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To define molecular mechanisms controlling this progression, we probed five stages spanning the commitment process using deep sequencing RNA-seq and ChIP-seq methods to track genome-wide shifts in transcription, cohorts of active transcription factor genes, histone modifications at diverse classes of cis-regulatory elements, and binding patterns of GATA-3 and PU.1, transcription factors with complementary roles in T-cell development. The results locate potential promoter-distal cis-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 while 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. Overall design: Genome-wide expression profiles, global distributions of three different histone modifications, and global occupancies of two transcription factors were examined in five developmentally related immature T populations. High throughput sequencing generated on average 9-30 million of mappable reads (single-read) for each ChIP-seq sample, and 10-15 million (single-read) for RNA-seq. Independent biological replicates were analyzed for individual populations. Terminology: while FLDN1_H3Ac_sample1.1 and FLDN1_H3Ac_sample1.2 are two lanes from the same sample, FLDN1_H3Ac_sample1.X and FLDN1_H3Ac_sample2 are from independent biological replicates. The sequence data of the input DNA from the same cell type was used as ChIP-seq background control.xref:PubMed:22500808ENAMus musculus, Laboratory Mice., House, Mus, Laboratory, Swiss, Mus domesticus, mouse, Mus musculus domesticus, Swiss Mouse, mouse <Mus musculus>, Mouse, House Mice, Swiss Mice, house mouse, Mice, Laboratory Mouse, House Mouse, mice C57BL/6xCBA/CaJ hybrid, domesticus, Mus muscarisHITS-CLIP, High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, ChIP-Chip, Thymus-Dependent Lymphocytes, wide/broad, Chromatin Immuno-precipitation, Cross Linking and Immunoprecipitation Followed by Deep Sequencing, ChIP Sequencing, CLIP-Seq, T-Lymphocyte, broad, Assay for Transposase-Accessible Chromatin Using Sequencing, ChIP-PET, Cell, ChIP-Exo, T Lymphocyte, T-Cell, Chromatin Immunoprecipitation Sequencing-Chip, High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, immature T cell, T lymphocyte, Chromatin Immunoprecipitation Sequencing Chip, T-cell, Chromatin Immuno precipitation Sequencing, Genomes, Epigenetic, ChIP, T-Cells, Chromatin Immunoprecipitation Paired End Tag, Chromatin Immuno Precipitation Paired End Tag, Thymus-Dependent, Cross-Linking and Immunoprecipitation Followed by Deep Sequencing, T, Chromatin Immunoprecipitation, Lymphocytes, Chromatin Immuno-precipitation Sequencing, whole genome, ChIP Exonuclease, T-lymphocyte, ChIP-Seq, Sequencing, Epigenomic, Thymus-Dependent Lymphocyte, Assay for Transposase Accessible Chromatin Using Sequencing, Chromatin Immunoprecipitation Paired-End Tag, regulation of gene-specific transcription, T Cells, wide, T cell, ChIA-PET., mature T cell, Chromatin Immuno-Precipitation Paired-End Tag, Cells, ATAC-Seq, Chromatin Immunoprecipitation Sequencing-Chips, T Cell, Epigenetics, T Lymphocytes, ChIP-Exonuclease, Thymus Dependent Lymphocytes, LymphocytefalseMus musculusDynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity [ChIP-Seq]2025-09-242013-05-31PRJNA154107GSE312331009022500808