Charalampos Spilianakis

• MSc, PhD
• Professor at University of Crete & IMBB-FORTH

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 i...

Over the past decades, it has become increasingly clear that higher order chromatin folding and organization within the nucleus is involved in the regulation of genome activity and serves as an additional epigenetic mechanism that modulates cellular functions and gene expression programs in diverse biological processes. In particular, dynamic allel...

Mechanisms of tissue-specific gene expression regulation via 3D genome organization are poorly understood. Here we uncover the regulatory chromatin network of developing T cells and identify SATB1, a tissue-specific genome organizer, enriched at the anchors of promoter-enhancer loops. We have generated a T-cell specific Satb1 conditional knockout m...

In the heart of innate and adaptive immunity lies the proper spatiotemporal development of several immune cell lineages. Multiple studies have highlighted the necessity of epigenetic and transcriptional regulation in cell lineage specification. This mode of regulation is mediated by transcription factors and chromatin remodelers, controlling develo...

Intracellular space is demarcated into functional membraneless organelles and nuclear bodies via the process of phase separation. Phase transitions are involved in many functions linked to such bodies as well as in gene expression regulation and other cellular processes. In this work we describe how the genome organizer SATB1 utilizes its prion-lik...

The functional implications of the three-dimensional genome organization are becoming increasingly recognized. The Hi-C and HiChIP research approaches belong among the most popular choices for probing long-range chromatin interactions. A few methodical protocols have been published so far, yet their reproducibility and efficiency may vary. Most imp...

Mechanisms of tissue-specific gene expression regulation via spatial coordination of gene promoters and distal regulatory elements are still poorly understood. We investigated the 3D genome organization of developing murine T cells and identified SATB1, a tissue-specific genome organizer, enriched at the anchors of promoter-enhancer chromatin loops...

The regulatory circuits that define developmental decisions of thymocytes are still incompletely resolved. SATB1 protein is predominantly expressed at the CD4⁺CD8⁺cell stage exerting its broad transcription regulation potential with both activatory and repressive roles. A series of post-translational modifications and the presence of potential SATB...

microRNAs are of vital importance for the regulation of the adaptive and innate immune responses, modulating gene expression at the post transcriptional level. Although there is cumulative information regarding the steady state mature microRNA levels and their respective targets, little is known about the effect of the three-dimensional chromatin a...

The infiltration and subsequent in situ subtype specification of monocytes to effector/inflammatory and repair macrophages is indispensable for tissue repair upon acute sterile injury. However, the chromatin-level mediators and regulatory events controlling this highly dynamic macrophage phenotype switch are not known. In this study, we used a muri...

Skeletal muscle regeneration following injury is a complex process that involves inflammatory components. Macrophage infiltration to damaged tissues upon injuries and their in‐situ differentiation into effector/inflammatory and repair macrophages is indispensable for necrotic debris clearance, and for coordination of tissue repair. Regulatory event...

It is becoming increasingly appreciated that the non-coding genome may have a great impact on the regulation of chromatin structure and gene expression. The innate immune response can be mediated upon lipopolysaccharide stimulation of macrophages which leads to immediate transcriptional activation of early responsive genes including tumor necrosis...

Endotoxin tolerance occurs to protect the organism from hyperactivation of innate immune responses, primarily mediated by macrophages. Regulation of endotoxin tolerance occurs at multiple levels of cell responses and requires significant changes in gene expression. In the process of macrophage activation, induced expression of microRNA (miR)-155 an...

Significance Our study examines an important aspect of adaptive immunity, namely, the process of effector T-cell activation, which leads to the enhanced expression of lineage-specific cytokine genes upon T-cell receptor (TCR) re-engagement. We found that the TNF locus undergoes TCR-induced homologous allelic pairing, which correlates with biallelic...

Significance In diploid organisms, trans-allelic interactions control gene expression, providing a tight spatial and temporal level of transcription regulation. Although homologous trans-allelic interactions are quite abundant in various organisms such as Drosophila, plants, and fungi, they have not been widely reported in mammals. This article dem...

The T helper type 2 (Th2) cytokine genes Il4, Il5, and Il13 are contained within a 140-kb region of mouse chromosome 11 and their expression is controlled by a locus control region (LCR) embedded within this locus. The LCR is composed of a number of DNase I-hypersensitive sites (HSs), which are believed to encompass the regulatory core of the LCR....

Current research on the cytokine-mediated signalling towards the polarization and differentiation of a T-helper cell lineage lacks mechanistic insights on the transcriptional regulation of cytokine receptor genes. Here, we propose a new mechanism for the transcriptional regulation of the interferon gamma receptor 1 gene via long-range intrachromoso...

Nuclear architecture and chromatin reorganization have recently been shown to orchestrate gene expression and act as key players in developmental pathways. To investigate how regulatory elements in the mouse CD8 gene locus are arranged in space and in relation to each other, three-dimensional fluorescence in situ hybridization and chromosome confor...

The nucleus is an ordered three-dimensional entity, and organization of the genome within the nuclear space might have implications for orchestrating gene expression. Recent technological developments have revealed that chromatin is folded into loops bringing distal regulatory elements into intimate contact with the genes that they regulate. Such i...

Differentiation of T(H)1 and T(H)2 effector cells proceeds through several phases: First, naïve CD4(+) precursor cells are instructed to differentiate as appropriate to optimally fight the infectious threat encountered. This process is governed by the IL12 and IL4 cytokines, as well as by signaling through the Notch receptor. In response to these s...

The rates of activation and unitary properties of Na+-activated K+ (K(Na)) currents have been found to vary substantially in different types of neurones. One class of K(Na) channels is encoded by the Slack gene. We have now determined that alternative RNA splicing gives rise to at least five different transcripts for Slack, which produce Slack chan...

Cilia are present on nearly all cell types in mammals and perform remarkably diverse functions. However, the mechanisms underlying ciliogenesis are unclear. Here, we cloned a previously uncharacterized highly conserved gene, stumpy, located on mouse chromosome 7. Stumpy was ubiquitously expressed, and conditional loss in mouse resulted in complete...

Intensive characterization of the locus encoding interferon- provides new insight into how proper gene expression is achieved in polarizing T cells. NOTE: In the version of this News & Views initially published, the figure credit is missing. This figure should be credited to Ann Thomson. The error has been corrected in the HTML and PDF versions of...

Cytokine loci undergo changes in chromatin structure when naive CD4(+) T cells differentiate into Th1 or Th2 cells and have also been examined for regulatory sequences underlying such changes and their functional correlates. Studies have shown that distal regulatory elements control the Ifng and Th2 cytokine loci and are primary targets for tissue-...

Genes present on different chromosomes can be coordinately expressed through a transcription regulatory factor that brings them together in a region of active transcription in the nucleus.

The deacetylase inhibitor Trichostatin A (TSA) induces the transcription of the Major Histocompatibility Class II (MHC II) DRA gene in a way independent of the master coactivator CIITA. To analyze the molecular mechanisms by which this epigenetic regulator stimulates MHC II expression, we used chromatin immunoprecipitation (ChIP) assays to monitor...

The immune system is influenced by environmental factors such as hormones and nutrients. Previous studies have suggested that vitamins A and D influence the process of naive T helper (Th) cell differentiation into Th1 or Th2 cells. Vitamins A and D signal through the retinoid X receptor (RXR), which partners with either the retinoic acid receptor o...

The T-helper-cell 1 and 2 (T(H)1 and T(H)2) pathways, defined by cytokines interferon-gamma (IFN-gamma) and interleukin-4 (IL-4), respectively, comprise two alternative CD4+ T-cell fates, with functional consequences for the host immune system. These cytokine genes are encoded on different chromosomes. The recently described T(H)2 locus control reg...

Several regulatory regions are important for the expression of genes encoding T helper type 2 (T(H)2) cytokines, including T(H)2-specific DNase I hypersensitivity sites in the T(H)2 cytokine locus control region. Among these sites, Rad50 hypersensitive site 7 (RHS7) shows rapid T(H)2-specific demethylation after antigenic stimulation. To investigat...

The T helper type 2 (T(H)2) locus control region is important in the regulation of the genes encoding the cytokines interleukins 4, 5 and 13. Using the chromosome conformation capture technique, we found that in T cells, natural killer cells, B cells and fibroblasts, the promoters for the genes encoding T(H)2 cytokines are located in close spatial...

Tightly regulated expression of major histocompatibility complex (MHC) class II genes is critical for the immune system. A conserved regulatory module consisting of four cis-acting elements, the W, X, X2 and Y boxes, controls transcription of MHC class II genes. The X, X2, and Y boxes are bound, respectively, by RFX, CREB, and NF-Y to form a MHC cl...

We show here that steroid receptor coactivator 1 (SRC-1) is a coactivator of MHC class II genes that stimulates their interferon gamma (IFNgamma) and class II transactivator (CIITA)-mediated expression. SRC-1 interacts physically with the N-terminal activation domain of CIITA through two regions: one central [extending from amino acids (aa) 360-839...

We describe the temporal order of recruitment of transcription factors, cofactors and basal transcriptional components and the consequent biochemical events that lead to activation of the major histocompatibility class II (MHCII) DRA gene transcription by IFN-gamma. We found that the gene is 'poised' for activation since both the activators and a f...

Class II transactivator (CIITA) is the master regulator of major histocompatibility complex class II genes that regulates both B lymphocyte-specific and interferon gamma-inducible expression. Here we identify protein regions and examine mechanisms that determine the intracellular distribution of CIITA. We show that two separate regions of CIITA med...

The class II transactivator (CIITA), the master regulator of the tissue-specific and interferon gamma-inducible expression of major histocompatibility complex class II genes, synergizes with the histone acetylase coactivator CBP to activate gene transcription. Here we demonstrate that in addition to CBP, PCAF binds to CIITA both in vivo and in vitr...

The class II transactivator (CIITA) is a key regulatory factor that controls expression of the major histocompatibility complex (MHC) class II genes that are essential components for antigen presentation and thus regulation of the immune response. We show here that the adenovirus E1A protein interferes with the action of CIITA and inhibits both B-c...

During my PhD studies I worked on the mechanisms regulating the expression of Major Histocompatibility Complex class II genes. MHC class II antigens are dimeric membrane glycoproteins that recognize and present antigenic peptides to T-lymphocytes. Their expression is highly regulated in transcriptional level and their stimulation needs the existenc...

The factor CIITA (class II transactivator) is an essential transcriptional activator of the MHC class II genes. Here, we present the results of a primary work involving the mechanisms of its action in two directions: the construction of negative mutants and the investigation of its interactions with transcriptional coactivators. We found that mutan...