H3K36me3 by SET-2/KMT3, is associated with
facultative heterochromatin (see Sect. C2)
(Bicocca et al. 2018), in contrast to the
transcription-coupled H3K36 methylation by
SET-2/KMT3 at active genes. Widespread initiation from cryptic promoters has not been
reported for the N. crassa set-2 deletion strain,
but SET-2 is implicated in transcriptional
repression of the clock gene frequency (frq).
The large and accessible promoter region of
frq is highly regulated by multiple mechanisms,
including by a natural antisense RNA (Hurley
et al. 2015; Cha et al. 2015). Antisense transcription through the frq promoter leads to
transcription-dependent H3K36 methylation
by the SET-2/KMT3 histone methyltransferase
and subsequent gene repression (Xue et al.
2014). Other factors that serve to suppress
unregulated frq transcription include the transcriptional repressor RCO-1 (NCU06205) and
the chromatin remodeler CHD-1 (NCU03060)
(Zhou et al. 2013; Sun et al. 2016), the latter
suggesting that nucleosome positioning plays a
critical role in frq repression.
Euchromatin compartments are also highly
enriched for H3 that is dimethylated or trimethylated on lysine 4 (H3K4me2/3). Similar
to H3K36me3, H3K4 methylation is also cotranscriptionally deposited. In S. cerevisiae,
additionally, states of H3K4 methylation
exhibit a gradient of enrichment from the 5
0 to
3
0 end of genes, with trimethylated lysine 4
(H3K4me3) on histone H3 exhibiting highest
enrichment near the 5
0
end of genes,
H3K4me2 enrichment shifted towards the middle of the gene bodies, and peaks of monomethyl H3K4 enrichment shifted further
towards the 3
0 end of genes (Liu et al. 2005;
Pokholok et al. 2005). The enrichment of
H3K4 methylation occurs in most genes, yet
the absolute levels of enrichment are tightly
correlated with transcriptional levels: high
H3K4me corresponds to a high presence of
mRNA, although it is unclear if the H3K4me
causes elevated transcription or is simply a
result of transcriptional output. While the distribution of the different H3K4 methylation
states has not been well studied in N. crassa,
available data suggest that H3K4 methylation
has a complex regulatory network for deposition: for example, many expressed genes have
no H3K4 methylation. The function of different
H3K4 methylated states (H3K4me3/2/1) in N.
crassa is also understudied and poorly understood. Like H3K36me3, methylation of K4 on
H3 is linked to regulation of frq expression and
repression of gene expression (Raduwan et al.
2013; Zhu et al. 2019), though additional work
is needed to understand how H3K4 methylation
contributes to genome function. Additional
work is also needed to determine the mechanisms that control H3K4 methylation states and
levels at specific genes.
III. Heterochromatin
Emil Heitz coined the term “heterochromatin”
to describe structurally distinct segments of
chromosomes based on their cytological staining pattern (Heitz 1928; Zacharias 1995).
Subsequent genetic and molecular studies
revealed that (1) heterochromatin compartments are transcriptionally and recombinationally suppressed, (2) heterochromatin is
characterized by molecular features that are
conserved in many organisms, and (3) heterochromatin is important for critical cell functions such as genome defense, chromosome
segregation, gene regulation, and genome organization (Grewal and Jia 2007; Janssen et al.
2018). Heterochromatin domains can be subclassified into two types, constitutive and
facultative heterochromatin, which are functionally distinct and characterized by different
molecular components including a unique set
of posttranslational modifications on histones
deposited and bound by heterochromatinspecific proteins. These types of heterochromatin are discussed separately below. Notably,
Neurospora has served as an important model
system for understanding heterochromatin
because it shares many critical molecular features of heterochromatin with higher eukaryotes, including plants and animals. The
shared hallmarks of heterochromatin include
cytosine methylation on DNA and histone H3
methylated on lysine 9 (H3K9me) or lysine 27
(H3K27me). Notably, some or all of these fea1 Chromatin Structure and Function in Neurospora crassa
9
facultative heterochromatin (see Sect. C2)
(Bicocca et al. 2018), in contrast to the
transcription-coupled H3K36 methylation by
SET-2/KMT3 at active genes. Widespread initiation from cryptic promoters has not been
reported for the N. crassa set-2 deletion strain,
but SET-2 is implicated in transcriptional
repression of the clock gene frequency (frq).
The large and accessible promoter region of
frq is highly regulated by multiple mechanisms,
including by a natural antisense RNA (Hurley
et al. 2015; Cha et al. 2015). Antisense transcription through the frq promoter leads to
transcription-dependent H3K36 methylation
by the SET-2/KMT3 histone methyltransferase
and subsequent gene repression (Xue et al.
2014). Other factors that serve to suppress
unregulated frq transcription include the transcriptional repressor RCO-1 (NCU06205) and
the chromatin remodeler CHD-1 (NCU03060)
(Zhou et al. 2013; Sun et al. 2016), the latter
suggesting that nucleosome positioning plays a
critical role in frq repression.
Euchromatin compartments are also highly
enriched for H3 that is dimethylated or trimethylated on lysine 4 (H3K4me2/3). Similar
to H3K36me3, H3K4 methylation is also cotranscriptionally deposited. In S. cerevisiae,
additionally, states of H3K4 methylation
exhibit a gradient of enrichment from the 5
0 to
3
0 end of genes, with trimethylated lysine 4
(H3K4me3) on histone H3 exhibiting highest
enrichment near the 5
0
end of genes,
H3K4me2 enrichment shifted towards the middle of the gene bodies, and peaks of monomethyl H3K4 enrichment shifted further
towards the 3
0 end of genes (Liu et al. 2005;
Pokholok et al. 2005). The enrichment of
H3K4 methylation occurs in most genes, yet
the absolute levels of enrichment are tightly
correlated with transcriptional levels: high
H3K4me corresponds to a high presence of
mRNA, although it is unclear if the H3K4me
causes elevated transcription or is simply a
result of transcriptional output. While the distribution of the different H3K4 methylation
states has not been well studied in N. crassa,
available data suggest that H3K4 methylation
has a complex regulatory network for deposition: for example, many expressed genes have
no H3K4 methylation. The function of different
H3K4 methylated states (H3K4me3/2/1) in N.
crassa is also understudied and poorly understood. Like H3K36me3, methylation of K4 on
H3 is linked to regulation of frq expression and
repression of gene expression (Raduwan et al.
2013; Zhu et al. 2019), though additional work
is needed to understand how H3K4 methylation
contributes to genome function. Additional
work is also needed to determine the mechanisms that control H3K4 methylation states and
levels at specific genes.
III. Heterochromatin
Emil Heitz coined the term “heterochromatin”
to describe structurally distinct segments of
chromosomes based on their cytological staining pattern (Heitz 1928; Zacharias 1995).
Subsequent genetic and molecular studies
revealed that (1) heterochromatin compartments are transcriptionally and recombinationally suppressed, (2) heterochromatin is
characterized by molecular features that are
conserved in many organisms, and (3) heterochromatin is important for critical cell functions such as genome defense, chromosome
segregation, gene regulation, and genome organization (Grewal and Jia 2007; Janssen et al.
2018). Heterochromatin domains can be subclassified into two types, constitutive and
facultative heterochromatin, which are functionally distinct and characterized by different
molecular components including a unique set
of posttranslational modifications on histones
deposited and bound by heterochromatinspecific proteins. These types of heterochromatin are discussed separately below. Notably,
Neurospora has served as an important model
system for understanding heterochromatin
because it shares many critical molecular features of heterochromatin with higher eukaryotes, including plants and animals. The
shared hallmarks of heterochromatin include
cytosine methylation on DNA and histone H3
methylated on lysine 9 (H3K9me) or lysine 27
(H3K27me). Notably, some or all of these fea1 Chromatin Structure and Function in Neurospora crassa
9