Charalampos G. Spilianakis

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Charalampos G. Spilianakis

IMBB Group Leader (Associate Professor, University of Crete)

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).

Selected Publications
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Zelenka Τ, Klonizakis Α, Tsoukatou D, Papamatheakis D-A, Franzenburg S, Tzerpos P, Tzonevrakis I-R, Papadogkonas G, Kapsetaki M, Nikolaou C, Plewczynski D, Spilianakis C. (2022) The 3D enhancer network of the developing T cell genome is shaped by SATB1. Nat. Commun. 13:6954.

Zelenka T, Spilianakis C. (2021) HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells. Methods Protoc. 4:49.

Salataj E, Stathopoulou C, Hafþórsson RA, Nikolaou C, Spilianakis CG. (2019) Developmental Conservation of microRNA Gene Localization at the Nuclear Periphery. PLoS One. 14:e0223759.

Stathopoulou C, Kapsetaki M, Stratigi K, Spilianakis C. (2017) Long non-coding RNA SeT and miR-155 regulate the Tnfα gene allelic expression profile. PLoS One. 12:e0184788.

Stratigi K, Kapsetaki M, Aivaliotis M, Town T, Flavell RA, Spilianakis CG. (2015) Spatial proximity of homologous alleles and long noncoding RNAs regulate a switch in allelic gene expression. Proc Natl Acad Sci U S A. 112:E1577-86.

All Publications

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

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. doi: https://doi.org/10.1371/journal. 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: https://doi.org/10.4049/jimmunol.1900553

Long non-coding RNA SeT and miR-155 regulate the Tnfα gene allelic expression profile.
Stathopoulou C, Kapsetaki M, Stratigi K, Spilianakis C.
PLoS One 2017; 14;12(9):e0184788. doi: https://doi.org/10.1371/journal.pone.0184788

Coordinated Regulation of miR-155 and miR-146a Genes during Induction of Endotoxin Tolerance in Macrophages.
Doxaki C., Kampranis S.C., Eliopoulos A.G., Spilianakis C., Tsatsanis C.
J Immunol. 2015; 195(12):5750-5761. doi: https://doi.org/10.4049/jimmunol.1500615

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: https://doi.org/10.1073/pnas.1502182112

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: https://doi.org/10.1073/pnas.1502461112

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: https://doi.org/10.1073/pnas.1304720110

Long-range genomic interactions epigenetically regulate the expression of a cytokine receptor.
Deligianni C., Spilianakis C.G.
EMBO Rep. 2012; 13: 819-826 doi: https://doi.org/10.1038/embor.2012.112

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