AX is a novel mechanism of transcription initiation. Our results link H2AXS139ph to transcription, assigning a new function for this DNA damage marker. Controlled chromatin opening during transcription may involve intermediates with DNA breaks that may require mechanisms that ensure the integrity of the genome.
2020-12-15 | PXD016586 | Pride
Project description:This project aims to identify differentially expressed small non coding RNAs between young and old normal chondrocytes isolated from the metacarpophalangeal joint of 10 horses; 5 young and 5 old.
2021-04-30 | E-MTAB-8112 | biostudies-arrayexpress
Project description:The purpose of this experiment was to further our understanding of gene expression in the central nervous system (thalamus and cerebrum) after exposure to West Nile virus. To that end, three different analyses were performed. The first examined differences in gene expression between horses not vaccinated and exposed to WNV and normal control horses (exposure). The second examined differences in gene expression between horses not vaccinated and exposed to WNV and horses vaccinated and exposed to WNV (survival). And the third examined differences between the nonvaccinated cerebrum and nonvaccinated thalamus of horses exposed to WNV (location). Six conditions- Gene expression in the thalamus and cerebrum of three different groups of horses (Non-vaccinated horses exposed to West Nile virus, Vaccinated horses exposed to West Nile virus, normal horses not exposed to West Nile virus). Biological replicates- 6 normal cerebrums, 6 normal thalamus, 6 vaccinated and exposed cerebrums, 6 vaccinated and exposed thalamus, 6 non-vaccinated and exposed cerebrum, 6 non-vaccinated and exposed thalamus.
2011-08-31 | E-GEOD-30347 | biostudies-arrayexpress
Project description:To investigate the miR-219-5p decreases the resistance of OC cells to cisplatin via Wnt/β-catenin signaling and autophagy by regulating HMGA2, we tested the A2780 and A2780-DDP cell lines with miRNA-Seq.
2022-07-30 | GSE209922 | GEO
Project description:The high-mobility-group (HMG) proteins are the most abundant non-histone chromatin-associated proteins. Here we deciphered the role of the high mobility group AT-hook protein 2 (HMGA2) during lung development by analyzing the lung of Hmga2 deficient mice (Hmga2-/-).We found that Hmga2 is expressed in the mouse embryonic lung at the distal airways. Analysis of Hmga2-/- mice showed that Hmga2 is required for proper cell proliferation and distal epithelium differentiation during embryonic lung development. Hmga2 knockout (KO) led to enhanced canonical WNT signaling due to an increased expression of secreted WNT glycoproteins Wnt2b, Wnt7b and Wnt11 as well as a reduction of the WNT signaling antagonizing proteins GATA6 (GATA binding protein 6) and FZD2 (frizzled homolog 2). Comparison of Hmga2-/- with Hmga2+/+ mice by Affymetrix microarray-based expression analysis of embryonic lung revealed an increased expression of genes whose products participate in cell cycle and canonical Wnt signaling. Affymetrix microarray transcriptome analysis of Hmga2-/- and Hmga2+/+ embryonic lung (E18.5) was performed and analyzed
2014-03-07 | E-GEOD-55340 | biostudies-arrayexpress
Project description:Analysis of patient-specific nucleotide variants is a cornerstone of personalised medicine. Although only 2% of the genomic sequence is protein-coding, mutations occurring in these regions have the potential to influence protein structure and may have severe impact on disease aetiology. Of special importance are variants that affect modifiable amino acid residues, as protein modifications involved in signal transduction networks cannot be analysed by genomics. Proteogenomics enables analysis of proteomes in context of patient- or tissue-specific non-synonymous nucleotide variants. Here, we developed a proteogenomics workflow and applied it to study resistance to serine/threonine-protein kinase B-raf (BRAF) inhibitor (BRAFi) vemurafenib in malignant melanoma cell line A375. This approach resulted in high identification and quantification of non-synonymous nucleotide variants and (phospho)proteins. We integrated multi-omic datasets to reconstruct the perturbed signalling networks associated with BRAFi resistance and to predict drug therapies with the potential to disrupt BRAFi resistance mechanism in A375 cells. Notably, we showed that aurora kinase A (AURKA) inhibition is effective and specific against BRAFi resistant A375 cells. Furthermore, we investigated nucleotide variants that interfere with protein post-translational modification (PTM) status and potentially influence cell signalling. Mass spectrometry (MS) measurements confirmed variant-driven PTM changes in 12 proteins; among them was the runt-related transcription factor 1 (RUNX1) displaying a variant on a known phosphorylation site S(Ph)276L. We confirmed the loss of phosphorylation site by MS and demonstrated the impact of this variant on RUNX1 interactome.
2021-11-04 | PXD018305 | Pride