The 3D enhancer network of the developing T cell genome is controlled by SATB1 [Hi-C]

Mechanisms of tissue-specific gene expression regulation, particularly via spatial coordination of gene promoters and their regulatory elements are poorly understood. Here we investigated the 3D genome organization of developing murine T cells. We identified a tissue-specific genome organizer SATB1 as a factor enriched at the anchors of promoter-enhancer chromatin loops. To unravel its functions in T cells, we generated Satb1fl/flCd4-Cre+ (Satb1 cKO) conditional knockout animals. Satb1 cKO animals suffer from severe autoimmunity so we sought to investigate a potential link between the autoimmunity and putatively deregulated nuclear architecture caused by SATB1 depletion. This series of Hi-C and HiChIP experiments is a part of SuperSeries including also RNA-Seq and ATAC-Seq experiments to fully understand the deregulation of Satb1 cKO thymocytes and to unravel the roles of SATB1 in T cell chromatin organization. Utilizing the HiChIP data, we compared SATB1 and CTCF-mediated chromatin loops, revealing that SATB1 builds a more refined layer of genome organization upon the CTCF scaffold. Moreover, H3K27ac HiChIP and Hi-C experiments in WT and Satb1 cKO thymocytes helped us to assess the functional impact of SATB1 and its underlying genome-wide regulome. SATB1 primarily mediates promoter-enhancer loops affecting a number of master regulator genes whose deregulation in knockout animals may comprise a cell-intrinsic mechanism of the autoimmunity. Our findings indicate a possible existence of a special class of genome organizers controlling tissue and/or time-specific transcriptional programs via spatial chromatin arrangements that are complementary to the function of conventional ubiquitously expressed genome organizers. Overall design: Two biological replicates for each sample were used. We performed SATB1 HiChIP, CTCF HiChIP (both only in WT) and H3K27ac HiChIP in WT and Satb1fl/flCd4-Cre+ murine thymocytes. Moreover, we performed Hi-C experiments in WT and Satb1fl/flCd4-Cre+ murine thymocytes. All interaction matrices are provided as well as processed HiChIP loops and binding sites of the targeted factors derived from the HiChIP datasets. For SATB1 binding site identification, we used a different HiChIP dataset from an unsuccessful HiChIP experiment with high proportion of Dangling End Pairs (rep3, rep4), which is more suitable for SATB1 peak calling.