Regulation of chromatin organizer SATB1 via TCR induced alternative promoter switch during T- cell development

Abstract

SATB1 is a T-lineage-enriched chromatin organizer and global gene regulator. SATB1 regulates multitude of genes important for T-cell survival, positive and negative selection. SATB1 binds to its target loci and recruits chromatin modifying machinery onto them. However, the transcriptional regulation of SATB1 itself was not addressed. In this study, we focused on elucidating the molecular mechanisms of transcriptional regulation of Satb1. We show that Satb1 is regulated by alternative promoter switch during thymocyte development in mouse. Analysis of ChIP-seq occupancy of histone marks such as H3K4me3, H3K4me1 and H3K27me3 on Satb1 locus indicated existence of four different alternative promoters. Characterization of Satb1 transripts using 5’ RACE and analysis of RNA-seq reads further confirmed the usage of alternative promoters resulting in the generation of Satb1 transcript variants with distinct 5’ UTR sequences. Furthermore, we show that the expression of Satb1 alternative transcripts during thymic T-cell development is tightly regulated in a developmental stage-specific manner and is dependent on TCR signaling. Our study demonstrates that the differential translatability of each of the Satb1 transcript variants, and that their combinatorial expression drives SATB1 protein levels during development of thymocytes. Analysis of ATAC-seq data revealed that Satb1 alternative promoters exhibit lineage-specific chromatin accessibility during T-cell development from the precursor cells. We further identified the transcription factor machinery important for cell type specific expression of Satb1 alternative promoters and found that TCF1 plays a major role in AP usage. Collectively, these studies shed light on the complex regulation of Satb1 by alternative promoter switch during T-cell development.