repressive environment of the inactive Xchromosome (e.g., see Colognori et al. 2019),
yet a possible role of noncoding RNAs for fungal facultative heterochromatin has yet to be
explored.
2. Methylation of H3K36 by ASH1 at Facultative
Heterochromatin
Recently, it was determined that another epigenetic mark that is traditionally thought to
demarcate active genes, methylation of lysine
36 on histone H3 (H3K36me), is essential for
eukaryotic gene repression and establishment
of facultative heterochromatin. In Neurospora,
methylation of H3K36 is catalyzed by two different SET domain-containing proteins: the
RNA polymerase II (RNAPII)-associated SET2, which monomethylates, dimethylates, and
trimethylates H3K36 on actively transcribed
genes and ASH1, which acts independently of
RNAPII to dimethylate and occasionally trimethylate unmarked H3K36; the action of
both proteins provides the full complement of
H3K36me2 and H3K36me3 in wild-type Neurospora cells (Bicocca et al. 2018). In an elegant
series of experiments, Bicocca et al. (2018)
were able to separate the levels of H3K36me2
and H3K36me3 that were exclusively catalyzed
by ASH1 and found that ASH1-catalyzed
H3K36me2/3 demarcates lowly expressed
genes, in contrast to the enrichment of SET-2catalyzed H3K36me2/3 across the gene bodies
of highly transcribed genes (Fig. 1.2c). Thus,
ASH1-catalyzed H3K36me2 and H3K36me3
act as a repressive mark. Indeed, peaks of
ASH1-catalyzed H3K36me2 co-localize with
H3K27me2/3 enrichment at facultative heterochromatin (Bicocca et al. 2018), suggesting
ASH1 catalytic activity is also critical for gene
repression, although other ASH1-dependent
H3K36me2 peaks exist independent of PRC2
activity. Interestingly, in mutants that exhibit
alternative patterns of facultative heterochromatin relative to a wild-type strain, the newly
placed H3K27me2/3 co-localizes with ASH1catalyzed H3K36me2, and ~ 30% of
H3K27me2/3 domains first require the deposition of H3K36me2 by ASH-1, although ASH1catalyzed H3K36me2 can also inhibit
H3K27me2/3 deposition (Bicocca et al. 2018).
Together, these data suggest that for some
position-independent facultative heterochromatin domains, the initial dimethylation of
H3K36 by ASH1 may help recruit PRC2 for
dimethylation and trimethylation of H3K27,
although a direct interaction between these
complexes has not been reported to date and
it is unknown how ASH1 is recruited to these
sites. Thus, the power of the model organism
Neurospora crassa has helped elucidating a
complex dynamic between two histone marks
important for gene repression.
3. Functions of Facultative Heterochromatin
Facultative heterochromatin marked by PRC2catalyzed H3K27me2/3 and ASH1-catalyzed
H3K36me2 mainly functions to repress gene
expression (Jamieson et al. 2013; Basenko
et al. 2015; Klocko et al. 2016). As previously
mentioned, genes marked by H3K27me2/3 in a
wild-type strain are typically silent or expressed
at very low levels. Paradoxically, removal of the
H3K27me2/3 mark in a Dset-7 mutant only
derepressed a subset of the genes in facultative
heterochromatin at sub-telomeres, although
the overall low level of the messenger RNA
from these genes may confound any RNAsequencing analysis. It is probable that the
remaining association of the sub-telomeres at
the nuclear membrane (below) may continue to
enforce a repressive environment on these
genes (Klocko et al. 2016), or the presence of
ASH-1-catalyzed H3K36me2, which often colocalizes with the H3K27me2/3 mark inhibits
any remaining transcription initiation at these
promoters (Bicocca et al. 2018).
Facultative heterochromatin is an important determinant in organizing the Neurospora
genome. As detailed above, interactions
between H3K27me2/3-marked intrachromosomal and interchromosomal loci are some of the
strongest interactions within the wild-type
Neurospora genome and facilitate the formation of the “heterochromatin bundle” in Neurospora nuclei (Galazka et al. 2016). However,
the loss of H3K27me2/3 following the deletion
18
A. J. Courtney et al.
yet a possible role of noncoding RNAs for fungal facultative heterochromatin has yet to be
explored.
2. Methylation of H3K36 by ASH1 at Facultative
Heterochromatin
Recently, it was determined that another epigenetic mark that is traditionally thought to
demarcate active genes, methylation of lysine
36 on histone H3 (H3K36me), is essential for
eukaryotic gene repression and establishment
of facultative heterochromatin. In Neurospora,
methylation of H3K36 is catalyzed by two different SET domain-containing proteins: the
RNA polymerase II (RNAPII)-associated SET2, which monomethylates, dimethylates, and
trimethylates H3K36 on actively transcribed
genes and ASH1, which acts independently of
RNAPII to dimethylate and occasionally trimethylate unmarked H3K36; the action of
both proteins provides the full complement of
H3K36me2 and H3K36me3 in wild-type Neurospora cells (Bicocca et al. 2018). In an elegant
series of experiments, Bicocca et al. (2018)
were able to separate the levels of H3K36me2
and H3K36me3 that were exclusively catalyzed
by ASH1 and found that ASH1-catalyzed
H3K36me2/3 demarcates lowly expressed
genes, in contrast to the enrichment of SET-2catalyzed H3K36me2/3 across the gene bodies
of highly transcribed genes (Fig. 1.2c). Thus,
ASH1-catalyzed H3K36me2 and H3K36me3
act as a repressive mark. Indeed, peaks of
ASH1-catalyzed H3K36me2 co-localize with
H3K27me2/3 enrichment at facultative heterochromatin (Bicocca et al. 2018), suggesting
ASH1 catalytic activity is also critical for gene
repression, although other ASH1-dependent
H3K36me2 peaks exist independent of PRC2
activity. Interestingly, in mutants that exhibit
alternative patterns of facultative heterochromatin relative to a wild-type strain, the newly
placed H3K27me2/3 co-localizes with ASH1catalyzed H3K36me2, and ~ 30% of
H3K27me2/3 domains first require the deposition of H3K36me2 by ASH-1, although ASH1catalyzed H3K36me2 can also inhibit
H3K27me2/3 deposition (Bicocca et al. 2018).
Together, these data suggest that for some
position-independent facultative heterochromatin domains, the initial dimethylation of
H3K36 by ASH1 may help recruit PRC2 for
dimethylation and trimethylation of H3K27,
although a direct interaction between these
complexes has not been reported to date and
it is unknown how ASH1 is recruited to these
sites. Thus, the power of the model organism
Neurospora crassa has helped elucidating a
complex dynamic between two histone marks
important for gene repression.
3. Functions of Facultative Heterochromatin
Facultative heterochromatin marked by PRC2catalyzed H3K27me2/3 and ASH1-catalyzed
H3K36me2 mainly functions to repress gene
expression (Jamieson et al. 2013; Basenko
et al. 2015; Klocko et al. 2016). As previously
mentioned, genes marked by H3K27me2/3 in a
wild-type strain are typically silent or expressed
at very low levels. Paradoxically, removal of the
H3K27me2/3 mark in a Dset-7 mutant only
derepressed a subset of the genes in facultative
heterochromatin at sub-telomeres, although
the overall low level of the messenger RNA
from these genes may confound any RNAsequencing analysis. It is probable that the
remaining association of the sub-telomeres at
the nuclear membrane (below) may continue to
enforce a repressive environment on these
genes (Klocko et al. 2016), or the presence of
ASH-1-catalyzed H3K36me2, which often colocalizes with the H3K27me2/3 mark inhibits
any remaining transcription initiation at these
promoters (Bicocca et al. 2018).
Facultative heterochromatin is an important determinant in organizing the Neurospora
genome. As detailed above, interactions
between H3K27me2/3-marked intrachromosomal and interchromosomal loci are some of the
strongest interactions within the wild-type
Neurospora genome and facilitate the formation of the “heterochromatin bundle” in Neurospora nuclei (Galazka et al. 2016). However,
the loss of H3K27me2/3 following the deletion
18
A. J. Courtney et al.