Associate Professor

2003, University of Crete

Scientific interest: 
Biochemistry, Molecular Immunology, Molecular Biology, Epigenetics, Chromatin structure and function, cell nuclear organization
Office phone number: 
+30 2810 391163
Lab phone number: 
+30 2810 391173
+30 2810 391101


Full CV

PDF icon cv_spilianakis_en_2020.pdf384.21 KB


PhD in Molecular Biology and Biomedicine, Department of Biology - University of Crete, Greece. Laboratory of Prof. Joseph Papamatheakis.
MSc in Molecular Biology, Department of Biology - University of Crete, Greece. Laboratory of Prof. Joseph Papamatheakis.
Bachelor in Biology, Department of Biology - University of Crete, Greece.


Current Positions
11/2016-present: Associate Professor of Molecular Biology & Epigenetics
09/2009-10/2016: Assistant Professor of Biochemistry, Department of Biology - University of Crete, Greece (Tenured 03/2013)
09/2009-present: Principal Investigator, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Greece
Previous Positions
2008-2009: Research Assistant Professor, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Greece
2003-2007: Postdoctoral Fellow, Section of Immunobiology, Yale University School of Medicine and   Howard Hughes Medical Institute, New Haven, USA. Laboratory of Prof. Richard A. Flavell.

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

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: