Colognori D, Sunwoo H, Kriz AJ et al (2019) Xist Deletional analysis reveals an interdependency
between Xist RNA and Polycomb complexes for
spreading along the inactive X. Mol Cell 74:101–
117.e10
Connolly LR, Smith KM, Freitag M (2013) The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression
of secondary metabolite gene clusters. PLoS Genet
9:e1003916
Dang Y, Cheng J, Sun X et al (2016) Antisense transcription licenses nascent transcripts to mediate
transcriptional gene silencing. Genes Dev 30:2417–
2432
Dang Y, Li L, Guo W et al (2013) Convergent transcription induces dynamic DNA methylation at disiRNA loci. PLoS Genet 9:e1003761
Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science
295:1306–1311
Dickey JS, Redon CE, Nakamura AJ et al (2009) H2AX:
functional roles and potential applications. Chromosoma 118:683–692
Dong Q, Wang Y, Qi S et al (2018) Histone variant H2A.
Z antagonizes the positive effect of the transcriptional activator CPC1 to regulate catalase-3 expression under normal and oxidative stress conditions.
Free Radic Biol Med 121:136–148
Downs JA, Lowndes NF, Jackson SP (2000) A role for
Saccharomyces cerevisiae histone H2A in DNA
repair. Nature 408:1001–1004
Freitag M, Hickey PC, Khlafallah TK et al (2004a) HP1
is essential for DNA methylation in Neurospora.
Mol Cell 13:427–434
Freitag M, Lee DW, Kothe GO et al (2004b) DNA methylation is independent of RNA interference in
Neurospora. Science 304:1939
Freitag M, Williams RL, Kothe GO, Selker EU (2002) A
cytosine methyltransferase homologue is essential
for repeat-induced point mutation in Neurospora
crassa. Proc Natl Acad Sci U S A 99:8802–8807
Gacek-Matthews A, Berger H, Sasaki T et al (2016)
KdmB, a Jumonji histone H3 Demethylase, regulates genome-wide H3K4 trimethylation and is
required for normal induction of secondary
metabolism in Aspergillus nidulans. PLoS Genet
12:e1006222
Gacek-Matthews A, Noble LM, Gruber C et al (2015)
KdmA, a histone H3 demethylase with bipartite
function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. Mol
Microbiol 96:839–860
Galagan JE, Calvo SE, Borkovich KA et al (2003) The
genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859–868
Galagan JE, Selker EU (2004) RIP: the evolutionary cost
of genome defense. Trends Genet 20:417–423
Galazka JM, Klocko AD, Uesaka M et al (2016) Neurospora chromosomes are organized by blocks of
importin alpha-dependent heterochromatin that
are largely independent of H3K9me3. Genome
Res 26:1069–1080
Gessaman JD, Selker EU (2017) Induction of H3K9me3
and DNA methylation by tethered heterochromatin factors in. Proc Natl Acad Sci U S A 114:E9598–
E9607
Gladyshev E (2017) Repeat-induced point mutation and
other genome defense mechanisms in fungi.
Microbiol Spectr 5:FUNK-0042-2017. https://doi.
org/10.1128/microbiolspec.FUNK-0042-2017
Gladyshev E, Kleckner N (2017) DNA sequence homology induces cytosine-to-thymine mutation by a
heterochromatin-related pathway in Neurospora.
Nat Genet 49:887–894
Gong F, Chiu L-Y, Miller KM (2016) Acetylation reader
proteins: linking acetylation signaling to genome
maintenance and cancer. PLoS Genet 12:e1006272
Grewal SIS, Jia S (2007) Heterochromatin revisited. Nat
Rev Genet 8:35–46
Grimaldi B, Coiro P, Filetici P et al (2006) The Neurospora crassa White Collar-1 dependent blue light
response requires acetylation of histone H3 lysine
14 by NGF-1. Mol Biol Cell 17:4576–4583
Grimbergen AJ, Siebring J, Solopova A, Kuipers OP
(2015) Microbial bet-hedging: the power of being
different. Curr Opin Microbiol 25:67–72
Gu Q, Ji T, Sun X et al (2017) Histone H3 lysine 9
methyltransferase FvDim5 regulates fungal development, pathogenicity and osmotic stress
responses in Fusarium verticillioides. FEMS Microbiol Lett 364. https://doi.org/10.1093/femsle/fnx184
He M, Xu Y, Chen J et al (2018) MoSnt2-dependent
deacetylation of histone H3 mediates MoTordependent autophagy and plant infection by the
rice blast fungus Magnaporthe oryzae. Autophagy
14:1543–1561
Heitz E (1928) Das Heterochromatin der Moose
Henikoff S, Smith MM (2015) Histone variants and
epigenetics. Cold Spring Harb Perspect Biol 7:
a019364
Henriksen MA (2007) Epigenetics. In: Allis CD, Jenuwein T, Reinberg D, Caparros M-L (eds) The quarterly review of biology, vol 82. Cold Spring Harbor
Laboratory Press, New York, pp 416–416. $150.00.
x 502 p; ill.; index. ISBN: 0-87969-724-5. 2007
Honda S, Bicocca VT, Gessaman JD et al (2016) Dual
chromatin recognition by the histone deacetylase
complex HCHC is required for proper DNA methylation in Neurospora crassa. Proc Natl Acad Sci U
S A 113:E6135–E6144
Honda S, Lewis ZA, Huarte M et al (2010) The DMM
complex prevents spreading of DNA methylation
from transposons to nearby genes in Neurospora
crassa. Genes Dev 24:443–454
Honda S, Lewis ZA, Shimada K et al (2012) Heterochromatin protein 1 forms distinct complexes to direct
histone deacetylation and DNA methylation. Nat
Struct Mol Biol 19:471–477. S1
Honda S, Selker EU (2008) Direct interaction between
DNA methyltransferase DIM-2 and HP1 is
1 Chromatin Structure and Function in Neurospora crassa
21
between Xist RNA and Polycomb complexes for
spreading along the inactive X. Mol Cell 74:101–
117.e10
Connolly LR, Smith KM, Freitag M (2013) The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression
of secondary metabolite gene clusters. PLoS Genet
9:e1003916
Dang Y, Cheng J, Sun X et al (2016) Antisense transcription licenses nascent transcripts to mediate
transcriptional gene silencing. Genes Dev 30:2417–
2432
Dang Y, Li L, Guo W et al (2013) Convergent transcription induces dynamic DNA methylation at disiRNA loci. PLoS Genet 9:e1003761
Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science
295:1306–1311
Dickey JS, Redon CE, Nakamura AJ et al (2009) H2AX:
functional roles and potential applications. Chromosoma 118:683–692
Dong Q, Wang Y, Qi S et al (2018) Histone variant H2A.
Z antagonizes the positive effect of the transcriptional activator CPC1 to regulate catalase-3 expression under normal and oxidative stress conditions.
Free Radic Biol Med 121:136–148
Downs JA, Lowndes NF, Jackson SP (2000) A role for
Saccharomyces cerevisiae histone H2A in DNA
repair. Nature 408:1001–1004
Freitag M, Hickey PC, Khlafallah TK et al (2004a) HP1
is essential for DNA methylation in Neurospora.
Mol Cell 13:427–434
Freitag M, Lee DW, Kothe GO et al (2004b) DNA methylation is independent of RNA interference in
Neurospora. Science 304:1939
Freitag M, Williams RL, Kothe GO, Selker EU (2002) A
cytosine methyltransferase homologue is essential
for repeat-induced point mutation in Neurospora
crassa. Proc Natl Acad Sci U S A 99:8802–8807
Gacek-Matthews A, Berger H, Sasaki T et al (2016)
KdmB, a Jumonji histone H3 Demethylase, regulates genome-wide H3K4 trimethylation and is
required for normal induction of secondary
metabolism in Aspergillus nidulans. PLoS Genet
12:e1006222
Gacek-Matthews A, Noble LM, Gruber C et al (2015)
KdmA, a histone H3 demethylase with bipartite
function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. Mol
Microbiol 96:839–860
Galagan JE, Calvo SE, Borkovich KA et al (2003) The
genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859–868
Galagan JE, Selker EU (2004) RIP: the evolutionary cost
of genome defense. Trends Genet 20:417–423
Galazka JM, Klocko AD, Uesaka M et al (2016) Neurospora chromosomes are organized by blocks of
importin alpha-dependent heterochromatin that
are largely independent of H3K9me3. Genome
Res 26:1069–1080
Gessaman JD, Selker EU (2017) Induction of H3K9me3
and DNA methylation by tethered heterochromatin factors in. Proc Natl Acad Sci U S A 114:E9598–
E9607
Gladyshev E (2017) Repeat-induced point mutation and
other genome defense mechanisms in fungi.
Microbiol Spectr 5:FUNK-0042-2017. https://doi.
org/10.1128/microbiolspec.FUNK-0042-2017
Gladyshev E, Kleckner N (2017) DNA sequence homology induces cytosine-to-thymine mutation by a
heterochromatin-related pathway in Neurospora.
Nat Genet 49:887–894
Gong F, Chiu L-Y, Miller KM (2016) Acetylation reader
proteins: linking acetylation signaling to genome
maintenance and cancer. PLoS Genet 12:e1006272
Grewal SIS, Jia S (2007) Heterochromatin revisited. Nat
Rev Genet 8:35–46
Grimaldi B, Coiro P, Filetici P et al (2006) The Neurospora crassa White Collar-1 dependent blue light
response requires acetylation of histone H3 lysine
14 by NGF-1. Mol Biol Cell 17:4576–4583
Grimbergen AJ, Siebring J, Solopova A, Kuipers OP
(2015) Microbial bet-hedging: the power of being
different. Curr Opin Microbiol 25:67–72
Gu Q, Ji T, Sun X et al (2017) Histone H3 lysine 9
methyltransferase FvDim5 regulates fungal development, pathogenicity and osmotic stress
responses in Fusarium verticillioides. FEMS Microbiol Lett 364. https://doi.org/10.1093/femsle/fnx184
He M, Xu Y, Chen J et al (2018) MoSnt2-dependent
deacetylation of histone H3 mediates MoTordependent autophagy and plant infection by the
rice blast fungus Magnaporthe oryzae. Autophagy
14:1543–1561
Heitz E (1928) Das Heterochromatin der Moose
Henikoff S, Smith MM (2015) Histone variants and
epigenetics. Cold Spring Harb Perspect Biol 7:
a019364
Henriksen MA (2007) Epigenetics. In: Allis CD, Jenuwein T, Reinberg D, Caparros M-L (eds) The quarterly review of biology, vol 82. Cold Spring Harbor
Laboratory Press, New York, pp 416–416. $150.00.
x 502 p; ill.; index. ISBN: 0-87969-724-5. 2007
Honda S, Bicocca VT, Gessaman JD et al (2016) Dual
chromatin recognition by the histone deacetylase
complex HCHC is required for proper DNA methylation in Neurospora crassa. Proc Natl Acad Sci U
S A 113:E6135–E6144
Honda S, Lewis ZA, Huarte M et al (2010) The DMM
complex prevents spreading of DNA methylation
from transposons to nearby genes in Neurospora
crassa. Genes Dev 24:443–454
Honda S, Lewis ZA, Shimada K et al (2012) Heterochromatin protein 1 forms distinct complexes to direct
histone deacetylation and DNA methylation. Nat
Struct Mol Biol 19:471–477. S1
Honda S, Selker EU (2008) Direct interaction between
DNA methyltransferase DIM-2 and HP1 is
1 Chromatin Structure and Function in Neurospora crassa
21