of set-7 (kmt-6) did impact the 3D architecture
of Neurospora DNA, as monitored by Hi-C.
Namely, while the heterochromatin bundle
was still able to form in a Dset-7 strain, the
genome architecture of a Dset-7 strain showed
a decrease in contacts between intrachromosomal and interchromosomal subtelomeric
regions, as well as a moderate increase in contacts between centromeres and euchromatic
arms (Klocko et al. 2016). These changes
could be explained by the H3K27me2/3 subtelomeres becoming more detached from the
nuclear membrane. Indeed, microscopy of fluorescently labeled telomeres showed a greater
propensity of the telomere foci to be found in
the central part of the nucleus and less associated with the nuclear membrane (Klocko et al.
2016). In support, Hi-C of a strain lacking npf
(Neurospora P55), which causes the loss of only
subtelomeric H3K27me2/3, produced an almost
identical genome interaction map that supported sub-telomere detachment upon loss of
sub-telomeric facultative heterochromatin
(Klocko et al. 2016). Neurospora sub-telomeres
are unique in that these are the only genomic
loci in which both H3K9me3 and H3K27me2/3
co-localize in a wild-type strain; however,
removal of both histone marks in a Ddim-5;D
set-7 mutant did not exacerbate the telomere
detachment phenotype. Only a decrease in centromere flank interactions was evident in this
strain relative to a single Dset-7 mutant (Klocko
et al. 2016); this double mutant also refutes the
hypothesis that H3K27me2/3 relocalized to
centromeres in a Ddim-5 strain helps to maintain the heterochromatin bundle with compromised constitutive heterochromatin.
VI. Conclusions
Neurospora crassa has served as a powerful
model system for understanding chromatin
structure and function in fungi and in other
eukaryotes. Work in N. crassa has generated
important information about how chromatin
structure contributes to gene regulation within
euchromatin through studies of promoter
structure, DNA accessibility, activating epigenetic marks, and histone variants. Similarly, N.
crassa has played an important role in advancing our understanding of silent chromatin and
the factors necessary for its assembly and maintenance, from the permanent, or constitutive,
heterochromatin necessary to inactivate repetitive DNA to facultative heterochromatin that
silences a multitude of evolutionarily novel
genes. It is now, more than ever, clear that
chromatin—both activating and silencing—
impacts every genome function in the nucleus
from nucleotide base pairing to threedimensional organization of chromosomes. In
many ways, chromatin regulation in N. crassa
appears more complex than in the budding
yeast S. cerevisiae, primarily because a number
of key chromatin regulatory pathways are
absent from the Saccharomycotina. For this
reason, N. crassa is a more relevant model system for elucidating general principles and
mechanisms of chromatin structure in fungi
than the more extensively studied budding
yeast. Indeed, key discoveries in N. crassa
have motivated work in a number of other
fungal genera. Namely, work with species of
Aspergillus, Fusarium, Leptosphaeria, Magnaporthe, Zymoseptoria, and others has uncovered important roles for chromatin regulators
in secondary metabolite production and regulation of pathogenicity genes, highlighting the
need for future work [e.g., see Shwab et al. 2007;
Soukup et al. 2012; Palmer et al. 2013; Connolly
et al. 2013; Soyer et al. 2014; Gacek-Matthews
et al. 2015, 2016; Niehaus et al. 2016; Gu et al.
2017; Maeda et al. 2017; Janevska et al. 2018; He
et al. 2018; Pfannenstiel et al. 2018; Mo ¨ller et al.
2019; Lan et al. 2019; and others].
Despite a great deal of progress, many
important questions about chromatin structure
and function remain unanswered. Given the
importance of chromatin structure to fungal
pathogenesis and secondary metabolism, identification of chromatin-based mechanisms that
are fungal-specific could provide new avenues
to limit the economic costs of fungal disease
and crop contamination. A better understanding of chromatin regulatory processes could
also enable more efficient engineering of fungi
for biotechnology purposes. N. crassa is an
ideal experimental system to address key open
1 Chromatin Structure and Function in Neurospora crassa
19
of Neurospora DNA, as monitored by Hi-C.
Namely, while the heterochromatin bundle
was still able to form in a Dset-7 strain, the
genome architecture of a Dset-7 strain showed
a decrease in contacts between intrachromosomal and interchromosomal subtelomeric
regions, as well as a moderate increase in contacts between centromeres and euchromatic
arms (Klocko et al. 2016). These changes
could be explained by the H3K27me2/3 subtelomeres becoming more detached from the
nuclear membrane. Indeed, microscopy of fluorescently labeled telomeres showed a greater
propensity of the telomere foci to be found in
the central part of the nucleus and less associated with the nuclear membrane (Klocko et al.
2016). In support, Hi-C of a strain lacking npf
(Neurospora P55), which causes the loss of only
subtelomeric H3K27me2/3, produced an almost
identical genome interaction map that supported sub-telomere detachment upon loss of
sub-telomeric facultative heterochromatin
(Klocko et al. 2016). Neurospora sub-telomeres
are unique in that these are the only genomic
loci in which both H3K9me3 and H3K27me2/3
co-localize in a wild-type strain; however,
removal of both histone marks in a Ddim-5;D
set-7 mutant did not exacerbate the telomere
detachment phenotype. Only a decrease in centromere flank interactions was evident in this
strain relative to a single Dset-7 mutant (Klocko
et al. 2016); this double mutant also refutes the
hypothesis that H3K27me2/3 relocalized to
centromeres in a Ddim-5 strain helps to maintain the heterochromatin bundle with compromised constitutive heterochromatin.
VI. Conclusions
Neurospora crassa has served as a powerful
model system for understanding chromatin
structure and function in fungi and in other
eukaryotes. Work in N. crassa has generated
important information about how chromatin
structure contributes to gene regulation within
euchromatin through studies of promoter
structure, DNA accessibility, activating epigenetic marks, and histone variants. Similarly, N.
crassa has played an important role in advancing our understanding of silent chromatin and
the factors necessary for its assembly and maintenance, from the permanent, or constitutive,
heterochromatin necessary to inactivate repetitive DNA to facultative heterochromatin that
silences a multitude of evolutionarily novel
genes. It is now, more than ever, clear that
chromatin—both activating and silencing—
impacts every genome function in the nucleus
from nucleotide base pairing to threedimensional organization of chromosomes. In
many ways, chromatin regulation in N. crassa
appears more complex than in the budding
yeast S. cerevisiae, primarily because a number
of key chromatin regulatory pathways are
absent from the Saccharomycotina. For this
reason, N. crassa is a more relevant model system for elucidating general principles and
mechanisms of chromatin structure in fungi
than the more extensively studied budding
yeast. Indeed, key discoveries in N. crassa
have motivated work in a number of other
fungal genera. Namely, work with species of
Aspergillus, Fusarium, Leptosphaeria, Magnaporthe, Zymoseptoria, and others has uncovered important roles for chromatin regulators
in secondary metabolite production and regulation of pathogenicity genes, highlighting the
need for future work [e.g., see Shwab et al. 2007;
Soukup et al. 2012; Palmer et al. 2013; Connolly
et al. 2013; Soyer et al. 2014; Gacek-Matthews
et al. 2015, 2016; Niehaus et al. 2016; Gu et al.
2017; Maeda et al. 2017; Janevska et al. 2018; He
et al. 2018; Pfannenstiel et al. 2018; Mo ¨ller et al.
2019; Lan et al. 2019; and others].
Despite a great deal of progress, many
important questions about chromatin structure
and function remain unanswered. Given the
importance of chromatin structure to fungal
pathogenesis and secondary metabolism, identification of chromatin-based mechanisms that
are fungal-specific could provide new avenues
to limit the economic costs of fungal disease
and crop contamination. A better understanding of chromatin regulatory processes could
also enable more efficient engineering of fungi
for biotechnology purposes. N. crassa is an
ideal experimental system to address key open
1 Chromatin Structure and Function in Neurospora crassa
19