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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling by array of Taf10 KO livers

ABSTRACT: Transcriptional profiling of Taf10-/- livers as compared to age-matched wild_type controls.

ORGANISM(S): Mus musculus

SUBMITTER: George Garinis

PROVIDER: E-MEXP-3442 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Defective transcription initiation causes postnatal growth failure in a mouse model of nucleotide excision repair (NER) progeria.

Kamileri Irene I Karakasilioti Ismene I Sideri Aria A Kosteas Theodoros T Tatarakis Antonis A Talianidis Iannis I Garinis George A GA

Proceedings of the National Academy of Sciences of the United States of America 20120208 8

Nucleotide excision repair (NER) defects are associated with cancer, developmental disorders and neurodegeneration. However, with the exception of cancer, the links between defects in NER and developmental abnormalities are not well understood. Here, we show that the ERCC1-XPF NER endonuclease assembles on active promoters in vivo and facilitates chromatin modifications for transcription during mammalian development. We find that Ercc1(-/-) mice demonstrate striking physiological, metabolic and ...[more]

PMID: 22323595

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E-IMBB-Mm-1

Project description:Transcription profiling of mouse livers in adult males and embryos with wild-type and TAF10 -/- hepatocytes.

2008-11-08 | E-MTAB-3 | biostudies-arrayexpress

Transcriptome profiling of NER progeroid animals treated with an NF-kB inhibitor.

Project description:NBD treatment of animals: Sibling pairs of Ercc1-/delta mice housed in a single cage were treated with 8K-NBD or 8K-mNBD 10 mg/kg three times per week intraperitoneally by an investigator blinded as to the treatment group. Treatment began at 5 weeks of age before the animals were symptomatic and continued throughout their lifespan. Mice were euthanized via CO2 inhalation at 12 or 18-20 weeks of age and tissues isolated. 8K-NBD (KKKKKKKKGGTALDWSWLQTE) and inactive 8K-mutant NBD (8K-mNBD) (KKKKKKKKGGTALDASALQTE) were synthesized at the University of Pittsburgh Peptide facility. Peptides were dissolved in DMSO at 40uM and stored at -80 C until dilution in PBS directly before use.

2012-07-01 | E-MEXP-3615 | biostudies-arrayexpress

TAF8 MUTATION CAUSES INTELLECUAL DISABILITY, TFIID DISASSEMBLY WITH NO EFFECT ON RNA POLYMERASE II TRANSCRIPTION

Project description:The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID nucleates RNA Polymerase II (Pol II) preinitiation complex formation on gene promoters and thus, is crucial for Pol II transcription. Germline knock out of several mouse TFIID subunits (Tbp, Taf7, Taf8, and Taf10) results in lethality at embryonic day 4.0, demonstrating the fundamental role of holo-TFIID in transcription. We identified a child harboring a splice-site mutation in TAF8, who has intellectual disability, poor growth, progressive spasticity and microcephaly. The c.781-G>A TAF8 mutation in this patient resulted in a frame shift, which affected the final 50 carboxy terminal amino acids of TAF8. We found that the mutant TAF8 protein is unstable and the patient c.781-G>A TAF8 primary fibroblasts did not form canonical TFIID complexes. Astonishingly however, genome-wide RNA pol II occupancy and pre-mRNA transcription on the tested genes was unaffected in the patient’s primary fibroblasts. This study indicates that perturbed TFIID function is less deleterious for transcription in human cells than originally anticipated.

2018-04-16 | PXD008084 | Pride

High throughput RNA sequencing of hepatocellular carcinoma and pre tumor samples from Tdg fl/-; UBC-cre/ERT2+ mice livers and their age/sex matched Tdg fl/fl controls livers

Project description:We isolated whole livers from male TDG knockout livers (4-month post tamoxifen injection) and HCC, along with their age matched male control livers. RNA was extracted from the samples as per RNAzol manufacturer guidelines with DNase treatment. RNA was then analyzed by bioanalyzer and subjected to sequencing using the Illumina NextSeq 500 platform.

2020-03-06 | GSE146401 | GEO

The gene expression profiles of WT and NML-KO livers

Project description:To examine whether energy starvation caused by the increase in rRNA transcription affects liver metabolism, we compared the gene expression profiles of WT and NML-KO livers using Affymetrix microarray technology. We analyzed 5 livers of WT mice and 5 livers of NML-KO mice.

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SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells

Project description:Co-activator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved multisubunit co-activator complex with modular organization. The core module of SAGA constitutes the structural heart, composed of a histone octamer like structure and two additional proteins. The central histone octamer like core structure consists of six histone fold domain (HFD)-containing proteins, forming three HF pairs (TADA1/TAF12, TAF6L/TAF9/9b, and TAF10/SUPT7L) in the mammalian SAGA complexes, to which adds SUPT3H, which contains an intramolecular HF pair. The yeast homologue of SUPT3H, called Spt3, was shown to interact genetically and biochemically with the TATA binding protein (TBP). Here we investigated the role of SUPT3H in human U2OS and mouse embryonic stem (ES) cells. Using immuno-purification coupled mass spectrometry experiments we show that both human and mouse SAGA can assemble without the double HFD-containing SUPT3H. Nascent RNA-seq experiments indicted that in either U2OS or mouse ESCs lacking SUPT3H only a small subset of genes is deregulated. Consequently, in mouse ESCs SUPT3H is not essential for mouse ESC survival, but is required for ESC growth and self-renewal. In addition, TBP recruitment experiments show no major change in TBP accumulation at gene promoters in the absence of SUPT3H in mouse and human cells. Taken together our data suggest in mammalian cells SUPT3H is not required for the assembly of SAGA, general TBP recruitment to genes and cell survival, but it is important for regulating a limited set of genes.

2022-07-26 | PXD026991 | Pride

mRNA seq of MOSAICS based Irs1 KO, Srebf1 KO, Tbx3 KO, Bcl6 KO, Smyd2 KO and control (sgGFP and sgLacZ) livers

Project description:To investigate expression changes of the KO vs. control livers under 3 months of Western Diet. We then performed mRNA seq analysis on MOSAICS based single-gene whole-liver KO samples and control samples

2024-09-01 | GSE212916 | GEO

Metabolic reprogramming in livers from LKB1 KO mice

Project description:Metabolic reprogramming in livers from LKB1 KO mice

| PRJNA791350 | ENA

The gene expression profiles of WT and NML-KO livers

2013-06-22 | GSE48191 | GEO

Gene expression analysis of PiZ mouse livers

Project description:Transgenic PiZ mice have been genetically engineered to express ATZ and have been a valuable experimental model for studing liver disease associated with AAT deficiency. ATZ accumulates in these mice within the ER of hepatocytes in a nearly identical manner to livers of affected patients. To investigate the pathogenesis of liver damage induced by ATZ, we performed gene expression analysis in livers of 6-week-old PiZ mice and strain-, age-, and gender-matched wild-type mouse controls. All samples were processed on Affymetrix Mouse 430A 2.0 arrays using GeneChip 3’-IVT Plus and Hybridization Wash and Stain kits by means of Affymetrix’s standard protocols. The analysis indicated that most genes upregulated in PiZ livers were associated with response to unfolded proteins, ER nuclear signaling pathway, and response to protein stimulus.

2017-03-23 | GSE93115 | GEO

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