Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

T cell development comprises a stepwise process of commitment from a multipotent precursor. To define molecular mechanisms controlling this progression, we probed five stages spanning the commitment process using RNA-seq and ChIP-seq to track genome-wide shifts in transcription, cohorts of active transcription factor genes, histone modifications at diverse classes of cis-regulatory elements, and binding repertoire of GATA-3 and PU.1, transcription factors with complementary roles in T cell development. The results highlight potential promoter-distal cis-regulatory elements in play and reveal both activation sites and diverse mechanisms of repression that silence genes used in alternative lineages. Histone marking is dynamic and reversible, and though permissive marks anticipate, repressive marks often lag behind changes in transcription. In vivo binding of PU.1 and GATA-3 relative to epigenetic marking reveals distinctive factor-specific rules for recruitment of these crucial transcription factors to different subsets of their potential sites, dependent on dose and developmental context. [Display omitted] ► Genome-wide RNA, promoter, and distal chromatin changes dissect T cell commitment ► Multipotency to commitment: alternative fates excluded by distinct repression modes ► Dynamic and reversible epigenetic marking responds to transcriptional regulators ► Distinct regimes of binding by dose and epigenetic interaction for PU.1 and GATA-3 Examining the epigenetic changes that define the stepwise maturation of T cells from multipotent precursors reveals the complexity in the mechanisms that silence genes used in alternative lineages and shows that, although permissive histone marks anticipate changes in transcription, repressive marks often lag behind.