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. 
  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
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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: 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: 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: 

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

CD8 locus nuclear dynamics during thymocyte development. 
Ktistaki E., Garefalaki A., Williams A., Andrews S.R., Bell D.M., Foster K.E., Spilianakis C.G., Flavell R.A., Kosyakova N., Trifonov V., Liehr T., Kioussis D
J Immunol. 2010; 184: 5686-5695 doi: 

Interchromosomal association and gene regulation in trans. 
Williams A., Spilianakis C.G., Flavell R.A. 
Trends Genet. 2020; 26: 188-197 doi: 10.1016/j.tig.2010.01.007

How are T(H)1 and T(H)2 effector cells made? 
Amsen D., Spilianakis C.G., Flavell R.A.
Curr Opin Immunol. 2009; 21: 153-160 doi: 10.1016/j.coi.2009.03.010

Amino-termini isoforms of the Slack K+ channel, regulated by alternative promoters, differentially modulate rhythmic firing and adaptation. 
Brown M.R., Kronengold J., Gazula V.R., Spilianakis C.G., Flavell R.A., von Hehn C.A., Bhattacharjee A., Kaczmarek L.K.  
J Physiol. 2008; 586: 5161-5179 doi: 10.1113/jphysiol.2008.160861

The stumpy gene is required for mammalian ciliogenesis. 
Town T., Breunig J.J., Sarkisian M.R., Spilianakis C.G., Ayoub A.E., Liu X., Ferrandino A.F., Gallagher A.R., Li M.O., Rakic P., Flavell RA. 
Proc Natl Acad Sci USA 2008; 105: 2853-2858 doi: 10.1073/pnas.0712385105

Epigenetic regulation of Ifnγ expression. 
Spilianakis C.G., Flavell R.A.
Nat Immunol. 2007; 8: 681-683 doi: https://doi.org/10.1038/ni0707-681

Managing associations between different chromosomes. 
Spilianakis C.G., Flavell R.A. 
Science 2006; 312: 207-208 doi: 10.1126/science.1126689

T helper cell differentiation: Regulation by cis-elements and epigenetics. 
Lee G.R., Kim S.T., Spilianakis C.G., Fields P.E., Flavell R.A. 
Immunity 2006; 4: 369-379 doi: https://doi.org/10.1016/j.immuni.2006.03.007

Coordinated changes of histone modifications and HDAC mobilization regulate the induction of MHC class II genes by Trichostatin A. 
Gialitakis M., Kretsovali A., Spilianakis C.G., Kravariti, L., Mages J., Hoffmann R., Hatzopoulos A.K., Papamatheakis J. 
Nucleic Acids Res. 2006; 34: 765-772 doi: https://doi.org/10.1093/nar/gkj462

Twisting the Th1/Th2 immune response via the retinoid X receptor: Lessons from a genetic approach. 
Spilianakis C.G., Lee G.R., Flavell R.A. 
Eur J Immunol. 2005; 35: 3400-3404 doi: https://doi.org/10.1002/eji.200535588

Interchromosomal associations between alternatively expressed loci. 
Spilianakis C.G., Lalioti M., Town T., Lee G.R., Flavell R.A. 
Nature 2005; 435: 637-645 doi: 10.1038/nature03574

Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions. 
Lee G.R., Spilianakis C.G., Flavell R.A. 
Nat Immunol. 2005; 6: 42-48 doi:  https://doi.org/10.1038/ni1148

Long-range intrachromosomal interactions in the T helper type-2 cytokine locus. 
Spilianakis C.G., Flavell R.A. 
Nat Immunol. 2004; 5: 1017-1027 doi:  https://doi.org/10.1038/ni1115

The S box of major histocompatibility complex class II promoters is a key determinant for recruitment of the transcriptional co-activator CIITA. 
Muhlethaler-Mottet A., Krawczyk M., Masternak K., Spilianakis C.G., Kretsovali A., Papamatheakis J., Reith W.
J Biol Chem. 2004; 279: 40529-40535 doi: https://doi.org/10.1074/jbc.M406585200

Steroid receptor coactivator 1 links the steroid and interferon gamma response pathways. 
Tzortzakaki E., Spilianakis C.G., Zika E., Kretsovali A., Papamatheakis J. 
Mol Endocrinol. 2003; 12: 2509-2518 doi: https://doi.org/10.1210/me.2002-0439

CIITA regulates transcription onset viaSer5-phosphorylation of RNA Pol II. 
Spilianakis C.G.*, Kretsovali A.*, Agalioti T.*, Makatounakis T., Thanos D., Papamatheakis J. 
EMBO J. 2003; 22: 5125-5136 doi:  https://doi.org/10.1093/emboj/cdg496

Self-association of class II transactivator correlates with its intracellular localization and transactivation. 
Spilianakis C.G., Kretsovali A., Dimakopoulos A., Makatounakis T., Papamatheakis J.
J Biol Chem. 2001; 276: 32191-32197 doi: https://doi.org/10.1074/jbc.M103164200

Acetylation by PCAF enhances CIITA nuclear accumulation and transactivation of major histocompatibility complex class II genes. 
Spilianakis C.G., Papamatheakis J., Kretsovali A. 
Mol Cell Biol. 2000; 22: 8489-8498 doi:  https://doi.org/10.1128/MCB.20.22.8489-8498.2000

Involvement of CREB binding protein in expression of major histocompatibility complex class II genes via interaction with the class II transactivator. 
Kretsovali A., Agalioti T., Spilianakis C.G., Tzortzakaki E., Merika M., Papamatheakis J. 
Mol Cell Biol. 1998; 18: 6777-6783 doi:   https://doi.org/10.1128/MCB.18.11.6777