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Article

Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters.
Trovato, M., Bunina, D., Yildiz, U., Fernandez-Novel Marx, N., Uckelmann, M., Levina, V., Perez, Y., Janeva, A., Garcia, B.A., Davidovich, C., Zaugg, J.B. 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., Arnold, C., Claringbould, A., Moussa, R., Servaas, N.H., Kholmatov, M., Daga, N., Nogina, D., Mueller-Dott, S., Reyes-Palomares, A., Palla, G., Sigalova, O., Bunina, D., Pabst, C. and Zaugg, J.B.
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., 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., 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., Bunina, D., Sidoli, S., Lübke, M.J., Diaz, N., Trovato, M., Garcia, B.A., Zaugg, J.B. and Noh, K.M.
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., 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., 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., 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., 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., 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., 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., Ul'ianov, S.V., Gavrilov, A.A. and Razin, S.V.
Molekulyarnaya Biologiya 45 (4): 662-667. July 2011