Sansom Stephen N, Shikama-Dorn Noriko, Zhanybekova Saule, Nusspaumer Gretel, Macaulay Iain C, Deadman Mary E, Heger Andreas, Ponting Chris P, Holländer Georg A
MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom;
Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland;
Genome Res. 2014 Dec;24(12):1918-31. doi: 10.1101/gr.171645.113. Epub 2014 Sep 15.
Promiscuous gene expression (PGE) by thymic epithelial cells (TEC) is essential for generating a diverse T cell antigen receptor repertoire tolerant to self-antigens, and thus for avoiding autoimmunity. Nevertheless, the extent and nature of this unusual expression program within TEC populations and single cells are unknown. Using deep transcriptome sequencing of carefully identified mouse TEC subpopulations, we discovered a program of PGE that is common between medullary (m) and cortical TEC, further elaborated in mTEC, and completed in mature mTEC expressing the autoimmune regulator gene (Aire). TEC populations are capable of expressing up to 19,293 protein-coding genes, the highest number of genes known to be expressed in any cell type. Remarkably, in mouse mTEC, Aire expression alone positively regulates 3980 tissue-restricted genes. Notably, the tissue specificities of these genes include known targets of autoimmunity in human AIRE deficiency. Led by the observation that genes induced by Aire expression are generally characterized by a repressive chromatin state in somatic tissues, we found these genes to be strongly associated with H3K27me3 marks in mTEC. Our findings are consistent with AIRE targeting and inducing the promiscuous expression of genes previously epigenetically silenced by Polycomb group proteins. Comparison of the transcriptomes of 174 single mTEC indicates that genes induced by Aire expression are transcribed stochastically at low cell frequency. Furthermore, when present, Aire expression-dependent transcript levels were 16-fold higher, on average, in individual TEC than in the mTEC population.
胸腺上皮细胞（TEC）的杂乱基因表达（PGE）对于产生耐受自身抗原的多样化T细胞抗原受体库至关重要，因此对于避免自身免疫也至关重要。然而，TEC群体和单细胞中这种异常表达程序的程度和性质尚不清楚。通过对精心鉴定的小鼠TEC亚群进行深度转录组测序，我们发现了一个PGE程序，该程序在髓质（m）和皮质TEC中是共有的，在mTEC中进一步细化，并在表达自身免疫调节基因（Aire）的成熟mTEC中完成。TEC群体能够表达多达19293个蛋白质编码基因，这是已知在任何细胞类型中表达的基因数量最多的。值得注意的是，在小鼠mTEC中，仅Aire表达就正向调节3980个组织限制性基因。值得注意的是，这些基因的组织特异性包括人类AIRE缺乏症中已知的自身免疫靶点。基于Aire表达诱导的基因通常在体细胞组织中以抑制性染色质状态为特征这一观察结果，我们发现这些基因与mTEC中的H3K27me3标记密切相关。我们的发现与AIRE靶向并诱导先前被多梳蛋白组蛋白表观遗传沉默的基因的杂乱表达一致。对174个单个mTEC转录组的比较表明，Aire表达诱导的基因在低细胞频率下随机转录。此外，当存在时，Aire表达依赖性转录水平在单个TEC中平均比在mTEC群体中高16倍。
