E-MTAB-1441 - Transcription profiling by array of bone marrow derived macrophages from LyzCre/Trim33+/+ mice and LyzCre/Trim33flox/flox mice to study the role of TRIM33 in the transcriptional response induced by pathogen receptors

Status
Last updated on 29 December 2014, released on 30 June 2015
Organism
Mus musculus
Samples (16)
Array (1)
Protocols (6)
Description
Macrophage activation during the innate immune response is tightly regulated to prevent tissue damage while activating the defense to cellular attack. Using a mouse model where Trim33 is specifically deleted in mature myeloid cells, we show that TRIM33 is essential for two aspects of the inflammatory response in vivo. Loss of TRIM33 attenuates the initiation of macrophage activation by lipopolysaccharide (LPS) and TRIM33 is necessary to switch off transcription of inflammatory genes during late stages of LPS activation. Using chromatin immunoprecipitation coupled to deep sequencing, we provide a link between TRIM33 binding, RNA Polymerase II occupancy and H3K4me3 spreading on inflammatory genes in macrophages and reveal novel insights concerning the transcriptional regulation of Ifn-beta where TRIM33 exerts a repressive function via a distal regulatory region during late stages of LPS activation of macrophages. These findings pinpoint TRIM33 as a major regulator of the resolution of inflammation and indicate that transcriptional regulators can fine-tune H3K4me3 spreading. To study the role of TRIM33 in the transcriptional response induced by pathogen receptors, we analyzed whether lack of TRIM33 in macrophages affected the TLR-mediated regulation of proinflammatory and antimicrobial genes. To study this role, we bred TRIM33fl/fl mice with Lyz-Cre mice (obtained from The Jackson Laboratory, Bar Harbor, Maine, USA) where the Cre recombinase gene is under the regulatory sequences of the Lyz gene that is expressed only in mature myeloid cells. Bone marrow cells from 2 LyzCre/Trim33+/+ mice and 2 LyzCre/Trim33flox/flox mice were then differentiated in macrophages and treated during 0h, 4h, 12h and 24h with LPS. Total RNA was extracted from macrophages and analysed using cDNA microarrays. The set of gene expression consists of 16 samples of RNA of bone marrow derived macrophages activated with 100ng/ml of LPS during 0h, 4h, 12h, 24h, 8 samples from 2 LyzCre/Trim33+/+ mice and 8 samples from 2 LyzCre/Trim33flox/flox mice.
Experiment types
transcription profiling by array, co-expression, compound treatment, genetic modification design, replicate, time series design
Contacts
Citation
TRIM33 is necessary for epigenetic modifications associated with resolution of inflammation. Federica Ferri, Aude Parcelier, Vanessa Petit, Nathalie Gault, Daniel Lewandowski, Vilma Barroca, Stephanie Le Gras, Elene Sapharikas, Veronique Baud, Fran�oise Porteu, Sophie Kusy, Steven Sensarn, Marie-Catherine Vozenin, Eric Soler, Frank Grosveld, Irwin Davidson and Paul-Henri Romeo.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-1441.idf.txt
Sample and data relationshipE-MTAB-1441.sdrf.txt
Raw data (1)E-MTAB-1441.raw.1.zip
Processed data (1)E-MTAB-1441.processed.1.zip
Array designA-MEXP-2171.adf.txt
Links