MRNA composition of IRP1 mRNPs in mouse tissues
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE17096 | GEO | 2011/12/09
SECONDARY ACCESSION(S): PRJNA117813
REPOSITORIES: GEO
Similar Datasets
Project description:Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRP1 (iron regulatory protein 1). Reference Sanchez at al., 2007 Nat. Protoc. Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the reported tissue of four to six C57BL6/J mice using Trizol reagent. mRNA from duodenum, liver and spleen were extracted from mice fed with an iron poor diet (<10mg/kg, Altromin Spezialfutter GmbH & Co, Lage, Germany) for 21 days starting from weaning age. mRNAs from bone marrow and brian were extracted from mice (8-10 weeks old) fed with an iron-normal diet. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 M-BM-5g of total RNA with purified recombinant IRP1 produced in E.coli and a rabbit polyclonal anti-IRP1 antibody. A control reaction in which the recombinant IRP1 was omitted was performed in parallel (referred with the word M-bM-^@M-^\controlM-bM-^@M-^] in the title). All the microarray procedures were conducted at the EMBL Genomics Core Facility using standard Affymetrix protocols. In brief, approximately 120ng of immunoprecipitated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array (Eukaryotic Sample and Array Processing manual 701024 Rev.3). Intensity values for the hybridizations were obtained either using RMA, calculations done in bioconductor (www.bioconductor.org) or MAS5, calculated using Affymetrix GCOS package. MAS5 calculated intensities were further quantile normalized using bioconductor.
2011-12-09 | E-GEOD-17096 | biostudies-arrayexpress
Project description:Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRP2 (iron regulatory protein 2).
2011-12-09 | GSE17097 | GEO
Project description:Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRP2 (iron regulatory protein 2). Reference Sanchez at al., 2007 Nat. Protoc. Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the reported tissue of four to six C57BL6/J mice using Trizol reagent. mRNA from duodenum, liver and spleen were extracted from mice fed with an iron poor diet (<10mg/kg, Altromin Spezialfutter GmbH & Co, Lage, Germany) for 21 days starting from weaning age. mRNAs from bone marrow and brian were extracted from mice (8-10 weeks old) fed with an iron-normal diet. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 M-BM-5g of total RNA with purified recombinant His-tagged IRP2 produced in E.coli and a mouse monoclonal anti-His tag antibody. A control reaction in which the recombinant IRP2 was omitted was performed in parallel (referred with the word M-bM-^@M-^\controlM-bM-^@M-^] in the title). All the microarray procedures were conducted at the EMBL Genomics Core Facility using standard Affymetrix protocols. In brief, approximately 120ng of immunoprecipitated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array (Eukaryotic Sample and Array Processing manual 701024 Rev.3). Intensity values for the hybridizations were obtained either using RMA, calculations done in bioconductor (www.bioconductor.org) or MAS5, calculated using Affymetrix GCOS package. MAS5 calculated intensities were further quantile normalized using bioconductor.
2011-12-09 | E-GEOD-17097 | biostudies-arrayexpress
Project description:Proteins regulate gene expression by controlling mRNA biogenesis, localization, translation and decay. Identifying the composition, diversity and function of mRNPs (mRNA protein complexes) is essential to understanding these processes. In a global survey of S. cerevisiae mRNA binding proteins we identified 120 proteins that cross-link to mRNA, including 66 new mRNA binding proteins. These include kinases, RNA modification enzymes, metabolic enzymes, and tRNA and rRNA metabolism factors. These proteins show dynamic subcellular localization during stress, including assembly into stress granules and P-bodies (Processing-bodies). CLIP (cross-linking and immunoprecipitation) analyses of the P-body components Pat1, Lsm1, Dhh1 and Sbp1 identified sites of interaction on specific mRNAs revealing positional binding preferences and co-assembly preferences. Taken together, this work defines the major yeast mRNP proteins, reveals widespread changes in their subcellular location during stress, and begins to define assembly rules for P-body mRNPs.
2013-04-18 | GSE46142 | GEO
Project description:Proteins regulate gene expression by controlling mRNA biogenesis, localization, translation and decay. Identifying the composition, diversity and function of mRNPs (mRNA protein complexes) is essential to understanding these processes. In a global survey of S. cerevisiae mRNA binding proteins we identified 120 proteins that cross-link to mRNA, including 66 new mRNA binding proteins. These include kinases, RNA modification enzymes, metabolic enzymes, and tRNA and rRNA metabolism factors. These proteins show dynamic subcellular localization during stress, including assembly into stress granules and P-bodies (Processing-bodies). CLIP (cross-linking and immunoprecipitation) analyses of the P-body components Pat1, Lsm1, Dhh1 and Sbp1 identified sites of interaction on specific mRNAs revealing positional binding preferences and co-assembly preferences. Taken together, this work defines the major yeast mRNP proteins, reveals widespread changes in their subcellular location during stress, and begins to define assembly rules for P-body mRNPs. CLIP-seq analysis of Dhh1, Lsm1, Pat1 and Sbp1
2013-04-18 | E-GEOD-46142 | biostudies-arrayexpress
Project description:To study the composition of mRNPs containing TcDhh1, we carried out immunoprecipitation assays with anti-TcDhh1 and epimastigotes lysates. Pre-immune serum was used as control. We also carried out a ribonomic approach to identify the mRNAs present within the TcDhh1 immunoprecipitated complexes. For this purpose, competitive microarray hibridizations were performed against negative controls, the non-precipitated fraction.
2010-10-31 | E-MEXP-2448 | biostudies-arrayexpress
Project description:Imbalances in testicular iron levels are linked to compromised sperm production and male infertility. Iron regulatory proteins (IRP) 1 and 2 play crucial roles in cellular iron regulation. We investigated the role of IRP1 on spermatogenesis using Irp1-deficient mice (Irp1-/-). Histological analysis of the testis of Irp1-/- mice revealed hypospermatogenesis with a significant reduction in the number of elongated spermatids and daily sperm production compared to wild-type (WT) mice. Flow cytometry of germ cells from WT and Irp1-/- mice showed reduction in spermatocytes, round and elongated spermatids, which was confirmed by histological and immunofluorescence quantification. Finally, stage VIII of spermatogenesis, crucial for spermatid maturation, was less frequent in Irp1-/- testicular cross-sections. Hypospermatogenesis worsened with age despite unchanged intratesticular iron levels. Mechanistically, this was due to increased oxidative stress indicated by elevated 8-Oxoguanine (8-OxoG) levels, a DNA lesion resulting from reactive oxygen species (ROS). Furthermore, bulk RNA-seq data indicated compromised DNA damage repair and cell cycle processes, including mitosis and meiosis, which may explain hypospermatogenesis.Our results suggest that IRP1 deletion leads to hypospermatogenesis due to impaired cell cycle progression, decreased DNA damage repair capacity and oxidative damage. Altogether, this study uncovers a role for IRP1, independent of traditional iron regulation mechanisms.
2024-12-30 | GSE273580 | GEO
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Project description:We isolated nuclear mRNPs from yeast using an endogenous bi-molecular tagging approach on Sub2 and Hpr1. To validate the nature of these isolated particles, extracted RNA was sequenced and differential enrichment, as well as metagene coverage analysis were performed.
2023-07-24 | GSE226854 | GEO