ZFIN ID: ZDB-PERS-960805-394
Müller, Ferenc
Email: f.mueller@bham.ac.uk
Affiliation: Ferenc Müller Lab
Address: Department of Medical and Molecular Genetics Division of Reproductive and Child Health Institute of Biomedical Research University of Birmingham, B15 2TT Edgbaston, Birmingham, D-76021 United Kingdom
Country: United Kingdom
Phone: +44 121 414 2895
Fax: +44 121 414 2538

1. Transcriptional regulation of the zebrafish shh gene.
2. Signal transduction pathways in floor plate differentiation.
3. Transcriptional regulation in early embryo development.

Jimenez-Gonzalez, A., Ansaloni, F., Nebendahl, C., Alavioon, G., Murray, D., Robak, W., Sanges, R., Müller, F., Immler, S. (2024) Paternal starvation affects metabolic gene expression during zebrafish offspring development and lifelong fitness. Molecular Ecology. 33(6):e17296
Jimenez Gonzalez, A., Baranasic, D., Müller, F. (2023) Zebrafish regulatory genomic resources for disease modelling and regeneration. Disease models & mechanisms. 16(8):
Hadzhiev, Y., Wheatley, L., Cooper, L., Ansaloni, F., Whalley, C., Chen, Z., Finaurini, S., Gustincich, S., Sanges, R., Burgess, S., Beggs, A., Müller, F. (2023) The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation. Developmental Cell. 58:155170.e8155-170.e8
Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F.M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S.E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A.C., Kopp, W., Chambers, E., Wang, D., Kim, H.R., Acemel, R.D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S.A., Burgess, S.M., Winata, C., van Eeden, F., Vaquerizas, J.M., Gómez-Skarmeta, J.L., Onichtchouk, D., Brown, B.J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F.C., Daub, C.O., Lenhard, B., Müller, F. (2022) Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics. 54(7):1037-1050
Shen, D., Song, C., Miskey, C., Chan, S., Guan, Z., Sang, Y., Wang, Y., Chen, C., Wang, X., Müller, F., Ivics, Z., Gao, B. (2021) A native, highly active Tc1/mariner transposon from zebrafish (ZB) offers an efficient genetic manipulation tool for vertebrates. Nucleic acids research. 49:2126-2140
D'Orazio, F.M., Balwierz, P.J., González, A.J., Guo, Y., Hernández-Rodríguez, B., Wheatley, L., Jasiulewicz, A., Hadzhiev, Y., Vaquerizas, J.M., Cairns, B., Lenhard, B., Müller, F. (2021) Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization. Developmental Cell. 56(5):641-656.e5
D'Orazio, F.M., Jasiulewicz, A., Hadzhiev, Y., Müller, F. (2021) Visualization of Transcriptional Activity in Early Zebrafish Primordial Germ Cells. Methods in molecular biology (Clifton, N.J.). 2218:185-194
Wragg, J.W., 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 research. 48(15):8374-8392
Nepal, C., Hadzhiev, Y., Balwierz, P., Tarifeño-Saldivia, E., Cardenas, R., Wragg, J.W., Suzuki, A.M., Carninci, P., Peers, B., Lenhard, B., Andersen, J.B., Müller, F. (2020) Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Nature communications. 11:168
Hadzhiev, Y., Qureshi, H.K., Wheatley, L., Cooper, L., Jasiulewicz, A., Van Nguyen, H., Wragg, J.W., Poovathumkadavil, D., Conic, S., Bajan, S., Sik, A., Hutvàgner, G., Tora, L., Gambus, A., Fossey, J.S., Müller, F. (2019) A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation. Nature communications. 10:691
Weger, M., Weger, B.D., Görling, B., Poschet, G., Yildiz, M., Hell, R., Luy, B., Akcay, T., Güran, T., Dickmeis, T., Müller, F., Krone, N. (2018) Glucocorticoid deficiency causes transcriptional and post-transcriptional reprogramming of glutamine metabolism. EBioMedicine. 36:376-389
Dong, X., Liao, Z., Gritsch, D., Hadzhiev, Y., Bai, Y., Locascio, J.J., Guennewig, B., Liu, G., Blauwendraat, C., Wang, T., Adler, C.H., Hedreen, J.C., Faull, R.L.M., Frosch, M.P., Nelson, P.T., Rizzu, P., Cooper, A.A., Heutink, P., Beach, T.G., Mattick, J.S., Müller, F., Scherzer, C.R. (2018) Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease. Nature Neuroscience. 21(10):1482-1492
Weger, M., Diotel, N., Weger, B.D., Beil, T., Zaucker, A., Eachus, H.L., Oakes, J.A., do Rego, J.L., Storbeck, K.H., Gut, P., Straehle, U., Rastegar, S., Mueller, F., Krone, N. (2018) Expression and activity profiling of the steroidogenic enzymes of glucocorticoid biosynthesis and the fdx1 co-factors in zebrafish. Journal of neuroendocrinology. 30(4):e12586
Eachus, H., Zaucker, A., Oakes, J.A., Griffin, A., Weger, M., Güran, T., Taylor, A., Harris, A., Greenfield, A., Quanson, J.L., Storbeck, K.H., Cunliffe, V.T., Müller, F., Krone, N. (2017) Genetic disruption of 21-hydroxylase in zebrafish causes interrenal hyperplasia. Endocrinology. 158(12):4165-4173
Crowcombe, J., Dhillon, S.S., Hurst, R.M., Egginton, S., Müller, F., Sík, A., Tarte, E. (2016) 3D Finite Element Electrical Model of Larval Zebrafish ECG Signals. PLoS One. 11:e0165655
Basu, S., Hadzhiev, Y., Petrosino, G., Nepal, C., Gehrig, J., Armant, O., Ferg, M., Strahle, U., Sanges, R., Müller, F. (2016) The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome. Scientific Reports. 6:33210
Nepal, C., Coolen, M., Hadzhiev, Y., Cussigh, D., Mydel, P., Steen, V.M., Carninci, P., Andersen, J.B., Bally-Cuif, L., Müller, F., Lenhard, B. (2016) Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs. Nucleic acids research. 44(7):3070-81
Griffin, A., Parajes, S., Weger, M., Zaucker, A., Taylor, A.E., O'Neil, D.M., Müller, F., Krone, N. (2016) Ferredoxin 1b (Fdx1b) is the essential mitochondrial redox partner for cortisol biosynthesis in zebrafish. Endocrinology. 157(3):1122-34
Wragg, J., Müller, F. (2016) Transcriptional Regulation During Zygotic Genome Activation in Zebrafish and Other Anamniote Embryos. Advances in genetics. 95:161-94
Hadzhiev, Y., Miguel-Escalada, I., Balciunas, D., Müller, F. (2016) Testing of Cis-Regulatory Elements by Targeted Transgene Integration in Zebrafish Using PhiC31 Integrase. Methods in molecular biology (Clifton, N.J.). 1451:81-91
Wai, H.A., Wada, H., Kawakami, K., Müller, F., Vernallis, A.B., Brown, G., Johnson, W.E. (2015) The development and growth of tissues derived from cranial neural crest and primitive mesoderm is dependent on the ligation status of retinoic acid receptor (RAR) γ: evidence that RARγ functions to maintain stem/progenitor cells in the absence of retinoic acid. Stem cells and development. 24(4):507-19
Zaucker, A., Bodur, T., Roest Crollius, H., Hadzhiev, Y., Gehrig, J., Loosli, F., Watson, C., Müller, F. (2014) Description of Embryonic Development of Spotted Green Pufferfish (Tetraodon nigroviridis). Zebrafish. 11(6):509-17
Haberle, V., Li, N., Hadzhiev, Y., Plessy, C., Previti, C., Nepal, C., Gehrig, J., Dong, X., Akalin, A., Suzuki, A.M., van IJcken, W.F., 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. 507(7492):381-385
Nepal, C., Hadzhiev, Y., Previty, C., Haberle, V., Li, N., Takahashi, H., Suzuki, A.M., Sheng, Y., Abdelhamid, R., Anand, S., Gehrig, J., Akalin, A., Kockx, C., van der Sloot, A., van Ijcken, W., Armant, O., Rastegar, S., Straehle, U., Stupka, E., Carninci, P., Lenhard, B., and Muller, F. (2013) Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome research. 23(11):1938-50
Feula, A., Dhillon, S.S., Byravan, R., Sangha, M., Ebanks, R., Hama Salih, M.A., Spencer, N., Male, L., Magyary, I., Deng, W.P., Muller, F., and Fossey, J.S. (2013) Synthesis of azetidines and pyrrolidines via iodocyclisation of homoallyl amines and exploration of activity in a zebrafish embryo assay. Organic & biomolecular chemistry. 11(31):5083-93
Parajes, S., Griffin, A., Taylor, A.E., Rose, I.T., Miguel-Escalada, I., Hadzhiev, Y., Arlt, W., Shackleton, C., Muller, F., and Krone, N. (2013) Redefining the initiation and maintenance of zebrafish interrenal steroidogenesis by characterizing the key enzyme Cyp11a2. Endocrinology. 154(8):2702-11
Bakos, K., Kovacs, R., Staszny, A., Sipos, D.K., Urbanyi, B., Muller, F., Csenki, Z., and Kovacs, B. (2013) Developmental toxicity and estrogenic potency of zearalenone in zebrafish (Danio rerio). Aquatic toxicology (Amsterdam, Netherlands). 136-137:13-21
Dhillon, S.S., Doro, E., Magyary, I., Egginton, S., Sik, A., and Muller, F. (2013) Optimisation of Embryonic and Larval ECG Measurement in Zebrafish for Quantifying the Effect of QT Prolonging Drugs. PLoS One. 8(4):e60552
Sanges, R., Hadzhiev, Y., Gueroult-Bellone, M., Roure, A., Ferg, M., Meola, N., Amore, G., Basu, S., Brown, E.R., De Simone, M., Petrera, F., Licastro, D., Strahle, U., Banfi, S., Lemaire, P., Birney, E., Muller, F., and Stupka, E. (2013) Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. Nucleic acids research. 41(6):3600-3618
Basu, S., Muller, F., and Sanges, R. (2013) Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements. BMC Bioinformatics. 14(7):S14
Astuti, D., Morris, M.R., Cooper, W.N., Staals, R.H., Wake, N.C., Fews, G.A., Gill, H., Gentle, D., Shuib, S., Ricketts, C.J., Cole, T., van Essen, A.J., van Lingen, R.A., Neri, G., Opitz, J.M., Rump, P., Stolte-Dijkstra, I., Muller, F., Pruijn, G.J., Latif, F., and Maher, E.R. (2012) Germline mutations in DIS3L2 cause the Perlman syndrome of overgrowth and Wilms tumor susceptibility. Nature Genetics. 44(3):277-284
Lindeman, L.C., Andersen, I.S., Reiner, A.H., Li, N., Aanes, H., Ostrup, O., Winata, C., Mathavan, S., Muller, F., Aleström, P., and Collas, P. (2011) Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation. Developmental Cell. 21(6):993-1004
Peravali, R., Gehrig, J., Giselbrecht, S., Lutjohann, D.S., Hadzhiev, Y., Muller, F., and Liebel, U. (2011) Automated feature detection and imaging for high-resolution screening of zebrafish embryos. Biotechniques. 50(5):319-324
Bem, D., Yoshimura, S., Nunes-Bastos, R., Bond, F.F., Kurian, M.A., Rahman, F., Handley, M.T., Hadzhiev, Y., Masood, I., Straatman-Iwanowska, A.A., Cullinane, A.R., McNeill, A., Pasha, S.S., Kirby, G.A., Foster, K., Ahmed, Z., Morton, J.E., Williams, D., Graham, J.M., Dobyns, W.B., Burglen, L., Ainsworth, J.R., Gissen, P., Muller, F., Maher, E.R., Barr, F.A., and Aligianis, I.A. (2011) Loss-of-Function Mutations in RAB18 Cause Warburg Micro Syndrome. American journal of human genetics. 88(4):499-507
Lang, M., Hadzhiev, Y., Siegel, N., Amemiya, C.T., Parada, C., Strähle, U., Becker, M.B., Muller, F., and Meyer, A. (2010) Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position. EvoDevo. 1(1):11
Kano, S., Xiao, J.H., Osorio, J., Ekker, M., Hadzhiev, Y., Muller, F., Casane, D., Magdelenat, G., and Retaux, S. (2010) Two lamprey hedgehog genes share non-coding regulatory sequences and expression patterns with gnathostome hedgehogs. PLoS One. 5(10):e13332
Southgate, L., Dafou, D., Hoyle, J., Li, N., Kinning, E., Critchley, P., Nemeth, A.H., Talbot, K., Bindu, P.S., Sinha, S., Taly, A.B., Raghavendra, S., Muller, F., Maher, E.R., and Trembath, R.C. (2010) Novel SPG11 mutations in Asian kindreds and disruption of spatacsin function in the zebrafish. Neurogenetics. 11(4):379-389
Yang, L., Ho, N.Y., Muller, F., and Strahle, U. (2010) Methyl mercury suppresses the formation of the tail primordium in developing zebrafish embryos. Toxicological sciences : an official journal of the Society of Toxicology. 115(2):379-390
Cullinane, A.R., Straatman-Iwanowska, A., Zaucker, A., Wakabayashi, Y., Bruce, C.K., Luo, G., Rahman, F., Gürakan, F., Utine, E., Ozkan, T.B., Denecke, J., Vukovic, J., Di Rocco, M., Mandel, H., Cangul, H., Matthews, R.P., Thomas, S.G., Rappoport, J.Z., Arias, I.M., Wolburg, H., Knisely, A.S., Kelly, D.A., Muller, F., Maher, E.R., and Gissen, P. (2010) Mutations in VIPAR cause an arthrogryposis, renal dysfunction and cholestasis syndrome phenotype with defects in epithelial polarization. Nature Genetics. 42(4):303-312
Csenki, Z., Zaucker, A., Kovacs, B., Hadzhiev, Y., Hegyi, R., Lefler, K.K., Muller, T., Kovacs, R., Urbanyi, B., Varadi, L., and Muller, F. (2010) Intraovarian transplantation of stage I-II follicles results in viable zebrafish embryos. The International journal of developmental biology. 54(4):585-589
Gehrig, J., Reischl, M., Kalmar, E., Ferg, M., Hadzhiev, Y., Zaucker, A., Song, C., Schindler, S., Liebel, U., and Muller, F. (2009) Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos. Nature Methods. 6(12):911-916
Muller, F., and Tora, L. (2009) TBP2 is a general transcription factor specialized for female germ cells. Journal of biology. 8(11):97
König, H., Matter, N., Bader, R., Thiele, W., and Müller, F. (2007) Splicing Segregation: The Minor Spliceosome Acts outside the Nucleus and Controls Cell Proliferation. Cell. 131(4):718-729
Ferg, M., Sanges, R., Gehrig, J., Kiss, J., Bauer, M., Lovas, A., Szabo, M., Yang, L., Straehle, U., Pankratz, M.J., Olasz, F., Stupka, E., and Müller, F. (2007) The TATA-binding protein regulates maternal mRNA degradation and differential zygotic transcription in zebrafish. The EMBO journal. 26(17):3945-3956
Ertzer, R., Muller, F., Hadzhiev, Y., Rathnam, S., Fischer, N., Rastegar, S., and Strähle, U. (2007) Cooperation of sonic hedgehog enhancers in midline expression. Developmental Biology. 301(2):578-589
Yang, L., Kemadjou, J.R., Zinsmeister, C., Legradi, J., Bauer, M., Muller, F., Pankratz, M., Jakel, J., and Straehle, U. (2007) Transcriptional profiling reveals barcode-like toxicogenomic responses in the zebrafish embryo. Genome biology. 8(10):R227
Yu, R.M., Lin, C.C., Chan, P.K., Chow, E.S., Murphy, M.B., Chan, B.P., Muller, F., Strähle, U., and Cheng, S.H. (2006) Four-dimensional Imaging and Quantification of Gene Expression in Early Developing Zebrafish (Danio rerio) Embryos. Toxicological sciences : an official journal of the Society of Toxicology. 90(2):529-538
Sanges, R., Kalmar, E., Claudiani, P., D'Amato, M., Muller, F., and Stupka, E. (2006) Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. Genome biology. 7(7):R56
Muller, F. (2005) Comparative Aspects of Alternative Laboratory Fish Models. Zebrafish. 2(1):47-54
Hwang, G., Müller, F., Rahman, M.A., Williams, D.W., Murdock, P.J., Pasi, K.J., Goldspink, G., Farahmand, H., and Maclean, N. (2004) Fish as Bioreactors: Transgene Expression of Human Coagulation Factor VII in Fish Embryos. Marine biotechnology (New York, N.Y.). 6(5):485-492
Shkumatava, A., Fischer, S., Müller, F., Strähle, U., and Neumann, C.J. (2004) Sonic hedgehog, secreted by amacrine cells, acts as a short-range signal to direct differentiation and lamination in the zebrafish retina. Development (Cambridge, England). 131(16):3849-3858
Bartfai, R., Balduf, C., Hilton, T., Rathmann, Y., Hadzhiev, Y., Tora, L., Orbán, L., and Muller, F. (2004) TBP2, a Vertebrate-Specific Member of the TBP Family, Is Required in Embryonic Development of Zebrafish. Current biology : CB. 14(7):593-598
Szabo, M., Müller, F., Kiss, J., Balduf, C., Strähle, U., and Olasz, F. (2003) Transposition and targeting of the prokaryotic mobile element IS30 in zebrafish. FEBS letters. 550(1-3):46-50
Albert, S., Müller, F., Fischer, N., Biellmann, D., Neumann, C., Blader, P., and Strähle, U. (2003) Cyclops-independent floor plate differentiation in zebrafish embryos. Developmental Dynamics : an official publication of the American Association of Anatomists. 226(1):59-66
Rastegar, S., Albert, S., Le Roux, I., Fischer, N., Blader, P., Müller, F., and Strähle, U. (2002) A floor plate enhancer of the zebrafish netrin1 gene requires Cyclops (Nodal) signalling and the winged helix transcription factor FoxA2. Developmental Biology. 252(1):1-14
Müller, F., Blader, P., and Strähle, U. (2002) Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elements. BioEssays : news and reviews in molecular, cellular and developmental biology. 24(6):564-572
Müller, F., Lakatos, L., Dantonel, J., Strähle, U., and Tora, L. (2001) TBP is not universally required for zygotic RNA polymerase II transcription in zebrafish. Current biology : CB. 11(4):282-287
Hill, A., Howard, V., Müller, F. and Cossins, A. (2001) Effect of 2,3,7,8-tetrachlorodibenzo-p dioxin on early development and the neurogenesis pathway in the zebrafish (Danio rerio). Organohalogen Compounds. 53:207-210
Müller, F., Albert, S., Blader, P., Fischer, N., Hallonet, M., and Strähle, U. (2000) Direct action of the Nodal-related signal Cyclops in induction of sonic hedgehog in the ventral midline of the CNS. Development (Cambridge, England). 127(18):3889-3897
Kiecker, C., Müller, F., Wu, W., Glinka, A., Strähle, U., and Niehrs, C. (2000) Phenotypic effects in Xenopus and zebrafish suggest that one-eyed pinhead functions as antagonist of BMP signalling. Mechanisms of Development. 94(1-2):37-46
Molina, A., Biemar, F., Müller, F., Iyengar, A., Prunet, P., Maclean, N., Martial, J.A., and Muller, M. (2000) Cloning and expression analysis of an inducible HSP70 gene from tilapia fish. FEBS letters. 474(1):5-10
Müller, F., Blader, P., Rastegar, S., Fischer, N., Knochel, W., Strähle, U. (1999) Characterization of zebrafish smad1, smad2 and smad5: the amino-terminus of Smad1 and Smad5 is required for specific function in the embryo. Mechanisms of Development. 88(1):73-88
Müller, F., Chang, B., Albert, S., Fischer, N., Tora, L., and Strähle, U. (1999) Intronic enhancers control expression of zebrafish sonic hedgehog in floor plate and notochord. Development (Cambridge, England). 126(10):2103-2116
Hanley, S., Smith, T.J., Müller, F., Maclean, N., Uzbekova, S., Prunet, P., Breton, B. (1998) Isolation and functional analysis of the histone H3 promoter from atlantic salmon (Salmo salar L.). Molecular marine biology and biotechnology. 7:165-172
Müller, F., Williams, D.W., Kobolak, J., Gauvry, L., Goldspink, G., Orbán, L., and Maclean, N. (1997) Activator effect of coinjected enhancers on the muscle-specific expression of promoters in zebrafish embryos. Molecular reproduction and development. 47(4):404-412
Williams, D. Müller, F., Lavender, F.L., Orbán, L., and Maclean, N. (1996) High transgene activity in the yolk syncytial layer affects quantitative transient expression assays in zebrafish (Danio rerio) embryos. Transgenic Research. 5:433-442
Müller, F., Gauvry, L., Williams, D., Kobolak, J., Maclean, N., Orbán, L., and Goldspink, G. (1996) The use of transient lacZ expression in fish embryos for comparative analysis of activity of cloned regulatory elements. In Gene expression and manipulation in aquatic organisms. S.J. Ennion and G. Goldspink, eds., Soc. Exp. Biol. Sem. Ser. 58, Cambridge, UK: Cambridge University Press. :175-199
Szelei, J., Varadi, L., Müller, F., Erdelyi, F., Orbán, L., Horvath, L, and Duda, E. (1994) Liposome-mediated gene transfer in fish embryos. Transgenic Research. 3:116-119
Müller, F., Lele, Z., Varadi, L., Menczel, L., and Orbán, L. (1993) Efficient transient expression system based on square pulse electroporation and in vivo luciferase assay of fertilized fish eggs. FEBS letters. 324:27-32
Müller, F., Ivics, Z., Erdelyi, F. Papp, T., Varadi, L., Horvath, L., Maclean, N., and Orbán, L. (1992) Introducing foreign genes into fish eggs with electroporated sperm as a carrier. Molecular marine biology and biotechnology. 1:276-281