Publications
Gene regulatory innovations from transposable elements in primate cerebellum development
Yamada, T., Sepp, M., Sarropoulos, I., Kaessmann, H.
Nature Communications, 2026 Link
PREPRINT: Conserved cerebellar rhombic lip compartmentalization and Eomes regulatory networks govern unipolar brush cell development
Akçay, V., Spänig, L.M., Vierdag, W.A., Joshi, P., Benites Gonçalves da Silva, P., Sanderson, A., Reinhardt, R., Sieber, L., Hofmann, N., Nolle, J., Schelb, F., Zuckermann, M., Kaessmann, H., Pfister, S.M., Sánchez-Danés, A., Sepp, M., Saka, S.K., Kutscher, L.M.
openRxiv, 2026 Link
PREPRINT: A multi-omics atlas of human hindbrain development
Joshi, P., Sepp, M., Sarropoulos, I., Trost, N., Okonechnikov, K., Yamada, T., Schneider, C., Schmidt, J., Perera, A.A., Wittmann, A., Blattner-Johnson, M., Jones, B., van Tilburg, C.M., Witt, O., Lisgo, S., Palkovits, M., Jones, D.T., Thongjuea, S., Kaessmann, H., Pfister, S.M., Kutscher, L.M.
openRxiv, 2026 Link
REVIEW: Evolutionary perspectives on the development of the mammalian cerebellum: From cellular diversity to gene regulatory programs
Yamada, T., Sarropoulos, I., Sepp, M.
Current Topics in Developmental Biology, 2026 Link
The evolution of gene regulation in mammalian cerebellum development
Sarropoulos, I., Sepp, M., Yamada, T., Schäfer, P.S.L., Trost, N., Schmidt, J., Schneider, C., Drummer, C., Mißbach, S., Taskiran, I.I., Hecker, N., Bravo González-Blas, C., Frömel, R., Joshi, P., Leushkin, E., Arnskötter, F., Leiss, K., Okonechnikov, K., Lisgo, S., Palkovits, M., Pääbo, S., Cardoso-Moreira, M., Kutscher, L.M., Behr, R., Pfister, S.M., Aerts, S., Kaessmann, H.
Science, 2026 Link
PREPRINT: The evolution of gene regulatory programs controlling gonadal development in primates
Trost, N., Fallahshahroudi, A., Sarropoulos, I., Schneider, C., Schmidt, J., Mbengue, N., Wolff, E., Drummer, C., Frömel, R., Lisgo, S., Murat, F., Sepp, M., Cardoso-Moreira, M., Behr, R., Kaessmann, H.
openRxiv, 2025 Link
Conference Report: Cerebellar Development and Disease at Single-Cell Resolution
Kutscher, L.M., Aprile, D., Bayin, N.S., Becker, E.B.E., Cerrato, V., Turrini, G., Coolen, M., Cantagrel, V., Durand, B.C., Evans II, M.K., Haldipur, P., Millen, K.J., Yeung, J., Goldowitz, D., Hatten, M.E., Joyner, A.L., Kebschull, J.M., Li, J.Y.H., Quadrato, G., Schmidt, C., Sepp, M., Silva, T.P., Testa, G., Tiberi, L., Mayer, S.
The Cerebellum, 2025 Link
Oncogene aberrations drive medulloblastoma progression, not initiation
Okonechnikov, K., Joshi, P., Körber, V., Rademacher, A., Bortolomeazzi, M., Mallm, J., Vaillant, J., da Silva, P.B.G., Statz, B., Sepp, M., Sarropoulos, I., Yamada, T., Wittmann, A., Schramm, K., Blattner-Johnson, M., Fiesel, P., Jones, B., Jäger, N., Milde, T., Pajtler, K.W., van Tilburg, C.M., Witt, O., Bochennek, K., Weber, K.J., Nonnenmacher, L., Reimann, C., Ghasemi, D.R., Schüller, U., Mynarek, M., Rutkowski, S., Jones, D.T.W., Korshunov, A., Rippe, K., Westermann, F., Thongjuea, S., Höfer, T., Kaessmann, H., Kutscher, L.M., Pfister, S.M.
Nature, 2025 Link
Developmental origins and evolution of pallial cell types and structures in birds
Zaremba, B., Fallahshahroudi, A., Schneider, C., Schmidt, J., Sarropoulos, I., Leushkin, E., Berki, B., Van Poucke, E., Jensen, P., Senovilla-Ganzo, R., Hervas-Sotomayor, F., Trost, N., Lamanna, F., Sepp, M., García-Moreno, F., Kaessmann, H.
Science, 2025 Link
Loss of Elp1 in cerebellar granule cell progenitors models ataxia phenotype of Familial Dysautonomia
Arnskötter, F., da Silva, P.B.G., Schouw, M.E., Lukasch, C., Bianchini, L., Sieber, L., Garcia-Lopez, J., Ahmad, S.T., Li, Y., Lin, H., Joshi, P., Spänig, L., Radoš, M., Roiuk, M., Sepp, M., Zuckermann, M., Northcott, P.A., Patrizi, A., Kutscher, L.M.
Neurobiology of Disease, 2024 Link
PREPRINT: Cell-state plasticity drives heterogeneity in Group 3/4 medulloblastoma
Joshi, P., da Silva, P.B.G., Okonechnikov, K., Stelzer, T., Sarropoulos, I., Sepp, M., Nolle, J., Pour-Jamnani, M.V., Rademacher, A., Yamada, T., Schneider, C., Schmidt, J., Bianchini, L., Schäfer, P., Leiss, K., Bortolomeazzi, M., Mallm, J., Statz, B., Wittmann, A., Schramm, K., Blattner-Johnson, M., Fiesel, P., Jones, B.C., Milde, T., Pajtler, K.W., van Tilburg, C.M., Witt, O., Rippe, K., Korshunov, A., Jones, D.T., Hovestadt, V., Northcott, P.A., Zuckermann, M., Thongjuea, S., Jäger, N., Kaessmann, H., Pfister, S.M., Kutscher, L.M.
openRxiv, 2024 Link
Cellular development and evolution of the mammalian cerebellum
Sepp, M., Leiss, K., Murat, F., Okonechnikov, K., Joshi, P., Leushkin, E., Spänig, L., Mbengue, N., Schneider, C., Schmidt, J., Trost, N., Schauer, M., Khaitovich, P., Lisgo, S., Palkovits, M., Giere, P., Kutscher, L.M., Anders, S., Cardoso-Moreira, M., Sarropoulos, I., Pfister, S.M., Kaessmann, H.
Nature, 2023 Link
A lamprey neural cell type atlas illuminates the origins of the vertebrate brain
Lamanna, F., Hervas-Sotomayor, F., Oel, A.P., Jandzik, D., Sobrido-Cameán, D., Santos-Durán, G.N., Martik, M.L., Stundl, J., Green, S.A., Brüning, T., Mößinger, K., Schmidt, J., Schneider, C., Sepp, M., Murat, F., Smith, J.J., Bronner, M.E., Rodicio, M.C., Barreiro-Iglesias, A., Medeiros, D.M., Arendt, D., Kaessmann, H.
Nature Ecology & Evolution, 2023 Link
Mapping pediatric brain tumors to their origins in the developing cerebellum
Okonechnikov, K., Joshi, P., Sepp, M., Leiss, K., Sarropoulos, I., Murat, F., Sill, M., Beck, P., Chan, K.C., Korshunov, A., Sah, F., Deng, M.Y., Sturm, D., DeSisto, J., Donson, A.M., Foreman, N.K., Green, A.L., Robinson, G., Orr, B.A., Gao, Q., Darrow, E., Hadley, J.L., Northcott, P.A., Gojo, J., Kawauchi, D., Hovestadt, V., Filbin, M.G., von Deimling, A., Zuckermann, M., Pajtler, K.W., Kool, M., Jones, D.T.W., Jäger, N., Kutscher, L.M., Kaessmann, H., Pfister, S.M.
Neuro-Oncology, 2023 Link
The molecular evolution of spermatogenesis across mammals
Murat, F., Mbengue, N., Winge, S.B., Trefzer, T., Leushkin, E., Sepp, M., Cardoso-Moreira, M., Schmidt, J., Schneider, C., Mößinger, K., Brüning, T., Lamanna, F., Belles, M.R., Conrad, C., Kondova, I., Bontrop, R., Behr, R., Khaitovich, P., Pääbo, S., Marques-Bonet, T., Grützner, F., Almstrup, K., Schierup, M.H., Kaessmann, H.
Nature, 2022 Link
Functional consequences of TCF4 missense substitutions associated with Pitt-Hopkins syndrome, mild intellectual disability, and schizophrenia
Sirp, A., Roots, K., Nurm, K., Tuvikene, J., Sepp, M., Timmusk, T.
Journal of Biological Chemistry, 2021 Link
Isoform-Specific Reduction of the Basic Helix-Loop-Helix Transcription Factor TCF4 Levels in Huntington’s Disease
Nurm, K., Sepp, M., Castany-Pladevall, C., Creus-Muncunill, J., Tuvikene, J., Sirp, A., Vihma, H., Blake, D.J., Perez-Navarro, E., Timmusk, T.
eneuro, 2021 Link
Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells
Sarropoulos, I., Sepp, M., Frömel, R., Leiss, K., Trost, N., Leushkin, E., Okonechnikov, K., Joshi, P., Giere, P., Kutscher, L.M., Cardoso-Moreira, M., Pfister, S.M., Kaessmann, H.
Science, 2021 Link
The Fuchs corneal dystrophy-associated CTG repeat expansion in the TCF4 gene affects transcription from its alternative promoters
Sirp, A., Leite, K., Tuvikene, J., Nurm, K., Sepp, M., Timmusk, T.
Scientific Reports, 2020 Link
Daughterless, the Drosophila orthologue of TCF4, is required for associative learning and maintenance of the synaptic proteome
Tamberg, L., Jaago, M., Säälik, K., Sirp, A., Tuvikene, J., Shubina, A., Kiir, C.S., Nurm, K., Sepp, M., Timmusk, T., Palgi, M.
Disease Models & Mechanisms, 2020 Link
Neuralized family member NEURL1 is a ubiquitin ligase for the cGMP-specific phosphodiesterase 9A
Taal, K., Tuvikene, J., Rullinkov, G., Piirsoo, M., Sepp, M., Neuman, T., Tamme, R., Timmusk, T.
Scientific Reports, 2019 Link
The Intellectual Disability and Schizophrenia Associated Transcription Factor TCF4 Is Regulated by Neuronal Activity and Protein Kinase A
Sepp, M., Vihma, H., Nurm, K., Urb, M., Page, S.C., Roots, K., Hark, A., Maher, B.J., Pruunsild, P., Timmusk, T.
The Journal of Neuroscience, 2017 Link
Partial deletion of TCF4 in three generation family with non-syndromic intellectual disability, without features of Pitt-Hopkins syndrome
Kharbanda, M., Kannike, K., Lampe, A., Berg, J., Timmusk, T., Sepp, M.
European Journal of Medical Genetics, 2016 Link
Nucleolar Enrichment of Brain Proteins with Critical Roles in Human Neurodevelopment
Slomnicki, L.P., Malinowska, A., Kistowski, M., Palusinski, A., Zheng, J., Sepp, M., Timmusk, T., Dadlez, M., Hetman, M.
Molecular & Cellular Proteomics, 2016 Link
Introducing Pitt-Hopkins syndrome-associated mutations of TCF4 to Drosophila daughterless
Tamberg, L., Sepp, M., Timmusk, T., Palgi, M.
Biology Open, 2015 Link
Characterization of the nuclear matrix targeting sequence (NMTS) of the BPV1 E8/E2 protein — the shortest known NMTS
Sankovski, E., Karro, K., Sepp, M., Kurg, R., Ustav, M., Abroi, A.
Nucleus, 2015 Link
Forkhead Transcription Factor FOXO3a Levels Are Increased in Huntington Disease Because of Overactivated Positive Autofeedback Loop
Kannike, K., Sepp, M., Zuccato, C., Cattaneo, E., Timmusk, T.
Journal of Biological Chemistry, 2014 Link
BAC-based cellular model for screening regulators of BDNF gene transcription
Jaanson, K., Sepp, M., Aid-Pavlidis, T., Timmusk, T.
BMC Neuroscience, 2014 Link
Pitt–Hopkins syndrome-associated mutations in TCF4 lead to variable impairment of the transcription factor function ranging from hypomorphic to dominant-negative effects
Sepp, M., Pruunsild, P., Timmusk, T.
Human Molecular Genetics, 2012 Link
Functional Diversity of Human Basic Helix-Loop-Helix Transcription Factor TCF4 Isoforms Generated by Alternative 5′ Exon Usage and Splicing
Sepp, M., Kannike, K., Eesmaa, A., Urb, M., Timmusk, T.
PLoS ONE, 2011 Link
Identification of cis-Elements and Transcription Factors Regulating Neuronal Activity-Dependent Transcription of Human BDNF Gene
Pruunsild, P., Sepp, M., Orav, E., Koppel, I., Timmusk, T.
The Journal of Neuroscience, 2011 Link
BAC transgenic mice reveal distal cis‐regulatory elements governing BDNF gene expression
Koppel, I., Aid‐Pavlidis, T., Jaanson, K., Sepp, M., Palm, K., Timmusk, T.
genesis, 2010 Link
NF‐κB‐dependent regulation of brain‐derived neurotrophic factor in hippocampal neurons by X‐linked inhibitor of apoptosis protein
Kairisalo, M., Korhonen, L., Sepp, M., Pruunsild, P., Kukkonen, J.P., Kivinen, J., Timmusk, T., Blomgren, K., Lindholm, D.
European Journal of Neuroscience, 2009 Link
Neuralized-2: Expression in human and rodents and interaction with Delta-like ligands
Rullinkov, G., Tamme, R., Sarapuu, A., Laurén, J., Sepp, M., Palm, K., Timmusk, T.
Biochemical and Biophysical Research Communications, 2009 Link
Tissue-specific and neural activity-regulated expression of human BDNF gene in BAC transgenic mice
Koppel, I., Aid-Pavlidis, T., Jaanson, K., Sepp, M., Pruunsild, P., Palm, K., Timmusk, T.
BMC Neuroscience, 2009 Link
N‐terminally truncated BAF57 isoforms contribute to the diversity of SWI/SNF complexes in neurons
Kazantseva, A., Sepp, M., Kazantseva, J., Sadam, H., Pruunsild, P., Timmusk, T., Neuman, T., Palm, K.
Journal of Neurochemistry, 2009 Link
Bovine papillomavirus type 1 E2 protein heterodimer is functional in papillomavirus DNA replication in vivo
Kurg, R., Uusen, P., Sepp, T., Sepp, M., Abroi, A., Ustav, M.
Virology, 2009 Link
Association of Bovine Papillomavirus E2 Protein with Nuclear Structures In Vivo
Kurg, R., Sild, K., Ilves, A., Sepp, M., Ustav, M.
Journal of Virology, 2005 Link