The main objective of our laboratory is to apply a combination of biocomputing, molecular, biochemical, imaging and genetic approaches in order to identify and characterize protein complexes that generate and/or maintain long range chromatin interactions in cell populations of the innate and adaptive immune system. We aim to provide substantial information on how the genome is shaped  and how the nuclear structure patterns in the context of distinct subnuclear microenvironments regulate gene expression.

(De)Regulation of high-order chromatin organization in T cells and the cause of autoimmunity

The adaptive immune response is fully dependent on the proper T cell development. Committed lymphoid progenitors in the thymus undergo a series of events including positive and negative selection, resulting in naïve T cells. The second pillar of the T cell function consists of the activation and differentiation processes of naive CD4+ precursor cells in response to cues provided by antigen presenting cells. The different CD4 T cell fates are determined via complex and cross-interactive networks consisted of cytokines and transcription factors. The co-expression of the latter affects the functional capabilities and the flexibility of the different CD4 T cell subsets.

Recently, the three-dimensional (3D) organization of chromatin has been recognized as a crucial regulator of gene expression. The factor CTCF has been proposed as a major player for establishing the 3D structure of genomes. However, the complex environment of developing T cells requires additional master regulators to operate the 3D interactome. The special AT-rich sequence binding protein 1 (SATB1) is a well-known genome organizer that has also been suggested to play this role. In the cell nucleus, SATB1 creates a cage-like protein structure providing a physical prop for DNA and also serving as a platform for other protein complexes. Its ability to create tetramers facilitates genome folding by creating DNA loops and such looping events may constitute one of the major mechanisms for gene expression regulation. The importance of SATB1 in thymocyte development has already been established and affects the proper function of the adaptive immune system.

SATB1 undergoes isoform-specific phase transitions in T cells
Tomas Zelenka, Petros Tzerpos, Giorgos Panagopoulos, Konstantinos Tsolis, Dionysios-Alexandros Papamatheakis, Vassilis M. Papadakis, David Stanek, Charalampos Spilianakis
bioRxiv 2021.08.11.455932; doi: https://doi.org/10.1101/2021.08.11.455932

The 3D enhancer network of the developing T cell genome is controlled by SATB1
Tomas Zelenka, Antonios Klonizakis, Despina Tsoukatou, Sören Franzenburg, Petros Tzerpos, Dionysios-AlexandrosPapamatheakis, Ioannis-Rafail Tzonevrakis, ChristoforosNikolaou, Dariusz Plewczynski, Charalampos Spilianakis
bioRxiv 2021.07.09.451769; doi: https://doi.org/10.1101/2021.07.09.451769

HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells.
Zelenka T, Spilianakis C.
Methods Protoc. 2021; 4(3):49. doi: https://doi.org/10.3390/mps4030049

SATB1-mediated chromatin landscape in T cells.
Zelenka T & Spilianakis C.G.
Nucleus 2020; 11: 117-131; doi: https://doi.org/10.1080/19491034.2020.1775037