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Michael Brunner 
Circadian Rhythms and Molecular Clocks

Groupleader: Michael Brunner

Shostak, A., Brunner, M. (2019) Help from my friends-cooperation of BMAL1 with noncircadian transcription factors. Genes Dev. Mar 1;33(5-6):255-257. doi: 10.1101/gad.324046.119

Upadhyay, A., Brunner, M., and Herzel, H. (2019). An Inactivation Switch Enables Rhythms in a Neurospora Clock Model. Int. J. Mol. Sci., DOI:


Ananthasubramaniam, B., Diernfellner, A., Brunner, M., and Herzel, H. (2018). Ultradian rhythms in the transcriptome of neurospora crassa. iScience, DOI:

Li C, Cesbron F, Oehler M, Brunner M, Höfer T (2018) Frequency Modulation of Transcription Bursting Enables Sensitive and Rapid Gene Regulation. Cell Systems 6 (4): 409-423. doi: 10.1016/j.cels.2018.01.012.

Lehmann R, Herzel HP, Brunner M, Sancar G, Sancar C, Ananthasubramaniam B (2018) Morning and Evening Peaking Rhythmic Genes are Regulated by Distinct Transcription Factors in Neurospora crassa. Martin Bossert (ed.), Information- and communication Theory in Molecular Biology. Springer: 199-210.


Shostak A, Ruppert B, Diernfellner A, Brunner M.
Correspondence: Reply to 'Oncogenic MYC persistently upregulates the molecular clock component REV-ERBα'.
Nat Commun. 2017; 8:14918. doi: 10.1038/ncomms14918.

Cemel IA, Ha N, Schermann G, Yonekawa S, Brunner M (2017) The coding and noncoding transcriptome of Neurospora crassa. BMC Genomics, 18(1), 978.
doi: 10.1186/s12864-017-4360-8.

Lauinger L, Li J, Shostak A, Cemel IA, Ha N, Zhang Y, Merkl PE, Obermeyer S, Stankovic-Valentin N, Schafmeier T, Wever WJ, Bowers AA, Carter KP, Palmer AE, Tschochner H, Melchior F, Deshaies RJ, Brunner M, Diernfellner A (2017) Thiolutin is a zinc chelator that inhibits the Rpn11 and other JAMM metalloproteases. Nat Chem Biol. 13(7):709-714. doi: 10.1038/nchembio.2370.


Shostak A, Diernfellner A, Brunner M (2016) MYC inhibits the clock and supports proliferation. Cell Cycle. 2016 Sep 7:1-2.

Shostak A, Ruppert B, Ha N, Bruns P, Toprak UH; ICGC MMML-Seq Project, Eils R, Schlesner M, Diernfellner A, Brunner M (2016) MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with cell cycle and proliferation. Nat Commun. 2016 Jun 24;7:11807. doi: 10.1038/ncomms11807.


Zhai Z, Kondo S, Ha N, Boquete JP, Brunner M, Ueda R, Lemaitre B (2015) Accumulation of differentiating intestinal stem cell progenies drives tumorigenesis. Nat Commun Dec 22;6:10219. doi: 10.1038/ncomms 10219.

Sancar C, Ha N, Yilmaz R, Tesorero R, Fisher T, Brunner M, Sancar G (2015) Combinatorial control of light induced chromatin remodeling and gene activation in Neurospora. PLoS Genet. 11(3):e1005105. doi: 10.1371/journal.pgen.1005105

Cesbron F, Oehler M, Ha N, Sancar G, Brunner M (2015) Transcriptional refractoriness is dependent on core promoter architecture. Nat Commun. 6:6753. doi: 10.1038/ncomms7753

Sancar C, Sancar G, Ha N, Cesbron F, Brunner M (2015) Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora. BMC Biol. Feb 24;13(1):17

Hoffmann J, Symul L, Shostak A, Fischer T, Naef F, Brunner M (2014) Non-circadian expression masking clock-driven weak transcription rhythms in U2OS cells. PLoS One 9: e102238

Lauinger L, Diernfellner A, Falk S, Brunner M (2014) The RNA helicase FRH is an ATP-dependent regulator of CK1a in the circadian clock of Neurospora crassa. Nat Commun 5: 3598

Lee CT, Malzahn E, Brunner M, Mayer MP (2014) Light-induced differences in conformational dynamics of the circadian clock regulator VIVID. J Mol Biol 426: 601-610

Ruger-Herreros C, Gil-Sanchez Mdel M, Sancar G, Brunner M, Corrochano LM (2014) Alteration of light-dependent gene regulation by the absence of the RCO-1/RCM-1 repressor complex in the fungus Neurospora crassa. PLoS One 9: e95069

Sancar G, Brunner M (2014) Circadian clocks and energy metabolism. Cell Mol Life Sci 71: 2667-2680

Cesbron F., Brunner M., Diernfellner A.C.R. (2013) Light-dependent and circadian transcription dynamics in vivo recorded with a destabilized luciferase reporter in Neurospora. PLoS One 8 (12), e83660.

Gin E., Diernfellner A.C.R., Brunner, M., Höfer T. (2013) The Neurospora photoreceptor VIVID exerts negative and positive control on light sensing to achieve adaptation. Mol Syst Biol. 28:9, 667.


Sancar, G., Sancar, C. and Brunner, M. (2012) Metabolic compensation of the Neurospora clock by a glucose-dependent feedback of the circadian repressor CSP1 on the core oscillator. Genes Dev 26, 2435-2442.

Tataroglu O., Lauinger L., Sancar G., Jakob K., Brunner M., Diernfellner A.C. (2012) Glycogen Synthase Kinase is a regulator of the circadian clock of Neurospora crassa. J Biol Chem 287, 36936-36943.

Diernfellner, A.C.R. and Brunner, M. (2012) O-GlcNAcylation of a circadian clock protein: dPER taking its sweet time. Genes Dev 226, 415-416.

Merrow M. and Brunner M. (eds.) (2011) Special Issue: Circadian Rhythms. FEBS Lett 585.

Querfurth, C., Diernfellner, A.C.R., Gin, E., Höfer, T. and Brunner M. (2011) Circadian conformational change of the Neurospora clock protein FREQUENCY triggered by clustered hyperphosphorylation of a basic domain. Mol Cell 43, 713-722.

Sancar, G., Sancar C., Brügger, B., Ha, N. Sachsenheimer, T., Gin, E., Wdowik, S., Lohmann, I., Wieland, F., Hoefer, T., Diernfellner, A. and Brunner, M. (2011) A global circadian repressor controls anti-phasic expression of metabolic genes in Neurospora. Mol. Cell 44, 687-697.

Schafmeier T. and Diernfellner A.C.R. (2011) Light input and processing in
the circadian clock of Neurospora. FEBS Lett 585, 1467-73.

Diernfellner, A.C.R. and Schafmeier, T. (2011) Phosphorylations: making the
Neurospora crassa circadian clock tick. FEBS Lett 585, 1461-66.

Rey, G., Cesbron, F., Rougemont, J., Reinke, H., Brunner, M. and Naef, F.
(2011) Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control
circadian output functions in mouse liver. PLoS Biol. 9:e1000595.

Tataroğlu, O. and Schafmeier, T. (2010) Of switches and hourglasses:
regulation of subcellular traffic in circadian clocks by phosphorylation.
EMBO reports 12, 927-935.

Malzahn, E., Ciprianidis S., Kaldi, K., Schafmeier, T. and Brunner, M. (2010)
Photoadaptation in Neurospora by competitive interaction of activating and
inhibitory LOV domains. Cell 142, 762-772.

Smith, K.M., Sancar, G., Dekhang, R., Sullivan, C.M., Li, S., Tag, A.G., Sancar, C., Bredeweg, E.L., Priest, H.D., Mccormick, R.F., Thomas, T.L., Carrington J.C., Stajich, J.E., Bell-Pedersen, D., Brunner, M. and Freitag, M. (2010) Transcription factors in light and circadian clock signaling networks revealed by genome-wide mapping of direct targets for neurospora white collar complex. Eukaryot Cell 9, 1549-1556.

Diernfellner, A.C.R., Querfurth, C., Salazar, C., Höfer, T., Brunner, M. (2009) Phosphorylation modulates rapid nucleo-cytoplasmic shuttling and cytoplasmic accumulation of Neurospora clock protein FRQ on a
circadian time scale. Genes Dev 23, 2192-2200.

Sancar, G, Sancar, C, Brunner M and Schafmeier, T (2009) Activity of the
circadian transcription factor White Collar Complex is modulated by
phosphorylation of SP-motifs. FEBS Lett 583, 1833-1840.

Schafmeier, T, Diernfellner, A, Schäfer, A, Dintsis, O, Neiss, A, and
Brunner, M (2008) Circadian activity and abundance rhythms of the Neurospora
clock transcription factor WCC associated with rapid nucleo-cytoplasmic
shuttling. Genes Dev 22, 3397-3402.

Neiss, A, Schafmeier, T and Brunner, M (2008) Transcriptional regulation and function of the Neurospora clock gene white collar-2 and its isoforms. EMBO reports 9, 788-794.

Brunner M, Simons MJP, Merrow M (2008) Lego clocks: building a clock from parts. Genes Dev 22, 1422-1426.

Brunner, M and Merrow, M (2008) The green yeast uses its plant-like clock to
regulate its animal-like tail. Genes Dev 22, 825-831.

Brunner M and Káldi K (2008) Interlocked feedback loops of the circadian
clock of Neurospora crassa. Mol Microbiol 68, 255-262.

Diernfellner A, Colot HV, Dintsis O, Loros JJ, Dunlap JC, Brunner M (2007) Long and short isoforms of Neurospora clock protein FRQ support temperature-compensated circadian rhythms. FEBS Lett, 581, 5759-64.

Querfurth, C, Diernfellner, A, Heise, F, Lauinger, L, Neiss, A, Tataroglu, Ö, Brunner, M and Schafmeier, T (2007) Posttranslational Regulation of Neurospora Circadian Clock by CK1a-dependent Phosphorylation. Cold Spring Harbor Symp Quant Biol LXXII 72: 177-183.

Brunner, M and Diernfellner, A (2006) How temperature affects the circadian clock of Neurospora crassa. Chronobiol Int 23, 81-90.

Brunner, M and Schafmeier, T (2006) Transcriptional and post-transcriptional regulation of the circadian clock of cyanobacteria and Neurospora. Genes Dev 20, 1061-1074.

Schafmeier, T, Káldi, K, Diernfellner, A, Mohr, CA and Brunner, M (2006) Phosphorylation dependent maturation of Neurospora circadian clock protein from a nuclear repressor towards a cytoplasmic activator. Genes Dev 20, 297-306.

Káldi, K, Herreros González, B and Brunner, M (2006) A positive feedback loop of the Neurospora circadian clock gene wc-1 modulates the phase of circadian output. EMBO reports 7, 199-204.

Diernfellner, ACR, Schafmeier, T, Merrow, MW and Brunner, M (2005) Molecular mechanism of temperature-sensing by the circadian clock of Neurospora crassa. Genes Dev 19, 1968-1973 [Abstract]

Schafmeier, T, Haase, A, Káldi, K, Scholz, J, Fuchs, M and Brunner, M (2005) Transcriptional feedback of Neurospora circadian clock gene by phosphorylation-dependent inactivation of its transcription factor. Cell 122, 235-246[Abstract]

Okamoto, K, Brinker, A, Moarefi, I, Hayer-Hartl, M, Neupert, W and Brunner, M (2002) Unfolding of Preproteins by the Mitochondrial Import Motor: Evidence for a Brownian Ratchet Mechanism. EMBO J 21, 3659-3671.

Moro, F, Okamoto, K, Donzeau, M, Neupert, W and Brunner, M (2002) Mitochondrial protein import: Molecular basis of the ATP-dependent interaction of mt-Hsp70 with Tim44. J Biol Chem 277, 6874-6880.

Görl, M, Merrow, M, Huttner, B, Johnson, J, Roenneberg, T and Brunner, M (2001) A PEST-like element in FREQUENCY determines the length of the circadian period in Neurospora crassa. EMBO J 20, 7074-7084.

Rothbauer, U, Hofmann, S, Mühlenbein, N, Paschen, SA, Gerbitz, KD, Neupert, W, Brunner, M and Bauer, MF (2001) Role of the DDP1-hTim13 complex in import of human Tim23 into the inner membrane of mitochondria. J Biol Chem 276, 37327-37334.

Milisav, I, Moro, F, Neupert, W and Brunner, M (2001) Modular structure of the TIM23 preprotein translocase of mitochondria. J Biol Chem 276, 25856-25861.

Merrow, M, Franchi, L, Dragovic, Z, Görl, M, Johnson, J, Brunner, M, Macino, G and Roenneberg, T (2001) Circadian Regulation of the Light Input Pathway in Neurospora crassa. EMBO J 20, 307-315.

Paschen, SA, Rothbauer, U, Káldi, K, Bauer, MF, Neupert, W and Brunner, M (2000) The role of the TIM8/13 complex in the import of Tim23 into mitochondria. EMBO J 19, 6392-6400.

Bauer MF Paschen SA, Neupert W and Brunner M (2000) Mechanisms of mitochondrial protein import. Protoplasma 213, 1-10.

Donzeau, M, Káldi, K, Adam, A, Paschen, SA, Wanner, G, Guiard, B, Bauer, MF, Neupert, W and Brunner, M (2000) TIM 23 Links the Inner and Outer Mitochondrial Membranes. Cell 101, 401-412.

Bauer, MF, Hofmann, S, Neupert, W and Brunner, M (2000) Protein translocation into mitochondria: the role of TIM complexes. Trends Cell Biol 10, 25-31.

Bauer, MF, Rothbauer, U, Muhlenbein, N, Smith, RJH, Gerbitz, KD, Neupert, W, Brunner, M and Hofmann, S (1999) The mitochondrial TIM22 preprotein translocase is highly conserved throughout the eukaryotic kingdom. FEBS Lett 464, 41-47.

Moro, F, Sirrenberg, C, Schneider, C, Neupert, W and Brunner, M The Tim17-23 preprotein translocase of mitochondria: composition and function in protein transport into the matrix. EMBO J 18, 3667-3675.

Endres, M, Neupert, W and Brunner, M (1999) Transport of the ADP/ATP carrier of mitochondria from the TOM complex to the TIM22_54 complex. EMBO J 18, 3214-3221.

Hofmann, S, Gempel, K, Reichert, A, Lichtner, P, Gerbitz, K-D, Neupert, W, Brunner, M and Bauer, MF (1999) Genetic and structural characterization of the human mitochondrial inner membrane translocase. J Mol Biol 289, 69-82.

Merrow, M, Brunner, M and Roenneberg, T (1999) Novel assignment of circadian function for the Neurospora clock gene frequency. Nature 399, 584-586.

Adam, A, Endres, M, Sirrenberg, C, Lottspeich, F, Neupert, W and Brunner, M (1999) Tim9, a new component of the TIM22-54 translocase in mitochondria. EMBO J 18, 313-319.

Bauer, MF, Künkele, K-P, Neupert, W and Brunner, M (1998) Proteine auf Reisen. Einsichten 2, 14-17.

Fölsch, H, Gaume, B, Brunner, M, Neupert, W and Stuart, RA (1998) C-terminal to N-terminal translocation of preproteins into mitochondria. EMBO J 17, 6508-6515.

Gaume, B, Klaus, C Ungermann, C, Guiard, B, Neupert, W and Brunner, M (1998) Unfolding of preproteins upon import into mitochondria. EMBO J 17, 6497-6507.

Kaldi, C, Bauer, MF, Sirrenberg, C, Neupert, W and Brunner, M (1998) Biogenesis of Tim23 and Tim17, integral components of the TIM machinery for matrix targeted preproteins. EMBO J 17, 1569-1576.

Rapaport, D, Brunner, M, Neupert, W and Westermann, B (1998) Fzo1p is a mitochondrial outer membrane protein essential for the biogenesis of functional mitochondria in Saccharomyces cerevisiae. J Biol Chem 273, 20150-20155.

Sirrenberg, C, Endres, M, FÖlsch, H, Stuart, RA, Neupert, W and Brunner, M (1998) Carrier protein import into mitochondria mediated by the intermembrane proteins Tim10/Mrs11 and Tim12/Mrs5. Nature 391, 912-915.

Sirrenberg, C, Endres, M, Becker, K, Bauer, MF, Walther, E, Neupert, W and Brunner, M (1997) Functional cooperation and stoichiometry of protein translocases of the outer and inner membranes of mitochondria. J Biol Chem 272, 29963-29966.

Arnold, I, Bauer, MF, Brunner, M Neupert, W and Stuart, R (1997) Yeast mitochondrial F1F0-ATPase: The novel subunit e is identical to Tim11. FEBS Lett 411, 195-200.

Bauer, MF, Sirrenberg, C, Neupert, W and Brunner, M (1996) Role of Tim23 as voltage sensor and presequence receptor in protein import into mitochondria. Cell 87, 33-41.

Klaus, C, Guiard, B, Neupert, W and Brunner, M (1996) Determinants in the presequence of cytochrome b2 for import and for proteolytic processing. Eur J Biochem 236, 856-861.

Schneider, H-C, Berthold, J, Bauer, MF, Klaus, C, Neupert, W and Brunner, M (1996) Protein import across the inner mitochondrial membrane. NATO ASI Series H96, 157-165.

Schneider, H-C, Westermann, B, Neupert, W and Brunner, M (1996) The nucleotide exchange factor MGE exerts a key function in the ATP-dependent cycle of mt-Hsp70-Tim44 interaction driving mitochondrial protein import. EMBO J 15, 5796-5803.

Sirrenberg, C, Bauer, MF, Guiard, B, Neupert, W and Brunner, M (1996) Import of carrier proteins into the mitochondrial inner membrane mediated by Tim22. Nature 384, 582-585.

Berthold, J, Bauer, MF, Schneider, H-C, Klaus, C, Dietmeier, K, Neupert, W and Brunner, M (1995) The MIM complex mediates preprotein translocation across the mitochondrial inner membrane and couples it to the mt-Hsp70/ATP driving system. Cell 81, 1085-1093.

Brunner, M and Neupert, W (1995) Purification and characterization of the mitochondrial processing peptidase of Neurospora crassa. Meth Enzymol 248, 325-342.

Brunner, M, Schneider, HC, Lill, R and Neupert, W (1995) Dissection of protein translocation across the mitochondrial outer and inner membranes. Cold Spring Harbor Symp LX, 619-627.

Arretz, M, Schneider, H, Guiard, B, Brunner, M and Neupert, W (1994) Characterization of the mitochondrial processing peptidase of Neurospora crassa. J Biol Chem , 269, 464-467.

Bassham, DC, Creighton, AM, Arretz, M, Brunner, M and Robinson, C (1994) Efficient but aberrant cleavage of mitochondrial precursor proteins by the chloroplast stromal processing peptidase. Eur J Biochem 221, 523-528.

Brunner, M, Klaus, C and Neupert, W (1994) The mitochondrial processing peptidase. In Heijne, G (ed) Signal Peptidases, RG Landes Comp, 73-86.

Brunner, M and Whiteheart, SW (1994) Mammalian Proteins involved in membrane traffic in the Golgi and to the cell surface - SNAP. In Rothblatt, J, Novick, P and Stevens, T (eds) Guidebook to the secretory pathway, Sambrook and Tooze publication at Oxford University press, 180-181.

Schneider, H-C, Berthold, J, Bauer, M, Dietmeier, K, Guiard, B, Brunner, M and Neupert, W (1994) Mitochondrial Hsp70/MIM44 complex facilitates import. Nature 371, 768-774.

Whiteheart, SW, Rossnagel, K, Buhrow, SA, Brunner, M, Jaenicke, R and Rothman, JE (1994) NSF: A trimeric ATPase whose hydrolysis of ATP is required for membrane fusion. J Biol Chem 126, 945-954.

Whiteheart, SW, Griff, I, Brunner, M, Clary, DO, Mayer, T, Buhrow, SA and Rothman, JE (1993) SNAP family of NSF attachment proteins includes a brain-specific isoform. Nature 1993 362, 353-355.

Söllner, T, Whiteheart, SW, Brunner, M, Erdjument-Bromage, H, Geromanos, S, Tempst, P and Rothman, JE (1993) SNAP receptors implicated in vesicle targetting and fusion. Nature 362, 318-324.

Tagaya, M Whiteheart, SW, Brunner, M, Arango, N and Rothman, JE (1993) Domain structure of N-ethylmaleimide-sensitive fusion protein involved in vesicular transport. J Biol Chem 268, 2662-2666.

Whiteheart, SW, Brunner, M, Wilson, DW, Wiedmann, M and Rothman, JE (1992) Soluble N-ethylmaleimide-sensitive fusion attachment proteins (SNAPs) bind to a multi-SNAP receptor complex in Golgi membranes. J Biol Chem 267 12239-12243.

Wilson, DW, Whiteheart, SW, Wiedmann, M, Brunner, M and Rothman, JE (1992) A multisubunit particle implicated in membrane fusion. J Cell Biol 117, 531-538.

Serafini, T, Orci, L, Amherdt, M, Brunner, M, Kahn, RA and Rothman, JE (1991) ADP-ribosylation factor is a subunit of the coat of Golgi-derived COP-coated vesicles: A novel role for a GTP-binding protein. Cell 67, 239-253.

Brunner, M and Bujard, H (1987) Promoter recognition and promoter strength in Escherichia coli. EMBO J 6, 3139-3144.

Bujard, H, Brunner, M Deuschle, U, Kammerer, W and Knaus, R (1987) Structure-function relationship of Ecoli promoters. In Reznikoff WE (ed) RNA-polymerase and regulation of transcription, Elsevier Scientific Publishing Co