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)
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)
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
Link to the publication
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
Link to the publication
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
Link to the publication
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
Link to the publication
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
Link to the publication
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
Link to the publication
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
Link to the publication
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
Link to the publication