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E-GEOD-47494 - A pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics

Status
Released on 5 August 2013, last updated on 3 May 2014
Organism
Mus musculus
Samples (6)
Protocols (6)
Description
Pseudogenes are thought to be inactive gene sequences, but recent evidence of extensive pseudogene transcription raised the question of potential function. Here we discover and characterize the sets of lncRNAs induced by inflammatory signaling via TNFα. TNFα regulates hundreds of lncRNAs, including 54 pseudogene lncRNAs, several of which show exquisitely selective expression in response to specific cytokines and microbial components in a NF-κB-dependent manner. Lethe, a pseudogene lncRNA, is selectively induced by proinflammatory cytokines via NF-κB or glucocorticoid receptor agonist, and functions in negative feedback signaling to NF-κB. Lethe interacts with NF-κB subunit RelA to inhibit RelA DNA binding and target gene activation. Lethe level decreases with organismal age, a physiological state associated with increased NF-κB activity. These findings suggest that expression of pseudogenes lncRNAs are actively regulated and constitute functional regulators of inflammatory signaling. RNA profiles of wild type (WT) MEFs treated with TNF-alpha were generated by deep sequencing using Illumina GAIIx. Examination of H3K4me3 histome modification in MEF.
Experiment types
ChIP-seq, RNA-seq of coding RNA 
Contacts
Kun Qu <kqu@stanford.edu>, Howard Y Chang, Jiangjing Zhang, Nicole A Rapicavoli
Citation
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-47494.idf.txt
Sample and data relationshipE-GEOD-47494.sdrf.txt
Processed data (1)E-GEOD-47494.processed.1.zip
Additional data (1)E-GEOD-47494.additional.1.zip
Links