Associate Professor


                                           PHD:           2003, University of Crete

Full CV


Scientific interests

Regulation of gene expression can be accomplished “in cis ” by several regulatory elements exerting their action on physically linked genes on the same chromosome. A “ trans” regulation aspect of gene expression has also recently been brought to light by studies of the interactions and function of regulatory elements located on a chromosome different from the one that carries the regulated gene. Such regulatory elements include enhancers or locus control regions that are shown to be able to regulate the expression not only of cis linked genes but also of genes located on different chromosomes, in trans.

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 chromosomal interactions in cell populations of the innate and adaptive immune system. We aim to provide substantial information on how the genome is shaped as a whole and how the nuclear structure patterns in the context of distinct subnuclear microenvironments regulate global gene expression (3D epigenetics).

Recent publications

    • Single-cell detection of primary transcripts, their genomic loci and nuclear factors by immuno-3D RNA/DNA FISH in T cells. Eralda Salataj, Charalampos Spilianakis, Julie Chaumeil. Front. Immunol. 2023, 14:2023 |
    • 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells. George Papadogkonas , Dionysios-Alexandros Papamatheakis and Charalampos Spilianakis. Front. Immunol. 2022, 13:921375. doi: 10.3389/fimmu.2022.921375
    • The 3D enhancer network of the developing T cell genome is shaped by SATB1. Tomas Zelenka, Antonios Klonizakis, Despina Tsoukatou, Dionysios-AlexandrosPapamatheakis, Sören Franzenburg, Petros Tzerpos, , Ioannis-Rafail Tzonevrakis, George Papadogkonas, Manouela Kapsetaki, ChristoforosNikolaou, Dariusz Plewczynski and Charalampos Spilianakis. Nat. Communications 2022, 13(1): 6954  doi:  10.1038/s41467-022-34345-y
    • HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells. Zelenka T, Spilianakis C. Methods Protoc. 2021; 4(3):49. doi: 
    • SATB1-mediated chromatin landscape in T cells. Zelenka T & Spilianakis C.G. Nucleus 2020; 11: 117-131; doi:
    • Developmental Conservation of microRNA Gene Localization at the Nuclear Periphery.  Salataj E, Stathopoulou  C, Hafþórsson  RA, Nikolaou  C, Spilianakis  C.G. PLoS One 2019; 14(11):e0223759. pone.0223759 
    • The BACH1-HMOX1 Regulatory Axis Is Indispensable for Proper Macrophage Subtype Specification and Skeletal Muscle Regeneration. Patsalos A, Tzerpos P, Halasz L, Nagy G, Pap A, Giannakis N, Lyroni K, Koliaraki V, Pintye E, Dezso B, Kollias G, Spilianakis CG, Nagy L. J Immunol. 2019; 203(6):1532-1547 . doi:
    • Myosin VI regulates gene pairing and transcriptional pause release in T cells. Zorca CE, Kim LK, Kim YJ, Krause MR, Zenklusen D, Spilianakis CG, Flavell RA. Proc Natl Acad Sci USA 2015; 112(13):E1587-1593 doi: 10.1073/pnas.1502461112
    • Spatial proximity of homologous alleles and long noncoding RNAs regulate a switch in allelic gene expression. Stratigi K., Kapsetaki M., Aivaliotis M., Town T., Flavell RA., Spilianakis CG. Proc Natl Acad Sci USA 2015; 112(13):E1577-1586 doi:
    • Hypersensitive site 6 of the TH2 locus control region is essential for TH2 cytokine expression. Williams A., Lee G.R., Spilianakis C.G., Hwang S.S., Eisenbarth S.C., Flavell R.A. Proc Natl Acad Sci USA 2013; 110(17): 6955-6960 doi:
    , E.D. Ozkan, M. Fowler, F.J. White, C. Philips, and D.C. Cooper (2009) Dopamine modulates an mGluR5-induced depolarization underlying prefrontal persistent activity, Nature Neuroscience, 2009, 12(2): 190-199