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.

Thymic epithelial cell differentiation, growth and function depend on the expression of the transcription factor Foxn1, however its target genes have never been physically identified. Using novel static and inducible genetic model systems and chromatin studies, we provide now a genome wide map of direct Foxn1 target genes for postnatal thymic epithelia and define the Foxn1 binding motif. We detail the function of Foxn1 in these cells and demonstrate that in addition to the transcriptional control of genes involved in the attraction and lineage commitment of T cell precursors, Foxn1 regulates the expression of genes involved in antigen processing and thymocyte selection. Thus, critical events in thymic lympho-stromal cross-talk and T cell selection are indispensably choreographed by Foxn1.

The thymus provides multiple microenvironments that are essential for the development and repertoire selection of T lymphocytes. The thymic cortex induces the generation and positive selection of T lymphocytes, whereas the thymic medulla establishes self-tolerance among the positively selected T lymphocytes. Cortical thymic epithelial cells (cTECs) and medullary TECs (mTECs) constitute the major stromal cells that structurally form and functionally characterize the cortex and the medulla, respectively. cTECs and mTECs are both derived from the endodermal epithelium of the third pharyngeal pouch. However, the molecular and cellular characteristics of the progenitor cells for the distinct TEC lineages are unclear. Here we report the preparation and characterization of mice that express the recombinase Cre instead of β5t, a proteasome subunit that is abundant in cTECs and not detected in other cell types, including mTECs. By crossing β5t-Cre knock-in mice with loxP-dependent GFP reporter mice, we found that β5t-Cre-mediated recombination occurs specifically in TECs but not in any other cell types in the mouse. Surprisingly, in addition to cTECs, β5t-Cre-loxP-mediated GFP expression was detected in almost all mTECs. These results indicate that the majority of mTECs, including autoimmune regulator-expressing mTECs, are derived from β5t-expressing progenitor cells.T hymic epithelial cells (TECs) are derived from the endodermal epithelium of the third pharyngeal pouch (1-3). Cortical TECs (cTECs) provide a microenvironment that induces the generation of T cells and the positive selection of functionally competent T cells, whereas medullary TECs (mTECs) essentially contribute to the establishment of self-tolerance by the deletion of self-reactive T cells and the generation of regulatory T cells (4, 5). The nuclear protein Autoimmune regulator (Aire) expressed by a subpopulation of mTECs is essential, especially during the perinatal period, for the establishment of selftolerance in T cells (6, 7). Although the importance of the forkhead transcription factor Foxn1 for the development of both cTECs and mTECs has been established (2, 8), it remains unknown how the endodermal epithelium of the third pharyngeal pouch gives rise to cTECs and mTECs. In particular, the molecular and cellular mechanisms underlying the separate development of the cTEC and mTEC lineages remain unclear.We previously reported β5t, a proteasome subunit expressed in cTECs (9, 10). β5t is pivotal for the positive selection of immunocompetent CD8 + T cells (11,12). β5t mRNA and protein are prominently expressed in cTECs and not detected in other cell types, including mTECs (10). To examine whether β5t-expressing cells could contribute to the development of cells other than cTECs, we engineered mice in which the β5t-encoding genomic sequence was replaced with the sequence that encodes the loxP-specific recombinase Cre. Analyzing mice that are crossed to carry the β5t-Cre knock-in allele and the loxPdependent GFP reporter allele, we demonstrate that β5t-Cr...

Thymic T cell development is dependent on a specialized epithelial microenvironment mainly composed of cortical and medullary thymic epithelial cells (TECs). The molecular programs governing the differentiation and maintenance of TECs remain largely unknown. Wnt signaling is central to the development and maintenance of several organ systems but a specific role of this pathway for thymus organogenesis has not yet been ascertained. In this report, we demonstrate that activation of the canonical Wnt signaling pathway by a stabilizing mutation of β-catenin targeted exclusively to TECs changes the initial commitment of endodermal epithelia to a thymic cell fate. Consequently, the formation of a correctly composed and organized thymic microenvironment is prevented, thymic immigration of hematopoietic precursors is restricted, and intrathymic T cell differentiation is arrested at a very early developmental stage causing severe immunodeficiency. These results suggest that a precise regulation of canonical Wnt signaling in thymic epithelia is essential for normal thymus development and function.

Plant viruses act as triggers and targets of RNA silencing and have evolved proteins to suppress this plant defense response during infection. Although Tobacco mosaic tobamovirus (TMV) triggers the production of virus-specific small interfering RNAs (siRNAs), this does not lead to efficient silencing of TMV nor is a TMV-green fluorescent protein (GFP) hybrid able to induce silencing of a GFP-transgene in Nicotiana benthamiana, indicating that a TMV silencing suppressor is active and acts downstream of siRNA production. On the other hand, TMV-GFP is unable to spread into cells in which GFP silencing is established, suggesting that the viral silencing suppressor cannot revert silencing that is already established. Although previous evidence indicates that the tobamovirus silencing suppressing activity resides in the viral 126-kDa small replicase subunit, the mechanism of silencing suppression by this virus family is not known. Here, we connect the silencing suppressing activity of this protein with our previous finding that Oilseed rape mosaic tobamovirus infection leads to interference with HEN1-mediated methylation of siRNA and micro-RNA (miRNA). We demonstrate that TMV infection similarly leads to interference with HEN1-mediated methylation of small RNAs and that this interference and the formation of virus-induced disease symptoms are linked to the silencing suppressor activity of the 126-kDa protein. Moreover, we show that also Turnip crinkle virus interferes with the methylation of siRNA but, in contrast to tobamoviruses, not with the methylation of miRNA.RNA silencing is a posttranscriptional, RNA-guided, gene regulatory mechanism that operates through RNA-mediated sequence-specific interactions in the cytoplasm of eukaryotes, including plants (5,47,57).RNA silencing is generally induced by double-stranded RNA (dsRNA), which can originate from various sources, such as transgenes, viral replication intermediates, or experimentally introduced dsRNA sequences. Central to the silencing process are dicers or "dicer-like" enzymes that cleave dsRNA into small double-stranded fragments, called small interfering RNAs (siRNAs). Single-stranded siRNAs are then incorporated into multicomponent RNA-induced silencing complexes (RISC), which contain an "argonaute" (AGO) family protein (in plants usually AGO1) (3) and inactivate homologous RNA through endonucleolytic cleavage. In addition to siRNAs, which are usually derived from foreign elements such as transgenes and viruses, other small RNA (sRNA) species are encoded by specific noncoding RNA genes. Among these, micro-RNAs (miRNAs) have predominant roles during plant development (28) and are processed from miRNA precursors encoded by miRNA genes. Similarly to siRNAs, miRNAs are incorporated into AGO-containing RISC complexes to guide the recognition of target RNAs. In plants, miRNA-RISC complexes usually cause target RNA cleavage, whereas in most mammalian cases miRNA-RISC inhibits translation of target mRNA (37). Plant siRNAs and miRNAs (commonly referred to as sRNAs) ...

Intrathymic T‐cell development is critically dependent on cortical and medullary thymic epithelial cells (TECs). Both epithelial subsets originate during early thymus organogenesis from progenitor cells that express the thymoproteasome subunit β5t, a typical feature of cortical TECs. Using in vivo lineage fate mapping, we demonstrate in mice that β5t+ TEC progenitors give rise to the medullary TEC compartment early in life but significantly limit their contribution once the medulla has completely formed. Lineage‐tracing studies at single cell resolution demonstrate for young mice that the postnatal medulla is expanded from individual β5t+ cortical progenitors located at the cortico‐medullary junction. These results therefore not only define a developmental window during which the expansion of medulla is efficiently enabled by progenitors resident in the thymic cortex, but also reveal the spatio‐temporal dynamics that control the growth of the thymic medulla.

Thymic epithelial cells provide unique cues for the life-long selection and differentiation of a repertoire of functionally diverse T cells. Rendered miRNA deficient, these stromal cells in the mouse lose their capacity to instruct the commitment of haematopoietic precursors to a T cell fate, to effect thymocyte positive selection and to achieve promiscuous gene expression required for central tolerance induction. Over time, the microenvironment created by miRNA-deficient thymic epithelia assumes the cellular composition and structure of peripheral lymphoid tissue where thympoiesis fails to be supported. These findings emphasize a global role for miRNA in the maintenance and function of the thymic epithelial cell scaffold and establish a novel mechanism how these cells control peripheral tissue antigen expression to prompt central immunological tolerance.

Thymic epithelial cells (TEC) effect crucial roles in thymopoiesis including the control of negative thymocyte selection. This process depends on their capacity to express promiscuously genes encoding tissue-restricted antigens. This competence is accomplished in medullary TEC (mTEC) in part by the presence of the transcriptional facilitator AutoImmune REgulator, AIRE. AIRE-regulated gene transcription is marked by repressive chromatin modifications, including H3K27me3. When during TEC development these chromatin marks are established, however, remains unclear. Here we use a comprehensive ChIP-seq dataset of multiple chromatin modifications in different TEC subtypes to demonstrate that the chromatin landscape is established early in TEC differentiation. Much of the chromatin architecture found in mature mTEC was found to be present already over earlier stages of mTEC lineage differentiation as well as in non-TEC tissues. This was reflected by the fact that a machine learning approach accurately classified genes as AIRE-induced or AIRE-independent both in immature and mature mTEC. Moreover, analysis of TEC specific enhancer elements identified candidate transcription factors likely to be important in mTEC development and function. Our findings indicate that the mature mTEC chromatin landscape is laid down early in mTEC differentiation, and that AIRE is not required for large-scale re-patterning of chromatin in mTEC.