TY - JOUR
T1 - Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells
AU - Giraud, Matthieu
AU - Yoshid, Hideyuki
AU - Abramson, Jakub
AU - Rahl, Peter B.
AU - Young, Richard A.
AU - Mathis, Diane
AU - Benoist, Christophe
N1 - We thank S. Davis, G. Frampton, and H. Paik for help with computational analysis. This work was supported by National Institutes of Health Grants R01-DK060027 and R01-AI088204 (to D.M. and C.B.) and R01-HG002668 and R01CA46455 (to R.A.Y.). M.G. received fellowships from the Campbell and Hall Charity Fund, The Harold Whitworth Pierce Charitable Trust, and the Philippe Foundation. H.Y. was supported by a fellowship from the Human Frontier Science Program, J.A. by Juvenile Diabetes Research Foundation Fellowships 10-2007-601 and 03-2005-1138, and P.B.R. by American Cancer Society Postdoctoral Fellowship 120272-PF-11-042-01-DMC.
PY - 2012/1/10
Y1 - 2012/1/10
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84855995571&partnerID=8YFLogxK
U2 - 10.1073/pnas.1119351109
DO - 10.1073/pnas.1119351109
M3 - مقالة
C2 - 22203960
SN - 0027-8424
VL - 109
SP - 535
EP - 540
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 2
ER -