Publications

Complete list of our publications

2025
Review Article
Ilik, I. A.; Yang, X.; Zhang, Z. Z.; Aktas, T.: Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease. Nature Reviews Molecular Cell Biology (2025)
Journal Article
Zhang, Y.; Stöppelkamp, I.; Fernandez-Pernas, P.; Allram, M.; Charman, M.; Magalhães, A. P.; Piedavent-Salomon, M.; Sommer, G.; Sung, Y.-C.; Meyer, K. et al.; Grams, N.; Halko, E.; Dongre, S.; Meierhofer, D.; Malszycki, M.; Ilik, I. A.; Aktas, T.; Kraushar, M. L.; Vastenhouw, N.; Weitzman, M. D.; Grebien, F.; Niskanen, H.; Hnisz, D.: Probing condensate microenvironments with a micropeptide killswitch. Nature (2025)
Journal Article
Martina, L.; Malszycki, M.; Aktas, T.: Distinct states of Nuclear Speckles emerge as new predictors of cancer prognosis. Cancer Research 85 (8), pp. 1352 - 1353 (2025)
2024
Journal Article
Stötzel, M.; Cheng, C.-Y.; Ilik, I. A.; Sampath Kumar, A.; Akbari-Omgba, P.; van der Weijden, V. A.; Zhang, Y.; Vingron, M.; Meissner, A.; Aktas, T. et al.; Kretzmer, H.; Bulut-Karslioglu, A.: TET activity safeguards pluripotency throughout embryonic dormancy. Nature Structural & Molecular Biology 31 (10), pp. 1625 - 1639 (2024)
Journal Article
Kellner, M.; Hörmann, J.; Fackler, S.; Yuanyu, H.; Tielin, Z.; Lin, L.; Ilik, I.; Aktas, T.; Feederle, R.; Hauck, S. M. et al.; Gires, O.; Gärtner, K.; Lietao, L.; Zeidler, R.: The Nuclear Speckles Protein SRRM2 Is Exposed on the Surface of Cancer Cells. Cells 13 (18), Article 1563 (2024)
Journal Article
Lisowski, P.; Lickfett, S.; Rybak-Wolf, A.; Menacho, C.; Le, S.; Pentimalli, T. M.; Notopoulou, S.; Dykstra, W.; Oehler, D.; López-Calcerrada, S. et al.; Mlody, B.; Otto, M.; Wu, H.; Richter, Y.; Roth, P.; Anand, R.; Kulka, L. A. M.; Meierhofer, D.; Glazar, P.; Legnini, I.; Telugu, N. S.; Hahn, T.; Neuendorf, N.; Miller, D. C.; Böddrich, A.; Polzin, A.; Mayatepek, E.; Diecke, S.; Olzscha, H.; Kirstein, J.; Ugalde, C.; Petrakis, S.; Cambridge, S.; Rajewsky, N.; Kühn, R.; Wanker, E. E.; Priller, J.; Metzger, J. J.; Prigione, A.: Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure. Nature Communications 15 (1), Article 7027 (2024)
Journal Article
Ilik, I. A.; Glažar, P.; Tse, K.; Brändl, B.; Meierhofer, D.; Müller, F.-J.; Smith, Z. D.; Aktas, T.: Autonomous transposons tune their sequences to ensure somatic suppression. Nature 626 (8001), pp. 1116 - 1124 (2024)
2023
Journal Article
Weigert, R.; Hetzel, S.; Bailly, N.; Haggerty, C.; Ilik, I. A.; Kwong Yung, P. Y.; Navarro, C.; Bolondi, A.; Sampath Kumar, A.; Anania, C. et al.; Brändl, B.; Meierhofer, D.; Lupiáñez, D. G.; Müller, F.-J.; Aktas, T.; Elsässer, S. J.; Kretzmer, H.; Smith, Z. D.; Meissner, A.: Dynamic antagonism between key repressive pathways maintains the placental epigenome. Nature Cell Biology 25 (4), pp. 579 - 591 (2023)
2022
Review Article
Ilik, I. A.; Aktas, T.: Nuclear speckles: dynamic hubs of gene expression regulation. The FEBS Journal 289 (22), pp. 7234 - 7245 (2022)
Journal Article
Bergfort, A.; Hilal, T.; Kuropka, B.; Ilik, I. A.; Weber, G.; Aktas, T.; Freund, C.; Wahl, M. C.: The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling. Nucleic Acids Research (London) 50 (5), pp. 2938 - 2958 (2022)
Journal Article
Aktas, T.: Transposons: catch them if you can. Nature Reviews Molecular Cell Biology 23 (5), 306 (2022)
Journal Article
Bergfort, A.; Preußner, M.; Kuropka, B.; Ilik, I. A.; Hilal, T.; Weber, G.; Freund, C.; Aktas, T.; Heyd, F.; Wahl, M. C.: A multi-factor trafficking site on the spliceosome remodeling enzyme BRR2 recruits C9ORF78 to regulate alternative splicing. Nature Communications 13 (1), Article 1132 (2022)
2020
Journal Article
Ilik, I. A.; Malszycki, M.; Lübke, A. K.; Schade, C.; Meierhofer, D.; Aktas, T.: SON and SRRM2 are essential for nuclear speckle formation. eLife 9, Article e60579 (2020)
Journal Article
Ilik, I. A.; Aktas, T.; Maticzka, D.; Backofen, R.; Akhtar, A.: FLASH: ultra-fast protocol to identify RNA-protein interactions in cells. Nucelic Acids Research 48 (3), Article e15 (2020)

Before 2019

Basilicata M.F., Bruel A.* , Semplicio G.*, Valsecchi-Keller C.*, Aktas T.* Duffourd Y., Rumpf T., Morton J., Gilissen C., El Chehadeh-Djebbar S., van der Burgt I., Pfundt R., Brunner H., Cho M., Vanakker O., Menten B., Vergult S., Lindstrom K., Reis A., Johnson D., Fryer A., McKay V., The DDD study , Fisher R., Thauvin-Robinet C., Faivre L., Kalscheuer V., Thevenon J., Akhtar A.; De novo mutations of MSL3 cause a novel X-linked syndrome marked by impaired histone H4 lysine 16 acetylation, Nature Genetics 2018
*equal contribution

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Maticzka D.*, Ilik I.A.*, Aktas T.*, Backofen R., Akhtar A.; uvCLAP: a fast, non-radioactive method to identify in vivo targets of RNA-binding proteins Nature Communication 2018
*equal contribution

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Aktas T.*; Ilik I.A.*; Maticzka D.; Bhardwaj V.; Rodrigues C.P.; Manke T.; Backofen R.; Akhtar A. DHX9 suppresses RNA processing defects originating from the Alu invasion of human genome. Nature 2017
* equal contribution

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Symmons O.; Pan L.; Remeseiro S.; Aktas T.; Klein F.; Huber W.; Spitz F. The Shh topological domain facilitates the action of remote enhancers by reducing the effects of genomic distances. Developmental Cell 2016

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Chelmicki T.; Dündar F.; Turley M.J.*; Khanam T.*; Aktas T.*; Ramirez F.; Gendrel A.V.; Wright P.R.; Videm P.; Manke T.; Backofen R.; Akhtar A. MOF-associated complexes ensure stem cell identity and Xist repression. eLife 2014
* equal contribution

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Rowe H.M.; Friedli M.; Offner S.; Verp S.; Mesnard D.; Marquis J.; Aktas T. Trono D.; De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET, Development 2013

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Marinic M.; Aktas T.; Ruf S.; Spitz F.; An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. Developmental Cell 2013

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Rowe H.M.; Jakobsson J.; Mesnard D.; Rougemont J.; Reynard S.; Aktas T.; Maillard P.V.; Layard-Liesching H.; Verp S.; Marquis J.; Spitz F.; Constam D.B.,Trono D. KAP1 controls endogenous retroviruses in embryonic stem cells. Nature 2010

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