Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA121673 | ENA |
REPOSITORIES: ENA
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Project description:Peptidylarginine deiminase IV (PADI4) catalyzes the conversion of positively charged arginine and methylarginine residues to neutrally charged citrulline residues on histone tails. This activity has been linked to the repression of gene transcription on a limited number of genes. To broaden our knowledge of the regulatory potential of PADI4, we utilized chromatin immunoprecipitation coupled with promoter tiling array (ChIP-chip) to more comprehensively investigate the range of PADI4 target genes across the genome in MCF-7 cells. Results showed that PADI4 is enriched in the gene promoter regions near the transcription start sites (TSSs) and, surprisingly, this pattern of binding is primarily associated with actively transcribed genes. Computational analysis found Elk-1, a member of the ETS oncogene family, to be highly enriched around PADI4 binding sites and coimmunoprecipitation analysis then confirmed that Elk-1 physically associates with PADI4. The expression of two well characterized Elk-1 target genes, c-fos and egr-1, was then found to be inhibited following treatment of MCF-7 cells with a PADI4 specific inhibitor. The inhibitor also significantly reduced levels of acetylation at H4 lysine 5 at these promoters suggesting that the activating function of PADI4 at these target genes is mediated, in part, by interplay between histone citrullination and HAT-mediated acetylation. These findings greatly expand our knowledge of the role of PADI4 in gene regulation by defining a new role for PADI4 catalyzed histone citrullination in mediating gene transactivation. Two PADI4 ChIP-chip biological replicates from MCF-7 human breast cancer cells are included.
2011-03-31 | E-GEOD-18755 | biostudies-arrayexpress
Project description:Peptidylarginine deiminase IV (PADI4) catalyzes the conversion of positively charged arginine and methylarginine residues to neutrally charged citrulline residues on histone tails. This activity has been linked to the repression of gene transcription on a limited number of genes. To broaden our knowledge of the regulatory potential of PADI4, we utilized chromatin immunoprecipitation coupled with promoter tiling array (ChIP-chip) to more comprehensively investigate the range of PADI4 target genes across the genome in MCF-7 cells. Results showed that PADI4 is enriched in the gene promoter regions near the transcription start sites (TSSs) and, surprisingly, this pattern of binding is primarily associated with actively transcribed genes. Computational analysis found Elk-1, a member of the ETS oncogene family, to be highly enriched around PADI4 binding sites and coimmunoprecipitation analysis then confirmed that Elk-1 physically associates with PADI4. The expression of two well characterized Elk-1 target genes, c-fos and egr-1, was then found to be inhibited following treatment of MCF-7 cells with a PADI4 specific inhibitor. The inhibitor also significantly reduced levels of acetylation at H4 lysine 5 at these promoters suggesting that the activating function of PADI4 at these target genes is mediated, in part, by interplay between histone citrullination and HAT-mediated acetylation. These findings greatly expand our knowledge of the role of PADI4 in gene regulation by defining a new role for PADI4 catalyzed histone citrullination in mediating gene transactivation.
2011-03-31 | GSE18755 | GEO
Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.
2010-09-25 | GSE24338 | GEO
Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
| S-EPMC2531291 | biostudies-literature
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO
Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression.
2011-02-19 | GSE20463 | GEO