Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA146011 | ENA |
REPOSITORIES: ENA
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Project description:MED12 is an X-chromosome member of the Mediator complex that is a key regulator of tissue specific gene expression and moderates intracellular signaling via multiple developmental pathways. Sequence variations in the carboxy-terminus of MED12, which contains a PQL and Opa domain, are associated with X-linked mental retardation behavioral syndromes and schizophrenia. Unfortunately, the mechanism(s) through which MED12 sequence variation in the carboxy-terminus could alter vulnerability to neurodevelomental and neuropsychiatric illnesses is yet unclear. In order to elucidate a better understanding of this process, we examined the role of the MED12 carboxy-terminus in cell cycle and gene expression with full-length and domain deleted overexpression constructs and RNA interference in HEK293 cells. Our microarray data show a set of genes differentially expressed in the experimental conditions versus the GFP control. The top 50 most differentially expressed genes in the experimental conditions versus the GFP control also show that MED12 expression level differentially affects stress response and transcriptional regulation pathways. These results are consistent with prior studies showing that MED12 has a key role in determining neuronal cell fate and our theoretical understanding of the biological basis of psychosis. They also lend further insight upon the pathways through which MED12 exerts its effects upon differentiation and disease pathogenesis, which may one day lead to new approaches to the treatment of MED12-related disorders. 12 samples were analyzed, being comprised of four conditions with three biological replicates. Comparisons were made between the GFP control to experimental condition (i.e. GFP vs MED12 FL; GFP vs MED12 PQL/Opa; and GFP vs MED12 shRNA 5)
2011-08-10 | E-GEOD-31327 | biostudies-arrayexpress
Project description:MED12 is an X-chromosome member of the Mediator complex that is a key regulator of tissue specific gene expression and moderates intracellular signaling via multiple developmental pathways. Sequence variations in the carboxy-terminus of MED12, which contains a PQL and Opa domain, are associated with X-linked mental retardation behavioral syndromes and schizophrenia. Unfortunately, the mechanism(s) through which MED12 sequence variation in the carboxy-terminus could alter vulnerability to neurodevelomental and neuropsychiatric illnesses is yet unclear. In order to elucidate a better understanding of this process, we examined the role of the MED12 carboxy-terminus in cell cycle and gene expression with full-length and domain deleted overexpression constructs and RNA interference in HEK293 cells. Our microarray data show a set of genes differentially expressed in the experimental conditions versus the GFP control. The top 50 most differentially expressed genes in the experimental conditions versus the GFP control also show that MED12 expression level differentially affects stress response and transcriptional regulation pathways. These results are consistent with prior studies showing that MED12 has a key role in determining neuronal cell fate and our theoretical understanding of the biological basis of psychosis. They also lend further insight upon the pathways through which MED12 exerts its effects upon differentiation and disease pathogenesis, which may one day lead to new approaches to the treatment of MED12-related disorders.
2011-08-11 | GSE31327 | GEO
Project description:To know target gene of IL-33 full-length, we generated IL-33 full length and IL-33 cytokine construct. After overexpression each construct in cell line, we did ChIP assay and analyzed ChIP-seq. As a result, we found different gene regulation by IL-33
2021-01-28 | GSE149575 | GEO
Project description:We report the genome-wide occupancy of exogenous DAXX (Myc-tagged), exogenous full length CBX2.1 (tagged with GAL4 DNA binding domain) and exogenous splice variant CBX2.2 (tagged with GAL4 DNA binding domain) in transiently transfected HEK293 cells. We observe that CBX2.1 but not CBX2.2 can efficiently target DAXX to chromatin.
2020-05-12 | GSE107348 | GEO
Project description:Purification of RNF43 interactors was performed with the following 4 different constructs: (i) empty vector (EV) as a control for background contaminants/non-specific protein binding; (ii) full-length RNF43 protein (RNF43 FL); (iii) deleted version of RNF43 harboring only the PA-TA domain (RNF43 Δ1); and (iv) deleted version of RNF43 harboring only the PA-TA-RING domain (RNF43 Δ3). HEK293T cells were transfected with pcDNA3-FLAG-HA- RNF43 (FL, Δ1 or Δ3).
2023-10-19 | PXD043151 | JPOST Repository
Project description:HDX-MS analysis of the protein ALT51, comparing deuterium uptake between the full length protein and a truncated construct missing the CBM-like domain
2023-02-22 | PXD034850 | Pride
Project description:As part of our study on human MASTL (microtubule-associated serine/threonine kinase-like), we used mass spectrometry (MS)-based proteomics in the aim to unravel novel aspects about MASTL activation, regulation and potential substrates. Specifically, we performed a phosphoproteomics-based kinase assay (essentially as in Xue et al. 2014) to identify MASTL substrates and analyzed different MASTL constructs to generate a “phosphorylation map” of the MASTL protein. siKALIP (Stable Isotope Labelled Kinase Assay-Linked Phosphoproteomics) Three MASTL variants, which we termed MASTL (full-length), MASTL450 (short) and Bonsai (truncated), were expressed in HEK293 cells and isolated using a tandem Strep and His-tag affinity purifications. For the in vitro kinase assay we used a dephosphorylated cell extract from interphase HEK293 cells to perform a slightly modified version of the siKALIP (described in Xue et al. 2014). Samples included an untreated basal sample, a dephosphorylated sample and samples for each of the three MASTL constructs. For label-free quantification, reactions were performed in quadruplicates for each MASTL construct. Explanation for MS raw files with MASTL construct included: FL: MASTL full-length. 450short: Shorter (consisting of the first 450 amino acid residues) MASTL. Bonsai: Truncated MASTL (consisting of amino acid residues 35-112, 113-180 and 728-879). MASTL phosphorylation map To analyse the phosphorylation state of MASTL we used isolated protein from an interphase HEK293 cell culture, either alone or incubated with mitotic extracts from HEK293 cells. Samples of different MASTL constructs were used for in-gel digestion and analysed by MS. Explanation for MS raw files with MASTL construct included: FL: MASTL full-length (“INACTIVE” indicates kinase-dead, “Dephos” indicates dephosphorylated FL protein, “Mit” indicates incubated with mitotic extracts). 450: Shorter (450 amino acids) MASTL (“KD” indicates kinase-dead). BONSAI: Truncated MASTL (“KD” indicates kinase-dead).
2020-01-09 | PXD007991 | Pride
Project description:HDX-MS analysis of the protein ALT51, comparing deuterium uptake between the full length protein and a truncated construct missing the CBM-like domain. Mass spectrometry was used to map the cleavage sites of CAT in a selection of representitive mucin-like glycoproteins.
2022-08-31 | PXD034904 | Pride
Project description:We report that full length TET1 (TET1-FL) overexpression fails to induce global DNA demethylation in HEK293T cells. The preferential binding of TET1-FL to hypomethylated CpG islands (CGIs) through its CXXC domain leads to its inhibited 5-hydroxymethylcytosine (5hmC) production as methylation level increases. TET1-FL-induced 5hmC accumulates at CGI edges, while TET1 knockdown induces methylation spreading from methylated edges into hypomethylated CGIs. However, TET1 can regulate gene transcription independent of its dioxygenase catalytic function. Thus, our results identify TET1 as a maintenance DNA demethylase that does not purposely decrease methylation levels, but specifically maintains the DNA hypomethylation state of CGIs in adult cells. Genome-wdie profiling of gene expression in HEK293T cells following overexpression of wild type or catalytically mutant TET1-FL or TET1-CD
2014-06-04 | E-GEOD-49833 | biostudies-arrayexpress
Project description:In this study on human Tousled-Like-Kinase 2 (TLK2) mass spectrometry-based analysis was applied as part of a molecular characterization of TLK2 in the aim to increase the understanding of the mode of activation of this protein. Specifically, different TLK2 constructs were expressed analyzed to generate a “phosphorylation map” of the TLK2 protein. To analyse the phosphorylation state of TLK2 we used recombinant protein purified from HEK293. Samples of different TLK2 constructs were used for in-gel digestion and analysed by mass spectrometry. All samples were prepared and run in triplicates for label-free quantification. Explanation for MS raw files with TLK2 construct included: KD: Kinase-dead TLK2 construct with mutation D613A, N-terminal His- and Strep-tag. wt: Active form of TLK2, canonical sequence, N-terminal His- and Strep-tag. full: Full-length canonical sequence (1-772), N-terminal His- and Strep-tag. trunc: Truncated TLK2 sequence (191-772), N-terminal His- and Strep-tag.
2018-09-04 | PXD009095 | Pride