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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Tribbles-1 regulates hepatic lipogenesis through post-transcriptional regulation of C/EBP? [ChIP-Seq]

ABSTRACT: We report ChIP-Seq data for C/EBPa in livers of mice with liver-specific KO (LSKO) of Trib1 as compared to WT controls, or in livers of mice overexpressing C/EBPa via adeno-associated virus (AAV) as compared to controls. 8-10 week old Trib1 flox/flox mice treated with AAV_Null (WT) or AAV_Cre (LSKO); 8-10 week old C57B/6 WT mice treated with AAV_Null or AAV_Cebpa.

ORGANISM(S): Mus musculus

SUBMITTER: Robert Bauer

PROVIDER: E-GEOD-70716 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Tribbles-1 regulates hepatic lipogenesis through post-transcriptional regulation of C/EBPα [ChIP-Seq]

Project description:We report ChIP-Seq data for C/EBPa in livers of mice with liver-specific KO (LSKO) of Trib1 as compared to WT controls, or in livers of mice overexpressing C/EBPa via adeno-associated virus (AAV) as compared to controls.

2015-07-14 | GSE70716 | GEO

Defining AP4- and MYC-regulated gene expression programs in germinal center B cells during cyclic re-entry

Project description:B cells diversify and affinity-mature their antigen receptor repertoire in germinal centers (GC). GC B cells receive help signals during transient interaction with T cells, yet it remains unknown how these transient T-B interactions sustain the subsequent proliferative program of selected B cells. Here we show that the transcription factor AP4 is required for sustained GC B cell proliferation and subsequent establishment of a diverse and protective antibody repertoire. AP4 is induced by c-MYC during the T-B interactions and maintained by T cell-derived IL-21. B cell-specific deletion of AP4 resulted in reduced GC sizes and somatic hypermutation and a failure to control chronic viral infection. These results indicate that AP4 integrates T cell-mediated selection and sustained expansion of GC B cells for humoral immunity. Splenic B cells activated with anti-IgM and CD40L in vitro and germinal center B cells sorted from C57BL/6 mice eight days after immunization with sheep red blood cells (SRBCs) were obtained and genome-wide occupancy of c-MYC, AP4 and active histone marks was profiled by chromatin immunoprecipitation and high-throughput sequencing. Gene expression in MYCâAP4â LZ, MYC+AP4+ LZ, AP4+ DZ, and APâ DZ GC B cells from SRBC-immunized AP4-mCherry / c-MYC-GFP dual reporter mice was profiled by RNA-seq.

2016-08-23 | E-GEOD-80669 | biostudies-arrayexpress

Natural genetic variation perturbs collaborative transcription factor binding required for enhancer selection and function

Project description:Natural genetic variation between two mouse strains was used as a natural mutagenesis screen to test various aspects of the proposed model for enhancer selection and function. Chromatin marks H3K4me2, H3K27Ac, and transcription factors PU.1, C/EBPa, and p65 were assessed by ChIP-Seq and GRO-Seq and RNA-Seq were used to measure gene expression in C57BL6/J and BALBc/J inbred mouse strains

2013-10-15 | E-GEOD-46494 | biostudies-arrayexpress

Trib1 promotes acute myeloid leukemia progression by modulating transcriptional programs of Hoxa9 [array]

Project description:The pseudokinase Trib1 functions as a myeloid oncogene that recruits E3 ubiquitin ligase COP1 to C/EBPa, and interacts with MEK1 to enhance ERK phosphorylation. Close genetic interaction between Trib1 and Hoxa9 has been observed in myeloid leukemogenesis as Trib1 overexpression significantly accelerates Hoxa9-induced leukemia onset. Yet the mechanism how Trib1 functionally modulates Hoxa9 transcription activity is unclear. Here we provide evidence that Trib1 modulates Hoxa9-associated super-enhancers. ChIP-seq analyses identified increased Histone H3K27Ac signals at the super-enhancers such as Erg, Aff3, Spns2 and Coro2 loci, as well as increased mRNA expression of these genes. The modification of super-enhancer activities is mostly achieved by degradation of C/EBPa by Trib1 and the MEK/ERK pathway only slightly contributes to the activities. Silencing of Erg abrogates the growth advantage acquired by Trib1 overexpression, indicating that Erg is a critical downstream target of the Trib1/Hoxa9 axis. Moreover, treatment of AML cells with the BRD4 inhibitor JQ1 showed growth inhibition in the Trib1/Erg-dependent manner. Upregulation of ERG by TRIB1 was also observed in human AML cell lines, suggesting that Trib1 is a potential target of Hoxa9-associated AML. We used microarrays to detail the global program of gene expression in mouse AML

2020-10-21 | GSE139641 | GEO

Transcription factor binding in liver tissue isolated from WT and GRdim mice

Project description:We report ChIP-seq and ChIP-exo data for GR in liver tissue isolated from WT and GRdim mice. Comparison of the mouse models reveals that GR interacts with the genome as both a monomer and dimer. Examination of GR, RNAPII and CEBPb binding in WT and GRdim mice on a genome-wide scale

2015-04-14 | E-GEOD-59752 | biostudies-arrayexpress

Tribbles-1 regulates hepatic lipogenesis through post-transcriptional regulation of C/EBPα [array]

Project description:Comparison of gene expression in livers of either WT mice or mice with hepatic specific deletion of the gene Tribbles1. Animal groups were both Trib1 cKO mice homozygous for a floxed allele of Trib1. Mice aged 8-10 weeks were treated with adeno associated virus (AAV) encoding Cre recombinase (AAV_Cre) or no gene (AAV_null). The WT group is mice treated with AAV_Null, the liver-specific KO group treated with AAV_Cre. Gene expression data was then used in Ingenuity Pathway analysis to attempt to identify upstream transcription factors that might be responsible for the gene expression changes observed. All animals were 8-10 weeks of age, and all animals were homozygous for the floxed allele of Trib1. WT animals were treated with AAV_Null, Trib1 liver specific KO mice were treated with AAV_Cre. Mice were euthanized at 1-week post injection of AAV, and RNA collected from whole liver tissue.

2015-07-14 | E-GEOD-70846 | biostudies-arrayexpress

Sox4 is a key oncogenic target in C/EBPa mutant Acute Myeloid Leukemia

Project description:Mutation or epigenetic silencing of the transcription factor C/EBPa is observed in ~10% of patients with acute myeloid leukemia (AML). In both cases, a common global gene expression profile is observed, but down-stream targets relevant for leukemogenesis are not known. Here we identify Sox4 as a direct target of C/EBPa whereby its expression is inversely correlated with C/EBPa activity. Downregulation of Sox4 abrogated increased self-renewal of leukemic cells and restored their differentiation. Gene expression profiles of leukemia initiating cells (LICs) from both Sox4 overexpression and murine mutant C/EBPa AML models clustered together, but differed from other types of AML. Our data demonstrate that Sox4 overexpression resulting from C/EBPa inactivation contributes to the development of leukemias with a distinct LIC phenotype. A ChIP-seq sample of C/EBPa in Macrophages is used in this study

2014-01-08 | E-GEOD-50565 | biostudies-arrayexpress

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

Project description:Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock.M-BM- We have determined the underlyingM-BM- mechanisms by measuring nascent RNA transcription around the clock in mouse liver. Unbiased examination of eRNAs that cluster in specific circadian phasesM-BM- identified functional enhancers driven by distinct transcription factors (TFs). We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression. Integrated genomicM-BM- analysesM-BM- also revealed novel mechanisms by which a single circadian factor controls opposing transcriptional phases. These findings shed new light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ. Nascent RNA transcripts in mouse liver were profiled at 8 time points of the 24 hour light-dark cycle. Static state mRNAs in WT and Rev-erbA -/- mice were profiled using microarray (GSE59460).

2014-11-21 | E-GEOD-59486 | biostudies-arrayexpress

Expression data of GMP and MDP from wild-type and Trib1-/- mice

Project description:Trib1 is critical for some myeloid cell differentiation. Therefore we used microarrays to investigate gene expression profiles in wild-type and Trib1-/- progenitor of myeloid cells. Progenitor cells, such as GMP and MDP, obtained from wild-type and Trib1-/- mice were sorted, followed by RNA extraction. Then hybridization on affymetrix microarrays was performed.

2013-01-18 | E-GEOD-43563 | biostudies-arrayexpress

Tribbles-1 regulates hepatic lipogenesis through post-transcriptional regulation of C/EBPα [array]

2015-07-14 | GSE70846 | GEO

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