The thymus in mice and humans originates from the third pharyngeal pouch
endoderm. This process is divided into early Foxn1-independent stages and later
Foxn1-dependent stages. Foxn1 is indispensible for the differentiation of thymic
epithelial progenitor cells (TEPCs) as the development of thymus in Foxn1 mutant
mice is arrested around E12.5. The transcriptional changes associated with the
developmental of the thymus are poorly understood. In particular, the transcriptional
regulation of Foxn1 in the developing thymic rudiment has not been definitively
identified. Recently, Pax1, Pax9, Tbx1, and E2Fs have been implicated in
transcriptional regulation of Foxn1. However, with the exception of E2Fs, evidence
regarding their direct involvement in regulating Foxn1 expression is missing.
Therefore, the aims of this thesis were to study the transcriptional regulation of
Foxn1 through identification of its regulatory regions and studying the transcriptional
changes associated with the developing thymus. These aims were addressed through
the use of chromatin-immunoprecipitation technique combined with next-generation
sequencing and gene expression analyses of the developing TEPCs. The data
presented in this thesis identified H3K4me3 and H3K27ac marked Foxn1 promoter
and five H3K4me1 and H3K27ac marked putative enhancer regions. The
combination of gene expression analyses and transcription factor binding sites within
the above regions suggested Ets1, Isl1, Foxc1, Nfia, Nfib, Srf, Foxo1, Nfatc2, Ing4,
Foxa2, Hes1, E2Fs, and p53 as candidate transcriptional regulators of Foxn1. Nfatc2
appears also to be a target of Foxn1 that could play an important role in thymus
development by regulating a large set of genes. Comparison of wild type and Foxn1
null thymus showed that Foxn1 could act as positive regulator of Pax1 and negative
regulator of Gata3 and Eya1, genes important for third pharyngeal pouch
development. The comparison of transcriptome of E10.5 and E11.5 third pharyngeal
pouch cells and E12.5 TEPCs showed that genes involved in tissue development are
downregulated while those involved in antigen presentation, a process important for
thymus function, are upregulated during development. These results also
demonstrated a decrease in the activity of transcription factor network involving Hox
genes and an increase in the activity of a network involving Nfkb, Rela, and Irf
genes. Analysis of signalling pathways suggested that the NFκB signalling pathway
could be important for thymus development after E12.5 while TGFβ signalling
pathway appeared to be detrimental to Foxn1 expression in thymic epithelial cells.
Together, I identified several transcription factors that could be involved in
transcriptional regulation of Foxn1 in TEPCs, several genes that could be a target of
FOXN1, changes in transcription factor network and signalling pathways associated
with the developing thymic rudiment