Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells
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Giraud-2012-Aire unleashes stall.pdf
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Author(s)
Giraud, Matthieu
Yoshida, Hideyuki
Abramson, Jakub
Rahl, Peter B.
Young, Richard A.
Mathis, Diane
Benoist, Christophe
Date Issued
January 2012
Journal
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Citation
Giraud, M. et al. “Aire Unleashes Stalled RNA Polymerase to Induce Ectopic Gene Expression in Thymic Epithelial Cells.” Proceedings of the National Academy of Sciences 109.2 (2012): 535–540. Copyright ©2012 by the National Academy of Sciences
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Final published version
Abstract
Aire is a transcriptional regulator that induces expression of peripheral tissue antigens (PTA) in thymic medullary epithelial cells (MECs), driving immunological self-tolerance in differentiating T cells. To elucidate its mechanistic pathways, we examined its transcriptional impact in MECs in vivo by microarray analysis with mRNA-spanning probes. This analysis revealed initiation of Aire-activated genes to be comparable in Aire-deficient and wild-type MECs, but with a block to elongation after 50–100 bp in the absence of Aire, suggesting activation by release of stalled polymerases by Aire. In contrast, patterns of activation by transcription factors such as Klf4 were consistent with regulation of initiation. Mapping of Aire and RNA polymerase-II (Pol-II) by ChIP and high-throughput sequencing (ChIP-seq) revealed that Aire bound all Pol-II–rich transcriptional start sites (TSS), irrespective of its eventual effect. However, the genes it preferentially activated were characterized by a relative surfeit of stalled polymerases at the TSS, which resolved once Aire was introduced into cells. Thus, transcript mapping and ChIP-seq data indicate that Aire activates ectopic transcription not through specific recognition of PTA gene promoters but by releasing stalled polymerases.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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DOI of Published Version
https://doi.org/10.1073/pnas.1119351109
