69. Studt L, Rosler SM, Burkhardt I, Arndt B, Freitag M, Humpf HU, et al. Knockdown of the methyltransferase Kmt6 relieves H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi. *Environ Microbiol.* 2016;18(11):4037–54.

70. Janevska S, Güldener U, Sulyok M, Tudzynski B, Studt L. Set1 and Kdm5 are antagonists for H3K4 methylation and regulators of the major conidiation-specific transcription factor gene *ABA1* in *Fusarium fujikuroi*. *Environ Microbiol.* 2018;20(9):3343–62.

71. Venkatasubrahmanyam S, Hwang WW, Meneghini MD, Tong AHY, Madhani HD. Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. *Proceedings of the National Academy of Sciences.* 2007;104(42):16609–14.

72. Creighton MP, Markoulaki S, Levine SS, Hanna J, Lodato MA, Sha K, et al. H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. *Cell.* 2008;135(4):649–61.

73. Illingworth RS, Botting CH, Grimes GR, Bickmore WA, Eskeland R. PRC1 and PRC2 are not required for targeting of H2A.Z to Developmental genes in embryonic stem cells. *PLoS ONE.* 2012;7(4):e34848.

74. Yu H, Wang J, Lackford B, Bennett B, Li J-L, Hu G. INO80 promotes H2A.Z occupancy to regulate cell fate transition in pluripotent stem cells. *Nucleic Acids Res.* 2021;49(12):e6739–55.

75. Santisteban MS, Kalashnikova T, Smith MM. Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. *Cell.* 2000;103(3):411–22.

76. Krijgsheld P, Bleichrodt R-J, van Veluw GJ, Wang FW, Müller WH, Dijksterhuis J, et al. Development in *Aspergillus*. *Study Mycol.* 2012;74:1–29.

77. Keller NP. Fungal secondary metabolism: regulation, function and drug discovery. *Nat Rev Microbiol.* 2019;17(3):167–80.

78. Niehaus E-M, Janevska S, Von Bargen KW, Sieber CMK, Harrer H, Humpf H-U, et al. Apicidin F: characterization and genetic manipulation of a new secondary metabolite gene cluster in the Rice Pathogen Fusarium fujikuroi. *PLoS ONE.* 2014;9(7):e103336.

79. Niehaus EM, Studt L, von Bargen KW, Kummer W, Humpf HU, Reuter G, et al. Sound of silence: the beauvericin cluster in *Fusarium fujikuroi* is controlled by cluster-specific and global regulators mediated by H3K27 modification. *Environ Microbiol.* 2016;18(11):4282–302.

80. Wiemann P, Willmann A, Straeten M, Kleigrewe K, Beyer M, Humpf H-U, et al. Biosynthesis of the red pigment bikaverin in *Fusarium fujikuroi*: genes, their function and regulation. *Mol Microbiol.* 2009;72(4):931–46.

81. Linnemannstöns P, Schulte J, Del Mar Prado M, Proctor RH, Avalos J, Tudzynski B. The polyketide synthase gene pks4 from *Gibberella fujikuroi* encodes a key enzyme in the biosynthesis of the red pigment bikaverin. *Fungal Genet Biol.* 2002;37(2):134–48.

82. Mihlan M, Homann V, Liu TW, Tudzynski B. AREA directly mediates nitrogen regulation of gibberellin biosynthesis in *Gibberella fujikuroi*, but its activity is not affected by NMR. *Mol Ecular Microbiol ogy.* 2003;47(4):975–91.

83. Linnemannstöns P, Voss T, Hedden P, Gaskin P, Tudzynski B. Deletions in the gibberellin biosynthesis gene cluster of *Gibberella fujikuroi* by restriction. enzyme-mediated integration and conventional transformation-mediated mutagenesis. *Appl Environ Microbiol.* 1999;65(6):2558–64.

84. Pontecorvo G, Roper JA, Hemmons LM, Macdonald KD, Bufton A. The genetics of aspergillus nidulans. *Adv Genet.* 1953;5:141–238.

85. Geissman TA, Verbiscar AJ, Phinney BO, Cragg GM. Studies on the biosynthesis of gibberellins from (–)-kaurenoic acid in cultures of *Gibberella fujikuroi*. *Phytochemistry.* 1966;5:933–47.

86. Darken MA, Jensen AL, Shu P. Production of gibberellic acid by fermentation. *Appl Microbiol.* 1959;7:301–3.

87. Janevska S, Arndt B, Baumann L, Apken L, Mauriz Marques L, Humpf H-U, et al. Establishment of the Inducible Tet-On System for the activation of the Silent Trichosetin Gene Cluster in *Fusarium fujikuroi*. *Toxins.* 2017;9(4):126–37.

88. Schumacher J. Tools for Botrytis Cinerea: new expression vectors make the gray mold fungus more accessible to cell biology approaches. *Fungal Genet Biol.* 2012;49(6):483–97.

89. Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, et al. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. *Proc Natl Acad Sci.* 2006;103(27):10352–7.

90. Staben C, Jensen B, Singer M, Pollock J, Schechtman M, Kinsey J et al. Use of a bacterial hygromycin B resistance gene as a dominant selectable marker in *Neurospora crassa* transformation. *Fungal Genetics Reports.* 1989;36 (22).

91. Christianson TW, Sikorski RS, Dante M, Shero JH, Hieter P. Multifunctional yeast high-copy-number shuttle vectors. *Gene.* 1992;110(1):119–22.

92. Winston F, Dollard C, Ricuperohovasse SL. Construction of a set of convenient *Saccharomyces cerevisiae* strains that are isogenic to S288C. *Yeast.* 1995;11(1):53–5.

93. Tudzynski B, Homann V, Feng B, Marzluf GA. Isolation, characterization and disruption of the *ara* nitrogen regulatory gene of *Gibberella fujikuroi*. *Mol Gen Genet.* 1999;261(1):106–14.

94. Cenis JL. Rapid extraction of fungal DNA for PCR amplification. *Nucleic Acids Res.* 1992;20(9):2380.

95. Atanasoff-Kardjalieff AK, Lünne F, Kalinina S, Strauss J, Humpf H-U, Studt L. Biosynthesis of Fusapyrone depends on the H3K9 methyltransferase, FmKmt1, in *Fusarium mangiferae*. *Front Fungal Biology.* 2021;2.

96. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. *Nucleic Acids Res.* 2001;29(9):45e.

97. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. *Bioinformatics.* 2014;30:2114–20.

98. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. *Bioinformatics.* 2009;25:1754–60.

99. Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. *Bioinformatics.* 2014;31:166–9.

100. Law CW, Chen Y, Shi W, Smyth GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. *Genome Biol.* 2014;15:R29–R.

101. Edgar R, Domrachev M, Lash AE. Gene expression Omnibus: NCBI gene expression and hybridization array data repository. *Nucleic Acids Res.* 2002;30(1):207–10.

102. Törönen P, Medlar A, Holm L. PANNZER2: a rapid functional annotation web server. *Nucleic Acids Res.* 2018;46:W84–W8.

103. Studt L, Janevska S, Arndt B, Boedi S, Sulyok M, Humpf HU, et al. Lack of the COMPASS component Ccl1 reduces H3K4 trimethylation levels and affects transcription of secondary metabolite genes in two plant-pathogenic fusarium species. *Front Microbiol.* 2016;7:2144.

104. Lawrence MF, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R et al. Software for Computing and Annotating genomic ranges. *PLoS Comput Biol.* 2013;9.

105. Pagès H, Aboyoun P, Gentleman R, DebRoy S, Biostrings. Efficient manipulation of biological strings 2023 [Available from: https://bioconductor.org/packages/Biostrings].

106. Schüller A, Wolansky L, Berger H, Studt L, Gacek-Matthews A, Sulyok M, et al. A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning. *Appl Microbiol Biotechnol.* 2020;104:9801–22.

107. Adams KJ, Pratt B, Bose N, Dubois LG, St. John-Williams L, Perrott KM, et al. Skyline for Small molecules: a Unifying Software Package for quantitative metabolomics. *J Proteome Res.* 2020;19(4):1447–58.

## Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
69. Studt L, Rosler SM, Burkhardt I, Arndt B, Freitag M, Humpf HU, et al. Knockdown of the methyltransferase Kmt6 relieves H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi. *Environ Microbiol.* 2016;18(11):4037–54.

70. Janevska S, Güldener U, Sulyok M, Tudzynski B, Studt L. Set1 and Kdm5 are antagonists for H3K4 methylation and regulators of the major conidiation-specific transcription factor gene *ABA1* in *Fusarium fujikuroi*. *Environ Microbiol.* 2018;20(9):3343–62.

71. Venkatasubrahmanyam S, Hwang WW, Meneghini MD, Tong AHY, Madhani HD. Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. *Proceedings of the National Academy of Sciences.* 2007;104(42):16609–14.

72. Creighton MP, Markoulaki S, Levine SS, Hanna J, Lodato MA, Sha K, et al. H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. *Cell.* 2008;135(4):649–61.

73. Illingworth RS, Botting CH, Grimes GR, Bickmore WA, Eskeland R. PRC1 and PRC2 are not required for targeting of H2A.Z to Developmental genes in embryonic stem cells. *PLoS ONE.* 2012;7(4):e34848.

74. Yu H, Wang J, Lackford B, Bennett B, Li J-L, Hu G. INO80 promotes H2A.Z occupancy to regulate cell fate transition in pluripotent stem cells. *Nucleic Acids Res.* 2021;49(12):e6739–55.

75. Santisteban MS, Kalashnikova T, Smith MM. Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. *Cell.* 2000;103(3):411–22.

76. Krijgsheld P, Bleichrodt R-J, van Veluw GJ, Wang FW, Müller WH, Dijksterhuis J, et al. Development in *Aspergillus*. *Stud Mycol.* 2012;74:1–29.

77. Keller NP. Fungal secondary metabolism: regulation, function and drug discovery. *Nat Rev Microbiol.* 2019;17(3):167–80.

78. Niehaus E-M, Janevska S, Von Bargen KW, Sieber CMK, Harrer H, Humpf H-U, et al. Apicidin F: characterization and genetic manipulation of a new secondary metabolite gene cluster in the Rice Pathogen Fusarium fujikuroi. *PLoS ONE.* 2014;9(7):e103336.

79. Niehaus EM, Studt L, von Bargen KW, Kummer W, Humpf HU, Reuter G, et al. Sound of silence: the beauvericin cluster in *Fusarium fujikuroi* is controlled by cluster-specific and global regulators mediated by H3K27 modification. *Environ Microbiol.* 2016;18(11):4282–302.

80. Wiemann P, Willmann A, Straeten M, Kleigrewe K, Beyer M, Humpf H-U, et al. Biosynthesis of the red pigment bikaverin in *Fusarium fujikuroi*: genes, their function and regulation. *Mol Microbiol.* 2009;72(4):931–46.

81. Linnemannstöns P, Schulte J, Del Mar Prado M, Proctor RH, Avalos J, Tudzynski B. The polyketide synthase gene pks4 from *Gibberella fujikuroi* encodes a key enzyme in the biosynthesis of the red pigment bikaverin. *Fungal Genet Biol.* 2002;37(2):134–48.

82. Mihlan M, Homann V, Liu TW, Tudzynski B. AREA directly mediates nitrogen regulation of gibberellin biosynthesis in *Gibberella fujikuroi*, but its activity is not affected by NMR. *Mol Ecular Microbiol ogy.* 2003;47(4):975–91.

83. Linnemannstöns P, Voss T, Hedden P, Gaskin P, Tudzynski B. Deletions in the gibberellin biosynthesis gene cluster of *Gibberella fujikuroi* by restriction. enzyme-mediated integration and conventional transformation-mediated mutagenesis. *Appl Environ Microbiol.* 1999;65(6):2558–64.

84. Pontecorvo G, Roper JA, Hemmons LM, Macdonald KD, Bufton A. The genetics of aspergillus nidulans. *Adv Genet.* 1953;5:141–238.

85. Geissman TA, Verbiscar AJ, Phinney BO, Cragg GM. Studies on the biosynthesis of gibberellins from (–)-kaurenoic acid in cultures of *Gibberella fujikuroi*. *Phytochemistry.* 1966;5:933–47.

86. Darken MA, Jensen AL, Shu P. Production of gibberellic acid by fermentation. *Appl Microbiol.* 1959;7:301–3.

87. Janevska S, Arndt B, Baumann L, Apken L, Mauriz Marques L, Humpf H-U, et al. Establishment of the Inducible Tet-On System for the activation of the Silent Trichosetin Gene Cluster in *Fusarium fujikuroi*. *Toxins.* 2017;9(4):126.

88. Schumacher J. Tools for Botrytis Cinerea: new expression vectors make the gray mold fungus more accessible to cell biology approaches. *Fungal Genet Biol.* 2012;49(6):483–97.

89. Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, et al. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. *Proc Natl Acad Sci.* 2006;103(27):10352–7.

90. Staben C, Jensen B, Singer M, Pollock J, Schechtman M, Kinsey J et al. Use of a bacterial hygromycin B resistance gene as a dominant selectable marker in *Neurospora crassa* transformation. *Fungal Genetics Reports.* 1989;36 (22).

91. Christianson TW, Sikorski RS, Dante M, Shero JH, Hieter P. Multifunctional yeast high-copy-number shuttle vectors. *Gene.* 1992;110(1):119–22.

92. Winston F, Dollard C, Ricuperohovasse SL. Construction of a set of convenient *Saccharomyces cerevisiae* strains that are isogenic to S288C. *Yeast.* 1995;11(1):53–5.

93. Tudzynski B, Homann V, Feng B, Marzluf GA. Isolation, characterization and disruption of the *ara* nitrogen regulatory gene of *Gibberella fujikuroi*. *Mol Gen Genet.* 1999;261(1):106–14.

94. Cenis JL. Rapid extraction of fungal DNA for PCR amplification. *Nucleic Acids Res.* 1992;20(9):2380.

95. Atanasoff-Kardjalieff AK, Lünne F, Kalinina S, Strauss J, Humpf H-U, Studt L. Biosynthesis of Fusapyrone depends on the H3K9 methyltransferase, FmKmt1, in *Fusarium mangiferae*. *Front Fungal Biology.* 2021;2.

96. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. *Nucleic Acids Res.* 2001;29(9):45e.

97. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. *Bioinformatics.* 2014;30:2114–20.

98. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. *Bioinformatics.* 2009;25:1754–60.

99. Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. *Bioinformatics.* 2014;31:166–9.

100. Law CW, Chen Y, Shi W, Smyth GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. *Genome Biol.* 2014;15:R29–R.

101. Edgar R, Domrachev M, Lash AE. Gene expression Omnibus: NCBI gene expression and hybridization array data repository. *Nucleic Acids Res.* 2002;30(1):207–10.

102. Törönen P, Medlar A, Holm L. PANNZER2: a rapid functional annotation web server. *Nucleic Acids Res.* 2018;46:W84–W8.

103. Studt L, Janevska S, Arndt B, Boedi S, Sulyok M, Humpf HU, et al. Lack of the COMPASS component Ccl1 reduces H3K4 trimethylation levels and affects transcription of secondary metabolite genes in two plant-pathogenic fusarium species. *Front Microbiol.* 2016;7:2144.

104. Lawrence MF, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R et al. Software for Computing and Annotating genomic ranges. *PLoS Comput Biol.* 2013;9.

105. Pagès H, Aboyoun P, Gentleman R, DebRoy S, Biostrings. Efficient manipulation of biological strings 2023 [Available from: https://bioconductor.org/packages/Biostrings].

106. Schüller A, Wolansky L, Berger H, Studt L, Gacek-Matthews A, Sulyok M, et al. A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning. *Appl Microbiol Biotechnol.* 2020;104:9801–22.

107. Adams KJ, Pratt B, Bose N, Dubois LG, St. John-Williams L, Perrott KM, et al. Skyline for Small molecules: a Unifying Software Package for quantitative metabolomics. *J Proteome Res.* 2020;19(4):1447–58.

**Publisher's Note**

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.