Dror I, Chitiashvili T, Tan SYX, Cano CT, Sahakyan A, Markaki Y, Chronis C, Collier AJ, Deng W, Liang G, Sun Y, Afasizheva A, Miller J, Xiao W, Black DL, Ding F, Plath K. XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells. Cell. 2024 Jan 4;187(1):110-129.e31. doi:10.1016/j.cell.2023.11.033.

Markaki Y*, Gan Chong J, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Schöneberg J, Heard E, Guttman M, Chou T*, Plath K*. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell. 2021 Dec 9;184(25):6174-6192.e32. doi: 10.1016/j.cell.2021.10.022. *corresponding authors

Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, Thai J, Plath K, Guttman M. RNA promotes the formation of spatial compartments in the nucleus. Cell. 2021 Nov 11;184(23):5775-5790.e30. doi: 10.1016/j.cell.2021.10.014. 

Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Leon WRM, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Sabri S, Leonhardt H, Zheng S, Guttman M, Black DL, Plath K. A protein assembly mediates Xist localization and gene silencing. Nature. 2020 Oct;586(7830):E30. doi: 10.1038/s41586-020-2790-y. 

Cremer M, Schmid VJ, Kraus F, Markaki Y, Hellmann I, Maiser A, Leonhardt H, John S, Stamatoyannopoulos J, Cremer T. Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters. Epigenetics Chromatin. 2017 Aug 7;10(1):39. doi: 10.1186/s13072-017 0146-0. 

Demmerle J, Innocent C, North AJ, Ball G, Müller M, Miron E, Matsuda A, Dobbie IM, Markaki Y, Schermelleh L. Strategic and practical guidelines for successful structured illumination microscopy. Nat Protoc. 2017 May;12(5):988-1010. doi: 10.1038/nprot.2017.019. 

Kraus F, Miron E, Demmerle J, Chitiashvili T, Budco A, Alle Q, Matsuda A, Leonhardt H, Schermelleh L, Markaki Y. Quantitative 3D structured illumination microscopy of nuclear structures. Nat Protoc. 2017 May;12(5):1011-1028. doi: 10.1038/nprot.2017.020. 

Cremer T, Cremer M, Hübner B, Strickfaden H, Smeets D, Popken J, Sterr M, Markaki Y, Rippe K, Cremer C. The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments. FEBS Lett. 2015 Oct 7;589(20 Pt A):2931-43. doi: 10.1016/j.febslet.2015.05.037.

Smeets D, Markaki Y, Schmid VJ, Kraus F, Tattermusch A, Cerase A, Sterr M, Fiedler S, Demmerle J, Popken J, Leonhardt H, Brockdorff N, Cremer T, Schermelleh L, Cremer M. Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics Chromatin. 2014 Apr 28;7:8. doi: 10.1186/1756-8935-7-8. 

Anton T, Bultmann S, Leonhardt H*, Markaki Y*. Visualization of specific DNA sequences in living mouse embryonic stem cells with a programmable fluorescent CRISPR/Cas system. Nucleus. 2014 Mar-Apr;5(2):163-72. doi: 10.4161/nucl.28488. *corresponding authors

Markaki Y, Smeets D, Cremer M, Schermelleh L. Fluorescence in situ hybridization applications for super-resolution 3D structured illumination microscopy. Methods Mol Biol. 2013;950:43-64. doi: 10.1007/978-1-62703-137-0_4.

Neumann LC, Markaki Y, Mladenov E, Hoffmann D, Buiting K, Horsthemke B. The imprinted NPAP1/C15orf2 gene in the Prader-Willi syndrome region encodes a nuclear pore complex associated protein. Hum Mol Genet. 2012 Sep 15;21(18):4038-48. doi: 10.1093/hmg/dds228. 

Markaki Y, Smeets D, Fiedler S, Schmid VJ, Schermelleh L, Cremer T, Cremer M. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture. Bioessays. 2012 May;34(5):412-26. doi: 10.1002/bies.201100176. 

Markaki Y, Christogianni A, Politou AS, Georgatos SD. Phosphorylation of histone H3 at Thr3 is part of a combinatorial pattern that marks and configures mitotic chromatin. J Cell Sci. 2009 Aug 15;122(Pt 16):2809-19. doi: 10.1242/jcs.043810.