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Rheostatic Chromatin Control of Promiscuous Transcription by Aire and Brg1 [Affymetrix]

ABSTRACT: Gene Expression Profiles of mTECs from Aire-/- and Brg1-/- mice and their littermate controls.

ORGANISM(S): Mus musculus

PROVIDER: GSE102525 | GEO | 2017/12/13

SECONDARY ACCESSION(S): PRJNA397971

REPOSITORIES: GEO

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Rheostatic Chromatin Control of Promiscuous Transcription by Aire and Brg1 [ATAC-Seq]

Project description:Chromatin Accessibility Profiles of mTECs from Aire-/- and Brg1-/- mice and their littermate controls.

2017-12-06 | GSE102526 | GEO

Rheostatic Chromatin Control of Promiscuous Transcription by Aire and Brg1

Project description:Rheostatic Chromatin Control of Promiscuous Transcription by Aire and Brg1

| PRJNA397973 | ENA

Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [Hi-C]

Project description:Hi-C analysis of Aire+/+ and Aire-/- mTECs

2021-07-30 | GSE180933 | GEO

Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [ChIP-seq]

Project description:ChIP-seq for proteins involved in Aire's functioning in Aire+/+ and Aire-/- mTECs

2021-07-30 | GSE180934 | GEO

Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [RNA-seq]

Project description:RNA-seq analysis of Aire+/+ and Aire-/- mTECs with or without deletion of STAG2 (SA-2).

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Transcriptional regulation by Aire in medullary thymic epithelial cells revisited

Project description:The deficiency of Aire, a transcriptional regulator whose defect results in the development of autoimmunity, is associated with reduced expression of tissue-restricted self-Ags (TRAs) in medullary thymic epithelial cells (mTECs). Although the mechanisms underlying Aire-dependent expression of TRAs need to be explored, the physical identification of the target(s) of Aire has been hampered by the low and promiscuous expression of TRAs. We have tackled this issue by engineering mice with augmented Aire expression. Integration of the transcriptomic data from Aire-augmented and Aire-deficient mTECs revealed that a large proportion of so-called Aire-dependent genes, including those of TRAs, may not be direct transcriptional targets downstream of Aire. Rather, Aire induces TRA expression indirectly through controlling the heterogeneity of mTECs, as revealed by single-cell analyses. In contrast, Ccl25 emerged as a canonical target of Aire, and we verified this both in vitro and in vivo. Our approach has illuminated the Aire?s primary targets while distinguishing them from the secondary targets.

2021-10-13 | GSE155331 | GEO

Identification of a novel Aire-regulating cis-regulatory element using H3K27ac ChIP-seq

Project description:Thymic central tolerance is essential to preventing autoimmunity. In medullary thymic epithelial cells (mTECs), the Autoimmune regulator (Aire) gene plays an essential role in this process by driving the expression of a diverse set of tissue-specific antigens (TSAs), which are presented and help tolerize self-reactive thymocytes. Interestingly, Aire has a highly tissue-restricted pattern of expression, with only mTECs and peripheral extrathymic Aire-expressing cells (eTACs) known to express detectable levels in adults. Despite this high level of tissue specificity, the cis-regulatory elements that control Aire expression have remained obscure. We used sequence conservation analysis and ChIP-seq against the enhancer-associated histone mark H3K27ac to identify a candidate Aire cis-regulatory element. There is enrichment of H3K27ac near this element, ACNS1, in mTECs and the element also has characteristics of being NF-ÎºB-responsive. Finally, we find that this element is essential for Aire expression in vivo and necessary to prevent spontaneous autoimmunity, reflecting the importance of this regulatory DNA element in promoting immune tolerance. Two experimental groups (GFP neg mTECs and GFP pos mTECs), each with three samples, and one control sample (D10 Th2 cells).

2015-10-23 | E-GEOD-74257 | biostudies-arrayexpress

Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [CUT&Tag]

Project description:NIPBL and IgG CUT&Tag in Aire+/+ mTECs

2021-07-30 | GSE180936 | GEO

Rheostatic Chromatin Control of Promiscuous Transcription by Aire and Brg1

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-12-06 | GSE102527 | GEO

The effect of the autoimmune regulator (Aire) gene on the transcriptional expression profile of 3.10 mTEC cell line.

Project description:Medullary thymic epithelial cells (mTECs) contribute to self-tolerance through the ectopic expression of peripheral tissue antigens (PTAs) in the thymus. PTA expression in mTECs is largely dependent on the autoimmune regulator (Aire) gene. Here we used a Mus musculus mTEC cell line (3.10 mTEC line, which constitutively express Aire in culture) to knockdown Aire gene by means of siRNA transfection. Aire knockdown was confirmed by means of qRT-PCR and RNA-FISH (for Aire mRNA levels), immunofluorescence and western blot (for AIRE protein levels).The Agilent oligo microarrays were used to determine the large scale transcriptional expression profiles of control or Aire-knockdown 3.10 mTECs.

2015-12-31 | E-MTAB-3879 | biostudies-arrayexpress

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