Wragg JW, White PL, Hadzhiev Y, Wanigasooriya K, Stodolna A, Tee L, Barros-Silva JD, Beggs AD, Müller F. (2024) Intra-promoter switch of transcription initiation sites in proliferation signaling-dependent RNA metabolism. Nat Struct Mol Biol. 2023 Dec;30(12):1970-1984.
Hadzhiev Y., Wheatley L., Cooper L., Ansaloni F., Whalley C., Chen Z., Finaurini S., Gustincich S., Sanges R., Burgess S., Beggs A. and Müller F. The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation. (2023) Developmental Cell, Jan 23;58(2):155-170.e8. doi: 10.1016/j.devcel.2022.12.007.
Baranasic D., Hörtenhuber M., Balwierz PJ., Zehnder T., Mukarram AK., Nepal C., Várnai C., Hadzhiev Y., Jimenez-Gonzalez A., Li N., Wragg J., D’Orazio FM., Relic D., Pachkov M., Díaz N., Hernández-Rodríguez B., Chen C., Stoiber M., Dong M., Stevens I., Ross SE., Eagle A., Martin R., Obasaju P., Rastegar S., McGarvey AC., Kopp W., Chambers E., Wang D., Kim HR., Acemel RD., Naranjo S., Łapiński M., Chong V., Mathavan S., Peers B., Sauka-Spengler T., Vingron M., Carninci P., Ohler U., Allen Lacadie S., Burgess S.M., Winata C., van Eeden F., Vaquerizas JM., Gómez-SkarmetaJL., Onichtchouk D., Brown BJ., Bogdanovic O., van Nimwegen E., Westerfield M., Wardle FC., Daub CO., Lenhard B. and Müller F. (2022) Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish. Nature Genetics, 54(7):1037-1050, doi: 10.1038/s41588-022-01089-w.
D’Orazio, F., Balwierz, P., Jimenez-Gonzalez, A., Guo, Y., Hernández-Rodríguez, B., Wheatley, L., Hadzhev, Y., Jasiulewicz, A., Vaquerizas, JM., Cairns, B., Lenhard B. and Müller F. (2021) Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalisation Developmental Cell 2021 Feb 24:S1534-5807(21)00118-0
Wragg JW, Roos L, Vucenovic D, Cvetesic N, Lenhard B, Müller F. (2020) Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation. Nucleic Acids Res. Jul 3. doi: 10.1093/nar/gkaa563.
Nepal C, Hadzhiev Y, Balwierz P, Tarifeño-Saldivia E, Cardenas R, Wragg JW, Suzuki AM, Carninci P, Peers B, Lenhard B, Andersen JB, Müller F. (2020) Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nat Commun. Jan 10;11(1):168
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.
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
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
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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