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Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells (RNA-seq)

ABSTRACT: PRDM proteins belong to the SET domain protein family, which is involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcriptional regulation remain to be delineated. In this study, we find that Prdm5 is highly expressed in mouse embryonic stem (mES) cells and exploit this cellular system to characterize molecular functions of Prdm5. By combining proteomics and next-generation sequencing technologies, we identify Prdm5 interaction partners and genomic occupancy. We demonstrate that although Prdm5 is dispensable for mES cell maintenance, it directly targets genomic regions involved in early embryonic development and affects the expression of a subset of developmental regulators during cell differentiation. Importantly, Prdm5 interacts with Ctcf, cohesin, and TFIIIC and cooccupies genomic loci. In summary, our data indicate how Prdm5 modulates transcription by interacting with factors involved in genome organization in mouse embryonic stem cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE51553 | GEO | 2013/10/31

SECONDARY ACCESSION(S): PRJNA225480

REPOSITORIES: GEO

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Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells (RNA-seq)

Project description:PRDM proteins belong to the SET domain protein family, which is involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcriptional regulation remain to be delineated. In this study, we find that Prdm5 is highly expressed in mouse embryonic stem (mES) cells and exploit this cellular system to characterize molecular functions of Prdm5. By combining proteomics and next-generation sequencing technologies, we identify Prdm5 interaction partners and genomic occupancy. We demonstrate that although Prdm5 is dispensable for mES cell maintenance, it directly targets genomic regions involved in early embryonic development and affects the expression of a subset of developmental regulators during cell differentiation. Importantly, Prdm5 interacts with Ctcf, cohesin, and TFIIIC and cooccupies genomic loci. In summary, our data indicate how Prdm5 modulates transcription by interacting with factors involved in genome organization in mouse embryonic stem cells. For each condition (ATRA-induced differentiation model and LIF cytokine deprivation) three replicate are available for both Prdm5 wt mES cells and Prdm5 KO mES cells, for a total of 12 samples

2013-10-31 | E-GEOD-51553 | biostudies-arrayexpress

Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells (ChIP-seq)

2013-10-31 | GSE51816 | GEO

Genomic and Proteomic Analyses of Prdm5 Reveal Interactions with Insulator Binding Proteins in Embryonic Stem Cells (ChIP-seq)

Project description:PRDM proteins belong to the SET domain protein family, which is involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcriptional regulation remain to be delineated. In this study, we find that Prdm5 is highly expressed in mouse embryonic stem (mES) cells and exploit this cellular system to characterize molecular functions of Prdm5. By combining proteomics and next-generation sequencing technologies, we identify Prdm5 interaction partners and genomic occupancy. We demonstrate that although Prdm5 is dispensable for mES cell maintenance, it directly targets genomic regions involved in early embryonic development and affects the expression of a subset of developmental regulators during cell differentiation. Importantly, Prdm5 interacts with Ctcf, cohesin, and TFIIIC and cooccupies genomic loci. In summary, our data indicate how Prdm5 modulates transcription by interacting with factors involved in genome organization in mouse embryonic stem cells. ChIP-Sequencing of fragments enriched by immunoprecipitation of Prdm5 in wild type mouse embryo fibroblasts (MEF) in duplicate. Background noise details obtained by ChIP-Sequencing of Prdm5 lacz/lacz MEF, in duplicate.

2013-10-31 | E-GEOD-51816 | biostudies-arrayexpress

Prdm5 suppresses ApcMin-driven intestinal adenomas and regulates monoacylglycerol lipase expression

Project description:PRDM proteins are tissue specific transcription factors often deregulated in diseases, particularly in cancer where different members have been found to act as oncogenes or tumor suppressors. PRDM5 is a poorly characterized member of the PRDM family for which several studies have reported a high frequency of promoter hypermethylation in cancers of gastrointestinal origin. We report here the characterization of Prdm5 knockout mice in the context of intestinal carcinogenesis. We demonstrate that loss of Prdm5 increases the number of adenomas throughout the murine small intestine on an ApcMin background. By genome-wide ChIP-seq and transcriptome analyses we identify loci encoding proteins involved in metabolic processes as prominent PRDM5 targets and characterize monoacylglycerol lipase (Mgll) as a direct PRDM5 target in human colon cancer cells and in Prdm5 mutant mouse intestines. Moreover, we report the downregulation of PRDM5 protein expression in human colon neoplastic lesions. In summary, our data provide the first causal link between Prdm5 loss and intestinal carcinogenesis and uncover an extensive and novel PRDM5 target repertoire likely facilitating the tumor suppressive functions of PRDM5.

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Prdm5 suppresses ApcMin-driven intestinal adenomas and regulates monoacylglycerol lipase expression

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PRDM5 regulates collagen gene transcription by association with RNA polymerase II in developing bone

Project description:PRDM family members are transcriptional regulators involved in tissue specific differentiation. PRDM5 has been reported to predominantly repress transcription, but a characterization of its molecular functions in a relevant biological context is lacking. We demonstrate here that Prdm5is highly expressed in developing bones; and, by genome-wide mapping of Prdm5 occupancy in pre-osteoblastic cells, we uncover a novel and unique role for Prdm5 in targeting all mouse collagen genes as well as several SLRP proteoglycan genes. In particular, we show that Prdm5 controls both Collagen I transcription and fibrillogenesis by binding inside the Col1a1 gene body and maintaining RNA polymerase II occupancy. In vivo, Prdm5 loss results in delayed ossification involving a pronounced impairment in the assembly of fibrillar collagens. Collectively, our results define a novel role for Prdm5 in sustaining the transcriptional program necessary to the proper assembly of osteoblastic extracellular matrix.

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Transcription profiling by array of human osteosarcoma U2OS cell line conditionally expressing HA-tagged PRDM5

Project description:PRDM5 is a recently identified member of the PRDM family of proteins, which functions as a transcriptional repressor by recruiting histone methyltransferase G9A to DNA, and behaves as a putative tumor suppressor in different types of cancer. We investigated PRDM5 function by identifying its target genes in U2OS cells at different time points after expression of PRDM5 protein. Experiment Overall Design: We analyzed gene expression profiles of a U2OS cell line conditionally expressing HA-tagged PRDM5 (U2OS-PRDM5), where PRDM5 is under the transcriptional control of a doxycycline-inducible promoter. Expression of PRDM5 protein is detectable after 8 hours of induction with 2ug/ml doxycycline, and increases steadily up to 48 hours, after which cells begin to undergo apoptosis. U2OS cells containing the empty cloning vector (U2OS-pSG213) were used as controls for each condition.

2009-01-31 | E-GEOD-10580 | biostudies-arrayexpress

Transcriptome analysis of Prdm11 knockout mice after OVA challenge

Project description:PRDM family members encode for progeins functionally associated with the control of cell proliferation, differentiation as well as apoptosis action in cell and tissue-specific menner. As important factors in maintenance and differentiation of human and mouse ES cells several PRDM family members were identified. Prdm11 has and outsider position within the PRDM family due to the lack of zinc-finger domains. However, a zic-finger binding motive i present and likely assue the function of protein-protein interactionl. Prdm11 was described as a candidate for tumor suppresser. However, the function of this gene is still unknown. Our study give evidence a new functional association of Prdm11 in allergic disease and asthma.

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Transcriptome analysis of Prdm11 knockout mice after OVA challenge

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