Mesenteric lymph node (mLN) T cells undergo tissue adaptation upon migrating to intestinallamina propria (LP) and intraepithelial (IE) compartments, ensuring appropriate balance between tolerance and resistance. By combining mouse genetics with single-cell and chromatin analyses, we addressed the molecular imprinting of gut epithelium on T cells. Transcriptionally, conventional and regulatory (Treg) CD4 + T cells from mLN, LP and IE segregate based on the gut layer they occupy; trajectory analysis suggests a stepwise loss of CD4-programming and acquisition of an intraepithelial profile. Treg fate-mapping coupled with RNA-and ATAC-sequencing revealed that the Treg program shuts down before an intraepithelial program becomes fully accessible at the epithelium. Ablation of CD4 lineage-defining transcription factor ThPOK results in premature acquisition of an IEL profile by mLN Tregs, partially recapitulating epithelium imprinting. Thus, coordinated replacement of circulating lymphocyte program with site-specific transcriptional and chromatin changes is necessary for tissue imprinting.conversion include co-expression of CD4 and the CD8aa homodimer which is induced by a switch from conventional CD4-to-CD8 lineage-defining transcription factors. CD4-IELs downregulate ThPOK (encoded by Zbtb7b), expressed by all conventional mature CD4 + T cells and upregulate the long form of Runx3, expressed by mature CD8 + T cells 9,12,16 . While environmental cues and transcription factors involved in the differentiation of naïve CD4 + T cells into gut-adapted T cell subsets have been described in the past decade, the transcriptional and chromatin changes that accompany such tissue-specific imprinting have not been elucidated.We used genetic fate-mapping and gene ablation mouse models coupled with single-cell RNA-, ATACand ChIP-sequencing approaches to uncover the molecular mechanisms of how the intestinal tissue can imprint T-cell fate decisions on migrating mLN CD4 + T cells. We found that gut-associated CD4 + T cell transcriptional profiles largely segregate by tissue location, indicating that upon leaving the gut-draining LNs, migrating cells quickly adapt to either LP or IE compartments; IE-adapted cells followed a stepwise acquisition of an IEL profile through a distinct pre-IEL stage. We specifically followed how the generally stable Treg phenotype is destabilized upon T cell migration to the IE compartment. We found that the Treg program is first downregulated at a pre-IEL stage before a cytotoxic IEL program is made accessible at the chromatin levels and then subsequently transcribed. Finally, we showed that while natural ThPOK downmodulation marks the pre-IEL stage, premature ThPOK loss in Tregs allows for the expression of the IEL profile before the Treg program is fully shut down. Our studies uncovered wide, tissue-specific and stepwise chromatin and transcriptional changes in T cells upon transitioning from tissue-draining LNs to tissue sites and revealed specific roles for lineage-defining transcription factors in drivi...