Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells
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...
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| Format: | Article |
| Language: | en_US |
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National Academy of Sciences
2012
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| Online Access: | http://hdl.handle.net/1721.1/72512 https://orcid.org/0000-0001-8855-8647 |
| _version_ | 1826209280159645696 |
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| author | Giraud, Matthieu Yoshida, Hideyuki Abramson, Jakub Rahl, Peter B. Young, Richard A. Mathis, Diane Benoist, Christophe |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Giraud, Matthieu Yoshida, Hideyuki Abramson, Jakub Rahl, Peter B. Young, Richard A. Mathis, Diane Benoist, Christophe |
| author_sort | Giraud, Matthieu |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T14:20:22Z |
| format | Article |
| id | mit-1721.1/72512 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:20:22Z |
| publishDate | 2012 |
| publisher | National Academy of Sciences |
| record_format | dspace |
| spelling | mit-1721.1/725122022-10-01T20:40:50Z Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells Giraud, Matthieu Yoshida, Hideyuki Abramson, Jakub Rahl, Peter B. Young, Richard A. Mathis, Diane Benoist, Christophe Massachusetts Institute of Technology. Department of Biology Young, Richard A. Young, Richard A. 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. National Institutes of Health (U.S.) (R01-HG002668) National Institutes of Health (U.S.) (Grant number R01CA46455) National Institutes of Health (U.S.) (Grant number R01-HG002668) 2012-09-04T20:30:28Z 2012-09-04T20:30:28Z 2012-01 2011-10 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/72512 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 https://orcid.org/0000-0001-8855-8647 en_US http://dx.doi.org/10.1073/pnas.1119351109 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences PNAS |
| spellingShingle | Giraud, Matthieu Yoshida, Hideyuki Abramson, Jakub Rahl, Peter B. Young, Richard A. Mathis, Diane Benoist, Christophe Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells |
| title | Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells |
| title_full | Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells |
| title_fullStr | Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells |
| title_full_unstemmed | Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells |
| title_short | Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells |
| title_sort | aire unleashes stalled rna polymerase to induce ectopic gene expression in thymic epithelial cells |
| url | http://hdl.handle.net/1721.1/72512 https://orcid.org/0000-0001-8855-8647 |
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