Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression data of untreated and RA-treated wild type and RXRÎ±-deficient mice liver

ABSTRACT: Our project focuses on retinoic acid (RA) effect on hepatic lipid homeostasis. Even though RA has more than one receptor including retinoids x receptor (RXR) and retinoic acid receptor (RAR), most probably, RA effect on lipid homeostasis is mediated by RXR and its partners such as PXR, FXR, and PPAR. So we treated the wild type and RXRÎ±-knockout mice by retinoic acid to check the global gene expression especially for lipid homeostasis genes. We used microarrays to observe the global gene expression underlying hepatic lipid homeostasis. We treated both the wild type and RXRÎ±-KO mice with normal diet and RA-containing diet for 7 days. For each group, three replicates were done. Liver total RNA were used to test global gene expression by microarray.

ORGANISM(S): Mus musculus

SUBMITTER: Yuqi He

PROVIDER: E-GEOD-50028 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The role of retinoic acid in hepatic lipid homeostasis defined by genomic binding and transcriptome profiling.

He Yuqi Y Gong Lei L Fang Yaping Y Zhan Qi Q Liu Hui-Xin HX Lu Yanliu Y Guo Grace L GL Lehman-McKeeman Lois L Fang Jianwen J Wan Yu-Jui Yvonne YJ

BMC genomics 20130828

<h4>Background</h4>The eyes and skin are obvious retinoid target organs. Vitamin A deficiency causes night blindness and retinoids are widely used to treat acne and psoriasis. However, more than 90% of total body retinol is stored in liver stellate cells. In addition, hepatocytes produce the largest amount of retinol binding protein and cellular retinoic acid binding protein to mobilize retinol from the hepatic storage pool and deliver retinol to its receptors, respectively. Furthermore, hepatoc ...[more]

PMID: 23981290

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Project description:In mouse embryonic cells, a retinoic acid (RA) stimulation triggers a massive change of gene expression leading the pluripotent, proliferating cells to a lineage-specific differentiation process. The retinoic acid receptor (RAR) plays a key role in this response by inhibiting pluripotency-maintaining genes and simultaneously activating some major actors of cell differentiation. To investigate the mechanism underlying this dual regulation, we performed joint RAR/RXR ChIP-seq and mRNA-seq time series during the first 48 hours of the RA-induced Primitive Endoderm differentiation process in F9 embryonic carcinoma cells. We detected significantly more RAR/RXR binding regions than previous studies and identified among them a handful of typical binding intensity patterns during differentiation. We demonstrate that these patterns are correlated with the coincidental binding of essential transcription factors (TFs) for pluripotency maintenance or PrE differentiation of embryonic stem (ES) cells, as well as the presence of variants of RAR binding motifs. Most importantly, early-bound regions coincide with pluripotency-associated transcription factor binding in ES (like Pou5f1, Sox2, Esrrb and Nr5a2) and display an increased frequency of the DR0 type RAR binding motifs; late-bound sites are associated to the PrE marker Sox17 and are enriched in the canonical DR5 binding motif. Our data offer an unprecedently detailed view on the action of RA in triggering pluripotent cell differentiation. Altogether, this work sheds light on the relocation of RAR/RXR binding sites throughout differentiation, and shows how RAR/RXR progressively shift from DR0 enriched regions, which were specifically identified in undifferentiated models, to canonical RAR binding sites containing loci. Time course (0, 2, 6, 12, 24, 48h) after stimulation of F9 cultured cells by retinoic acid: PanRAR and PanRXR ChIP-seq at 0, 2, 24 and 48h (no replicate); WCE-seq at 0h (no replicate); mRNA-seq at 0, 6, 12, 24, 48h (2 replicates except for time 0h, 4 replicates). Additionally, a control time course (culture in DMSO) sampled at 24 and 48h (no replicates).

Dataset Information

Gene expression data of untreated and RA-treated wild type and RXRÎ±-deficient mice liver

Publications

The role of retinoic acid in hepatic lipid homeostasis defined by genomic binding and transcriptome profiling.

Similar Datasets

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