Article

Distinct roles for MNK1 and MNK2 in social and cognitive behavior through kinase-specific regulation of the synaptic proteome and phosphoproteome.
Proce, Rosalba Olga, Steinecker, Maria, Giacomelli, Chiara ORCID: https://orcid.org/0000-0003-1466-1371, Uddström, Erika ORCID: https://orcid.org/0009-0009-5298-480X, Chatterjee, Anirban ORCID: https://orcid.org/0009-0002-8271-384X, Wüsthoff, Souhaila ORCID: https://orcid.org/0000-0001-7653-3565, Teixeira Alves, Luiz Gustavo ORCID: https://orcid.org/0000-0002-5822-4168, Popp, Oliver ORCID: https://orcid.org/0000-0001-6240-4666, Pohl, Tobias ORCID: https://orcid.org/0000-0001-8698-8475, Maxwell, Katie, Hortmann, Lucie, Kunz, Severine ORCID: https://orcid.org/0000-0002-0131-3506, Mertins, Philipp ORCID: https://orcid.org/0000-0002-2245-528X, Landthaler, Markus ORCID: https://orcid.org/0000-0002-1075-8734, Bunina, Daria ORCID: https://orcid.org/0000-0002-5885-7440 and Hörnberg, Hanna ORCID: https://orcid.org/0000-0001-9142-1932
Molecular Psychiatry 31 (6): 3446-3461. June 2026

A noncanonical role of glycolytic metabolites controlling the timing of mouse embryo segmentation.
Miyazawa, Hidenobu ORCID: https://orcid.org/0000-0001-6164-5134, Rada, Jona ORCID: https://orcid.org/0000-0001-8534-8708, Prior, Nicole ORCID: https://orcid.org/0000-0003-2856-7052, Sanchez, Paul Gerald Layague ORCID: https://orcid.org/0000-0001-6213-8927, Esposito, Emilia, Bunina, Daria ORCID: https://orcid.org/0000-0002-5885-7440, Girardot, Charles ORCID: https://orcid.org/0000-0003-4301-3920, Zaugg, Judith ORCID: https://orcid.org/0000-0001-8324-4040 and Aulehla, Alexander ORCID: https://orcid.org/0000-0003-3487-9239
Science Advances 11 (38): eadz9606. 19 September 2025

Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters.
Trovato, M. ORCID: https://orcid.org/0000-0003-0406-387X, Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Yildiz, U. ORCID: https://orcid.org/0000-0002-7175-362X, Fernandez-Novel Marx, N., Uckelmann, M., Levina, V., Perez, Y. ORCID: https://orcid.org/0000-0002-6674-4833, Janeva, A., Garcia, B.A. ORCID: https://orcid.org/0000-0003-3596-4750, Davidovich, C. ORCID: https://orcid.org/0000-0002-1085-6094, Zaugg, J.B. ORCID: https://orcid.org/0000-0001-8324-4040 and Noh, K.M.
Nature Communications 15 (1): 7557. 30 August 2024

GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks.
Kamal, A. ORCID: https://orcid.org/0000-0002-1584-5896, Arnold, C., Claringbould, A., Moussa, R. ORCID: https://orcid.org/0000-0002-5011-1695, Servaas, N.H. ORCID: https://orcid.org/0000-0002-9825-7554, Kholmatov, M., Daga, N., Nogina, D. ORCID: https://orcid.org/0000-0002-0593-2726, Mueller-Dott, S., Reyes-Palomares, A. ORCID: https://orcid.org/0000-0002-0289-6889, Palla, G., Sigalova, O. ORCID: https://orcid.org/0000-0001-8598-1079, Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Pabst, C. and Zaugg, J.B. ORCID: https://orcid.org/0000-0001-8324-4040
Molecular Systems Biology 19 (6): e11627. 12 June 2023

Donor cell memory confers a metastable state of directly converted cells.
Kim, K.P., Li, C., Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Jeong, H.W., Ghelman, J., Yoon, J., Shin, B., Park, H., Han, D.W., Zaugg, J.B., Kim, J., Kuhlmann, T., Adams, R.H., Noh, K.M., Goldman, S.A. and Schöler, H.R.
Cell Stem Cell 28 (7): 1291-1306. 1 July 2021

Genomic rewiring of SOX2 chromatin interaction network during differentiation of ESCs to postmitotic neurons.
Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Abazova, N., Diaz, N., Noh, K.M., Krijgsveld, J. and Zaugg, J.B.
Cell Systems 10 (6): 480-494. 24 June 2020

Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy.
Gehre, M. ORCID: https://orcid.org/0000-0001-6567-6464, Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Sidoli, S. ORCID: https://orcid.org/0000-0001-9073-6641, Lübke, M.J. ORCID: https://orcid.org/0000-0002-6330-5704, Diaz, N., Trovato, M., Garcia, B.A., Zaugg, J.B. ORCID: https://orcid.org/0000-0001-8324-4040 and Noh, K.M. ORCID: https://orcid.org/0000-0002-0708-787X
Nature Genetics 52 (3): 273-282. March 2020

Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities.
Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Štefl, M., Huber, F., Khmelinskii, A., Meurer, M., Barry, J.D., Kats, I., Kirrmaier, D., Huber, W. and Knop, M.
Nucleic Acids Research 45 (19): 11144-11158. 2 November 2017

Protein abundance control by non-coding antisense transcription.
Huber, F., Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Gupta, I., Khmelinskii, A., Meurer, M., Theer, P., Steinmetz, L.M. and Knop, M.
Cell Reports 15 (12): 2625-2636. 21 June 2016

PCR duplication: a one-step cloning-free method to generate duplicated chromosomal loci and interference-free expression reporters in yeast.
Huber, F., Meurer, M., Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Kats, I., Maeder, C.I., Stefl, M., Mongis, C. and Knop, M.
PLoS ONE 9 (12): e114590. 10 December 2014

Chromatin structure of the joint α/β-globin gene locus of Danio rerio.
Ioudinkova, E.S., Petrova, N.V., Bunina, D.A. ORCID: https://orcid.org/0000-0002-5885-7440, Vishniakova, H.S., Sklyar, I.V., Razin, S.V. and Iarovaia, O.V.
Doklady Biochemistry and Biophysics 448 : 59-61. January 2013

The inactivation of the π gene in chicken erythroblasts of adult lineage is not mediated by packaging of the embryonic part of the α-globin gene domain into a repressive heterochromatin-like structure.
Ioudinkova, E.S., Ulianov, S.V., Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Iarovaia, O.V., Gavrilov, A.A. and Razin, S.V.
Epigenetics 6 (12): 1481-1488. December 2011

Patterns of histone modifications across the chicken alfa-globin genes’ domain.
Yudinkova, E.S., Bunina, D.A. ORCID: https://orcid.org/0000-0002-5885-7440, Ulyanov, S. V., Gavrilov, A.A. and Razin, S.V.
Molecular Biology 45 (4): 608-613. 5 August 2011

[Patterns of the histone modifications across the chicken alpha-globin genes domain].
Iudinkova, E.S., Bunina, D.A. ORCID: https://orcid.org/0000-0002-5885-7440, Ul'ianov, S.V., Gavrilov, A.A. and Razin, S.V.
Molekulyarnaya Biologiya 45 (4): 662-667. July 2011

Preprint

High-throughput single-cell CRISPRi screens stratify neurodevelopmental functions of schizophrenia-associated genes.
Yildiz, U. ORCID: https://orcid.org/0000-0002-7175-362X, Claringbould, A. ORCID: https://orcid.org/0000-0002-9201-6557, Marttinen, M. ORCID: https://orcid.org/0000-0001-5861-4601, Campos-Fornés, V. ORCID: https://orcid.org/0000-0001-9992-1106, Lamprousi, M. ORCID: https://orcid.org/0000-0002-9149-9972, Saraswat, M. ORCID: https://orcid.org/0000-0002-1472-8049, Saver, M., Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Dorrity, M.W. ORCID: https://orcid.org/0000-0002-7691-6504, Zaugg, J. ORCID: https://orcid.org/0000-0001-8324-4040 and Noh, K.M. ORCID: https://orcid.org/0000-0002-0708-787X
bioRxiv : 2025.06.13.659629. 16 June 2025

Does age protect against loss of tonotopy after acute deafness in adulthood?
Rosskothen-Kuhl, N. ORCID: https://orcid.org/0000-0003-4724-5550, Green, S. ORCID: https://orcid.org/0000-0003-3085-5045 and Jakob, T.F.
bioRxiv : 2024.05.03.592347. 3 May 2024

Pathological LSD1 mutations repress enhancer-mediated gene regulatory networks in early differentiation.
Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Germain, P.L., Lopez Tobon, A., Fernandez-Novel Marx, N., Arnold, C., Ahern, A., Claringbould, A., Lai, M.C., Rangasamy, S., Narayanan, V., Lorentzen, P., Park, K.M., Adamo, A., Testa, G., Zaugg, J. and Noh, K.M.
bioRxiv : 2021.08.11.455900v2. 22 September 2021

Enhancer-priming in ageing human bone marrow mesenchymal stromal cells contributes to immune traits.
Lai, M.C. ORCID: https://orcid.org/0000-0002-8183-6103, Ruiz-Velasco, M., Arnold, C., Sigalova, O. ORCID: https://orcid.org/0000-0001-8598-1079, Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Berest, I., Ding, X., Hennrich, M.L., Poisa-Beiro, L., Claringbould, A., Mathioudaki, A., Pabst, C., Ho, A.D., Gavin, A.C. and Zaugg, J.B. ORCID: https://orcid.org/0000-0001-8324-4040
bioRxiv : 2021.09.03.458728. 5 September 2021

Dataset

RNA-seq of cortical synaptoneurosomes from MNK1 and MNK2 KO mice.
Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440 and Hörnberg, H. ORCID: https://orcid.org/0000-0001-9142-1932
[Dataset] 10 February 2026