Hadzhiev, Y., Qureshi, H., Wheatley, L., Cooper, L. Jasiulewicz, A., Wragg, J., Nguyen, H., Poovathumkadavil, D., Conic, S., Bajan, S., Sik, A., Hutvagner, G., Tora, L., Gambus, A., Fossey J., and Müller F. (2019) A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation Nature Communications 10(1):691. doi: 10.1038/s41467-019-08487-5.
Nepal, C., Hadzhiev, Y., Tarifeño-Saldivia, E., Carninci, P., Andersen, J.B., Peers, B., Lenhard B., and Müller F. (2019) Intertwined canonical and non-canonical initiation in dual promoters are pervasive and differentially regulate Polymerase II transcription preprint: BioRxiv 487496; doi: https://doi.org/10.1101/487496
Dong, X., Liao, Z., Gritsch, D., Hadzhiev, Y., Bai, Y., Locascio, J.J., Guennewig, B., Liu, G., Blauwendraat, C., Wang, T., Adler C.H., Frosch, M.P., Nelson, T.P., Rizzu, P., Cooper, A.A. Heutink, P., Beach, G.B, Mattick, J.S., Müller, F., and Scherzer C.R. (2018) An encyclopedia of transcribed elements in human brain dopamine neurons. (2018) Nature Neuroscience (10):1482-1492. doi: 10.1038/s41593-018-0223-0
Andersson R, Gebhard C, Miguel -Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Fantom Consortium, Forrest AR, Carninci P, Rehli M and Sandelin A (2014) An atlas of active enhancers across human cell types and tissues. Nature 507(7493):455-61
Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki A-M, van IJcken W, Armant O, Ferg M, Strähle U, Carninci P, Müller F* and Lenhard B (2014) Two independent transcription initiation codes overlap on vertebrate core promoters. Nature 207(7492):381-5
*co-corresponding author
Roberts JA, Miguel-Escalada I, Slovik KJ, Walsh KT, Hadzhiev Y, Sanges R, Stupka E, Balciuniene J, Marsh EK, Balciunas D and Müller F (2014) Targeted transgene integration overcomes variability of position effects in zebrafish. Development 141(3):715-24
Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki A-M S, Sheng Y, Abdelhamid RA, Anand S, Gehrig J, Akalin A, Kockx CEM, van der Sloot AAJ, van IJcken WFJ, Armant O, Rastegar S, Watson C, Strähle U, Stupka E, Carninci P, Lenhard B and Müller F (2013) Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Research 23(11):1938-50
Pasquali L, Gaulton KJ, Rodríguez-Seguí S, Mularoni L, Miquel-Escalada I, Akerman I, Tena JJ, Morán I, Gomez-Marin C, van de Bunt M, Ponsa-Cobas J, Castro N, Nammo T, Cebola I, García-Hurtado J, Maestro MA, Pattou F, Piemonti L, Berney T, Gloyn AL, Ravassard P, Skarmeta JL, Müller F, McCarthy M and Ferrer J (2014) Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nature Genetics 46(2):136-43
Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Ostrup O, Winata C, Mathavan S, Müller F, Aleström P and Collas P (2011) Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation. Dev Cell 21(6):993-1004
Cullinane AR, Straatman-Iwanowska A, Zaucker A, Wakabayashi Y, Bruce CK, Luo G, Rahman F, Gürakan F, Utine E, Ozkan TB, Denecke J, Vukovic J, Di Rocco M, Mandel H, Cangul H, Matthews RP, Thomas SG, Rappoport JZ, Arias IM, Wolburg H, Knisely AS, Kelly DA, Müller F, Maher ER and Gissen P (2010) Mutations in VIPAR cause an arthrogryposis, renal dysfunction and cholestasis syndrome phenotype with defects in epithelial polarization. Nat Genet 42(4):303-12
Gehrig J, Reischl M, Kalmar E, Ferg M, Hadzhiev Y, Zaucker A, Song C, Schindler S, Liebel U and Müller F (2009) Automated high throughput mapping of promoter-enhancer interactions in zebrafish embryos. Nature Methods 6(12):911-6
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