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SATB1 controls cell identity of DP thymocytes by repressing early expressing genes and activating DP-specific genes a Two-dimensional UMAP plot of thymocytes single-cell transcriptomes in vav-cre × Satb1fl/fl (Satb1cKO) and Satb1fl/fl (Satb1WT) mice. Each dot represents one cell and different areas identified by unsupervised clustering. b Violin plots showing Rag1 gene expression per cell in difference cell subsets from Satb1cKO and Satb1WT mice. c Volcano plot showing bulk RNA-seq differentially expressed genes (Satb1cKO vs Satb1WT) in sorted DP thymocytes. Three biological replicates were performed. The x- and y axis represent log2(fold change) and −log10(P value), respectively. Some genes are annotated. d Heatmap and e boxplot showing relative gene expression of the differentially expressed genes during the differentiation from DN1 to SP thymocytes. The differentially expressed genes contain 893 downregulated and 556 upregulated genes Box plots show median (center line), interquartile range (box), and tenth and ninetieth percentiles (whiskers). DEGs are from bulk RNA-seq data in c. Gene expression data from DN1 to SP stages are derived RNA-seq data from ImmGen datasets (GSE109125). f Gene-set enrichment analysis (GSEA)-enrichment plots for DN1- or DN3-specific genes showing a significant enrichment of the geneset in upregulated genes of Satb1cKO DP thymocytes. DN1 and DN3 genesets were generated according to the highest expression stage from DN1 to SP stages. The expression data are from bluk RNA-seq of sorted DP thymocytes from WT and Satb1cKO mice. Nominal P value, calculated as two-sided t test, no adjustment since only one geneset was tested. Source data are provided as a Source Data file.
Source publication
CD4⁺ and CD8⁺ double-positive (DP) thymocytes play a crucial role in T cell development in the thymus. DP cells rearrange the T cell receptor gene Tcra to generate T cell receptors with TCRβ. DP cells differentiate into CD4 or CD8 single-positive (SP) thymocytes, regulatory T cells, or invariant nature kill T cells (iNKT) in response to TCR signali...
Citations
... DDX5 exerts critical roles in RNA processing, including splicing, transcript stability, mRNA export, and microRNA processing. 55,106 In addition, DDX5 is involved in R-loop disassembly and promotes DNA repair. 107 DDX5 has been previously identified as a TET2 interacting partner in ESCs 52 and in MCF7 cells 45 (Table S2). ...
Ten-eleven translocation (TET) proteins are DNA dioxygenases that mediate active DNA demethylation. TET3 is the most highly expressed TET protein in thymic developing T cells. TET3, either independently or in cooperation with TET1 or TET2, has been implicated in T cell lineage specification by regulating DNA demethylation. However, TET-deficient mice exhibit complex phenotypes, suggesting that TET3 exerts multifaceted roles, potentially by interacting with other proteins. We performed liquid chromatography with tandem mass spectrometry in primary developing T cells to identify TET3 interacting partners in endogenous, in vivo conditions. We discover TET3 interacting partners. Our data establish that TET3 participates in a plethora of fundamental biological processes, such as transcriptional regulation, RNA polymerase elongation, splicing, DNA repair, and DNA replication. This resource brings in the spotlight emerging functions of TET3 and sets the stage for systematic studies to dissect the precise mechanistic contributions of TET3 in shaping T cell biology.
... Library concentration was quantified through Qubit 3.0, fragment length distribution was examined by DNF915, and libraries were sequenced on Illumina NovaSeq 6000 (Novogene, Tianjin, China). ATAC-seq data analysis was conducted as previously described [27,28]. Briefly, raw sequence reads were processed by Fastp (v 0.20.0) to remove adapters and low-quality reads. ...
Background
Growing evidence has suggested that Type I Interferon (I-IFN) plays a potential role in the pathogenesis of Down Syndrome (DS). This work investigates the underlying function of MX1, an effector gene of I-IFN, in DS-associated transcriptional regulation and phenotypic modulation.
Methods
We performed assay for transposase-accessible chromatin with high-throughout sequencing (ATAC-seq) to explore the difference of chromatin accessibility between DS derived amniocytes (DSACs) and controls. We then combined the annotated differentially expressed genes (DEGs) and enriched transcriptional factors (TFs) targeting the promoter region from ATAC-seq results with the DEGs in RNA-seq, to identify key genes and pathways involved in alterations of biological processes and pathways in DS.
Results
Binding motif analysis showed a significant increase in chromatin accessibility of genes related to neural cell function, among others, in DSACs, which is primarily regulated by members of the activator protein-1 (AP-1) transcriptional factor family. Further studies indicated that MX Dynamin Like GTPase 1 (MX1), defined as one of the key effector genes of I-IFN, is a critical upstream regulator. Its overexpression induced expression of AP-1 TFs and mediated inflammatory response, thus leading to decreased cellular viability of DS cells. Moreover, treatment with specific AP-1 inhibitor T-5224 improved DS-associated phenotypes in DSACs.
Conclusions
This study demonstrates that MX1-mediated AP-1 activation is partially responsible for cellular dysfunction of DS. T-5224 effectively ameliorated DS-associated phenotypes in DSACs, suggesting it as a potential treatment option for DS patients.
Supplementary Information
The online version contains supplementary material available at 10.1186/s40659-023-00474-x.
... The Section on Nuclear Organization and Dynamics has a wide range of expertise on its Editorial and Reviewer Boards and we have captured a snapshot of this in the set of papers highlighted in this Editor's Showcase. Zelenka et al. in previous studies of the T-cell CD4 + /CD8 + stage of development had noted that the transcription factor SATB1 had additional functional roles (Cai et al., 2003;Feng et al., 2022;Zelenka et al., 2022). They postulated that these roles might be supported by another splice variant of SATB1 and in "A novel SATB1 protein isoform with different biophysical properties" they identified this novel variant. ...
... Our group and others have recently identified the important role of the transcription factor and genome organizer SATB1 in DP thymocytes (Feng et al., 2022;Zelenka et al., 2022), where it is predominantly expressed (Zelenka and Spilianakis, 2020). SATB1 was primarily identified as a matrix associating region (MAR) binding protein (Dickinson et al., 1992;Alvarez et al., 2000). ...
... Loss of SATB1 leads to the developmental blockage of DP T cells and the ectopic activation of T cells. At the molecular level, SATB1 was shown to mediate the enhancer-promoter communication of immune related genes, that are essential for the proper commitment and development of T cells (Feng et al., 2022;Zelenka et al., 2022). Its association or dissociation with these genes is regulated by its phosphorylation and acetylation, respectively (Kumar et al., 2006). ...
Intra-thymic T cell development is coordinated by the regulatory actions of SATB1 genome organizer. In this report, we show that SATB1 is involved in the regulation of transcription and splicing, both of which displayed deregulation in Satb1 knockout murine thymocytes. More importantly, we characterized a novel SATB1 protein isoform and described its distinct biophysical behavior, implicating potential functional differences compared to the commonly studied isoform. SATB1 utilized its prion-like domains to transition through liquid-like states to aggregated structures. This behavior was dependent on protein concentration as well as phosphorylation and interaction with nuclear RNA. Notably, the long SATB1 isoform was more prone to aggregate following phase separation. Thus, the tight regulation of SATB1 isoforms expression levels alongside with protein post-translational modifications, are imperative for SATB1’s mode of action in T cell development. Our data indicate that deregulation of these processes may also be linked to disorders such as cancer.
... It is then reasonable to suppose that the ASE region is not active in the B-cell lineage, which could potentially explain normal Rag gene transcription in SATB1-deficient B-cell precursors. Given that SATB1 acts as a chromatin loop organizer in T cells [5,34,[52][53][54], we suspected a potential effect of its deletion on IgH V region accessibility in developing B cells. To assess this point, we examined VDJ recombination diversity by repertoire sequencing experiments on RNA samples (RepSeq) extracted from pre-B-cell-enriched bone marrow fractions. ...
... We show that SATB1 promotes Ig gene transcription in resting B cells, while in activated B cells, it acts as a repressor. In contrast to the T-cell lineage, where SATB1 is considered a major regulatory factor of the enhancer/superenhancer network [53,54], SATB1 deletion does not induce major disruptions in the B-cell transcriptome. Our invalidation model shows that only a reduced number of genes expressed during B differentiation are impacted by SATB1 deletion. ...
SATB1 (Special A-T rich Binding protein 1) is a cell type-specific factor that regulates the genetic network in developing T cells and neurons. In T cells, SATB1 is required for lineage commitment, VDJ recombination, development and maturation. Considering that its expression varies during B-cell differentiation, the involvement of SATB1 needs to be clarified in this lineage. Using a KO mouse model in which SATB1 was deleted from the pro-B-cell stage, we examined the consequences of SATB1 deletion in naive and activated B-cell subsets. Our model indicates first, unlike its essential function in T cells, that SATB1 is dispensable for B-cell development and the establishment of a broad IgH repertoire. Second, we show that SATB1 exhibits an ambivalent function in mature B cells, acting sequentially as a positive and negative regulator of Ig gene transcription in naive and activated cells, respectively. Third, our study indicates that the negative regulatory function of SATB1 in B cells extends to the germinal center response, in which this factor limits somatic hypermutation of Ig genes.
... For example, SATB1, a chromatin assembly protein and tissue-specific TF, is associated with T-cell development (128). Conditional depletion of SATB1 results in an autoimmune-like phenotype in mice because the obstructed promoter-enhancer loops in Satb1 cKO T cells result in downregulated expression of genes encoding for master regulators (such as Bcl6, Ets2, and Cd8b) and T-cell receptor locus (129,130). ...
Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin. Chromatin folding can be studied using chromosome conformation capture (3C) technology and 3C-based derivative sequencing technologies, including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), and high-throughput chromosome conformation capture (Hi-C), which allow scientists to capture 3D conformations from a single site to the entire genome. A comprehensive analysis of the relationships between various regulatory components and gene function also requires the integration of multi-omics data such as genomics, transcriptomics, and epigenomics. 3D genome folding is involved in immune cell differentiation, activation, and dysfunction and participates in a wide range of diseases, including autoimmune diseases. We describe hierarchical 3D chromatin organization in this review and conclude with characteristics of C-techniques and multi-omics applications of the 3D genome. In addition, we describe the relationship between 3D genome structure and the differentiation and maturation of immune cells and address how changes in chromosome folding contribute to autoimmune diseases.
Aging leads to an accumulation of cellular mutations and damage, increasing the risk of senescence, apoptosis, and malignant transformation. Cellular senescence, which is pivotal in aging, acts as both a guard against cellular transformation and as a check against cancer progression. It is marked by stable cell cycle arrest, widespread macromolecular changes, a pro‐inflammatory profile, and altered gene expression. However, it remains to be determined whether these differing subsets of senescent cells result from unique intrinsic programs or are influenced by their environmental contexts. Multiple transcription regulators and chromatin modifiers contribute to these alterations. Special AT‐rich sequence‐binding protein 1 (SATB1) stands out as a crucial regulator in this process, orchestrating gene expression by structuring chromatin into loop domains and anchoring DNA elements. This review provides an overview of cellular senescence and delves into the role of SATB1 in senescence‐related diseases. It highlights SATB1's potential in developing antiaging and anticancer strategies, potentially contributing to improved quality of life and addressing aging‐related diseases.
The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition and significance of the three-dimensional chromatin structure, summarize the technologies available for studying it, and describe the research progress on the chromatin spatial structure of dendritic cells, macrophages, T cells, B cells, and neutrophils.
Recombination activating gene (RAG) expression increases as thymocytes transition from the CD4 ⁻ CD8 ⁻ double-negative (DN) to the CD4 ⁺ CD8 ⁺ double-positive (DP) stage, but the physiological importance and mechanism of transcriptional up-regulation are unknown. Here, we show that a DP-specific component of the recombination activating genes antisilencer (DPASE) provokes elevated RAG expression in DP thymocytes. Mouse DP thymocytes lacking the DPASE display RAG expression equivalent to that in DN thymocytes, but this supports only a partial Tcra repertoire due to inefficient secondary Vα-Jα rearrangement. These data indicate that RAG up-regulation is required for a replete Tcra repertoire and that RAG expression is fine-tuned during lymphocyte development to meet the requirements of distinct antigen receptor loci. We further show that transcription factor RORγt directs RAG up-regulation in DP thymocytes by binding to the DPASE and that RORγt influences the Tcra repertoire by binding to the Tcra enhancer. These data, together with prior work showing RORγt to control Tcra rearrangement by regulating DP thymocyte proliferation and survival, reveal RORγt to orchestrate multiple pathways that support formation of the Tcra repertoire.
