Identification of TNFα-induced genes that are IRAK1BP1 dependent
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Maureen Harrington
PROVIDER: E-GEOD-44146 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The transcription factor NF-κB is considered the master regulator of the immune response but also acts broadly to regulate gene expression that influences cell survival, proliferation and differentiation. Post-translational modification of NF-κB, phosphorylation in particular, is essential for the transactivation activity of NF-κB. Emerging evidence suggests that the regulation of NF-κB in the nucleus is critical in controlling gene expression. Promyelocytic Leukemia (PML) is a nuclear protein that forms nuclear bodies (PML NBs), sub-nuclear structures that are associated with transcriptionally active genomic regions that have been implicated in multiple processes such as apoptosis, senescence and anti-viral responses. Chromosomal translocations leading to the expression of a PML-retinoic acid receptor-α (PML-RARα) fusion protein are causative for acute promyelocytic leukemia (APL) characterised by a differentiation block at the promyelocytic state of myeloid development. Here we demonstrate that PML is required for phosphorylation of NF-κB p65 and that PML is essential for NF-κB- induced transcriptional responses. Our analysis of available transcriptional profiles of all-trans retinoic acid treated acute promyelocytic leukemia (APL) cells identifies a NF-κB transcriptional programme suppressed by PML-RARα. We further demonstrate that PML-RARα inhibits NF-κB phosphorylation and transcriptional activity. Our findings demonstrate a critical role for PML in promoting NF-κB transcriptional activity which may contribute to APL initiation and maintenance. WT and PML-/- MEFs were analysed for gene expression analysis. Total of 12 samples, inlcluding triplicates were utilized. WT MEFs and PML-/- were stimulated with TNFα for three hours and analysed for gene expresison using unstimulated WT MEFs as control.
2016-06-01 | E-GEOD-47828 | biostudies-arrayexpress
Project description:HEK293T cells were transfected with the Rbp1-amr or slow (R729H-amr) α-amanitin resistant subunit of RNA Pol II and selected with α-amanitin 24 hours after transfection for additional 24 hours. Total RNA was extracted and global changes in gene expression were determined using microarray chips. MiRNAs are transcribed by RNA pol II but the transcriptional features influencing their synthesis are poorly defined. Here we report that a TATA-box in miRNA and a subset of protein-coding genes is associated with increased sensitivity to a slow rate of transcription elongation. We also show that promoters driven by TATA-box or NF-κB elicit high transcription re-initiation rate, but paradoxically lower levels of miRNA. Interestingly, miRNA synthesis was converted to a more productive mode by decreasing initiation rate, but less productive when the re-initiation rate increased. This phenomenon was found to be associated with a delay in miR-146a induction by NF-κB. We also demonstrate that miRNAs are remarkably strong pause sites. Our findings suggest that lower efficiency of miRNA synthesis directed by the TATA-box or NF-κB is a consequence of frequent transcription initiation that lead to Pol II crowding at pause sites, thereby increasing the chance of collision and premature termination. These findings highlight the importance of the transcription initiation mechanism for miRNA synthesis, and have implications for TATA-box promoters in general. HEK293T cells were transfected with plasmids directing the expression of α-amanitin-resistant variants of Pol II (Rpb1-amr and R749H-amr). α-amanitin was added and RNA was prepared 24 and 48 h later, respectively. The data provided is from 3 Rpb1-amr vs 3 R749H-amr (6 samples).
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2016-03-01 | E-GEOD-68760 | biostudies-arrayexpress
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2016-01-14 | E-GEOD-76804 | biostudies-arrayexpress
Project description:In this setup gene profiling of hair follicle keratinocytes with active nuclear NF-κB is used to further analyze the role of NF-κB in HF development. For this purpose an NF-κB-responsive EGFP reporter mouse has been constructed, which enables in vivo visualization of cells with NF-κB activity and their isolation via fluorescence assisted cell sorting (FACS). The isolated cells were used to establish a gene profile of early hair placode keratinocytes with NF-κB activity (E14.5).
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2016-02-29 | E-MTAB-4534 | biostudies-arrayexpress
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2016-07-03 | E-GEOD-70025 | biostudies-arrayexpress