Global dynamics of stage-specific transcription factor binding during thymocyte development

Abstract

In vertebrates, multiple transcription factors (TFs) bind to gene regulatory elements (promoters, enhancers, and silencers) to execute developmental expression changes. ChIP experiments are often used to identify where TFs bind to regulatory elements in the genome, but the requirement of TF-specific antibodies hampers analyses of tens of TFs at multiple loci. Here we tested whether TF binding predictions using ATAC-seq can be used to infer the identity of TFs that bind to functionally validated enhancers of the Cd4, Cd8, and Gata3 genes in thymocytes. We performed ATAC-seq at four distinct stages of development in mouse thymus, probing the chromatin accessibility landscape in double negative (DN), double positive (DP), CD4 single positive (SP4) and CD8 SP (SP8) thymocytes. Integration of chromatin accessibility with TF motifs genome-wide allowed us to infer stage-specific occupied TF binding sites within known and potentially novel regulatory elements. Our results provide genome-wide stage-specific T cell open chromatin profiles, and allow the identification of candidate TFs that drive thymocyte differentiation at each developmental stage.

A Gata3 enhancer necessary for ILC2 development and function

“…Given that Gata3 is expressed throughout T cell development in the thymus and in mature ILCs and differentiated T cells in the periphery, we next evaluated chromatin accessibility in these populations using publicly available ATAC-seq data (2,37). The distal Gata3 +674/762 region was conspicuously inaccessible in thymocytes, while Gata3 +278/285 accessibility persisted throughout T cell development, consistent with previously reported experiments (SI Appendix, Fig.…”

Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia

“…We obtained publicly available ATAC-seq data derived from cell types sorted ex vivo and brain single-nuclei analyses from mice (Supplemental Table S1; Mo et al 2015;Matcovitch-Natan et al 2016;Gray et al 2017;Hughes et al 2017;Hosoya et al 2018;McClymont et al 2018;Preissl et al 2018). In total, we obtained 25 mouse ATAC-seq open chromatin region (OCR) data sets encompassing subclasses of six broader cell types (dopaminergic neurons, excitatory neurons, glia, inhibitory neurons, retina cells, and T cells) (Supplemental Table S1).…”

The transcription factor BCL-6 controls early development of innate-like T cells

“…To investigate whether the early stages of the iNKT maturation program were critical for determining the chromatin accessibility profile of mature iNKTs, we performed ATAC-seq in ST0, ST1, and mature NKT1 (sorted as Tetr + TCRβ + CD24 − CD44 + NK1.1 + ) cells. To exclude loci that may be open transiently in ST0 cells due to positive selection and TCR signaling, we restricted our analysis in loci that were more accessible in mature NKT1 cells as compared to DP thymocytes 31 (iNKT-related regions). Our results showed that these regions were already accessible in ST0 cells ( Fig.…”