2013). Interestingly, the conserved RNA exonuclease enhanced RNAi-1 (ERI-1; NCU06684) is
necessary and sufficient for DNA methylation
at these sites (Fig. 1.2b)(Dang et al. 2016). Based
on these studies, a model for heterochromatin
formation at disiRNA-producing loci has been
proposed. In this model, convergent transcription is thought to stall RNA polymerase, allowing ERI1 binding to the nascent RNA and
resulting in subsequent recruitment of the heterochromatin machinery. It is important to
note that this process must only occur in a
small subset of nuclei. The observation that
frq is unmethylated in most nuclei but contains
dense cytosine methylation in a small fraction
of nuclei is consistent with the idea that ERI1induced deposition of H3K9me3 and 5
m C is a
rare event, which may explain the inability to
detect high levels of these chromatin modifications in genome-wide studies. Additional work
is needed to fully explain the role of ERI1induced heterochromatin in N. crassa. One
idea is that certain loci may be subject to occasional epigenetic silencing within a population
(i.e., multiple epialleles exist) as a form of epigenetic bet-hedging. In other words, epialleles
could create additional phenotypic diversity
that would allow certain individuals in a genetically identical population to thrive under different selective pressures (Grimbergen et al.
2015).
C. The Polycomb System and Facultative
Heterochromatin
One powerful advantage of N. crassa as a model
organism for epigenetic studies is the presence
of a conserved Polycomb repression system,
which in metazoans is important for assembling facultative, or temporary, heterochromatin which maintains cell type-specific or
environmentally specific gene repression
(Simon and Kingston 2013; Lewis 2017). In
animals, plants, and some fungi, facultative heterochromatin is demarcated by the presence of
histone H3 containing trimethylated lysine 27
(H3K27me3). In N. crassa, both dimethylated
and trimethylated H3K27 are found together
covering ~7% of the Neurospora genome.
These regions typically have high gene content,
in contrast to constitutive heterochromatin,
and are located near the telomeres of all the
seven chromosomes (Smith et al. 2008; Jamieson et al. 2013). Subtelomeric H3K27me2/3associated domains are highly enriched for
genes that are present only in fungi and are
less conserved with other eukaryotes, though a
few of these repressed and lowly expressed
genes have known functions (Jamieson et al.
2013).
1. Assembly of Facultative Heterochromatin by
Polycomb Repressive Complex-2
Recent efforts have focused on elucidating the
mechanisms that control methylation of H3
lysine 27 and assembly of facultative domains.
H3K27me2/3 is catalyzed by the Polycomb
Repressive Complex 2 (PRC2), a four-member
complex comprised of the histone methyltransferase SET-7/KMT6 (NCU07496) and three
additional members: EED (NCU05300), SUZ12
(NCU05460), and P55/CAC-3 (Neurospora p55/
chromatin assembly complex-3; NCU06679)
(Borkovich et al. 2004; Jamieson et al. 2013).
Neurospora PRC2 members are conserved with
related fungal species and with higher eukaryotes (Jamieson et al. 2013); however, genes
encoding members of the H3K27me2/3 reader
complex PRC1, found in Drosophila, mammals,
and plants, are not encoded in Neurospora
(Jamieson et al. 2013; Lewis 2017), leading to
the question of how the facultative heterochromatin mark is read and interpreted. Loss of
PRC2 in Neurospora does not confer any
noticeable growth defect (Jamieson et al.
2013), in contrast to other closely related fungal
species (Connolly et al. 2013; Studt et al. 2016).
Depending on the target locus, placement
of the H3K27me2/3 mark within chromosomal
domains can occur in a position-dependent or
position-independent manner (Fig. 1.2c)
(Jamieson et al. 2018). Analysis of H3K27me2/
3 in translocation strains revealed that new
telomere creation as a result of chromosome
rearrangement leads to establishment of a new
facultative heterochromatin domain adjacent to
the new chromosome end (Jamieson et al.
16
A. J. Courtney et al.
necessary and sufficient for DNA methylation
at these sites (Fig. 1.2b)(Dang et al. 2016). Based
on these studies, a model for heterochromatin
formation at disiRNA-producing loci has been
proposed. In this model, convergent transcription is thought to stall RNA polymerase, allowing ERI1 binding to the nascent RNA and
resulting in subsequent recruitment of the heterochromatin machinery. It is important to
note that this process must only occur in a
small subset of nuclei. The observation that
frq is unmethylated in most nuclei but contains
dense cytosine methylation in a small fraction
of nuclei is consistent with the idea that ERI1induced deposition of H3K9me3 and 5
m C is a
rare event, which may explain the inability to
detect high levels of these chromatin modifications in genome-wide studies. Additional work
is needed to fully explain the role of ERI1induced heterochromatin in N. crassa. One
idea is that certain loci may be subject to occasional epigenetic silencing within a population
(i.e., multiple epialleles exist) as a form of epigenetic bet-hedging. In other words, epialleles
could create additional phenotypic diversity
that would allow certain individuals in a genetically identical population to thrive under different selective pressures (Grimbergen et al.
2015).
C. The Polycomb System and Facultative
Heterochromatin
One powerful advantage of N. crassa as a model
organism for epigenetic studies is the presence
of a conserved Polycomb repression system,
which in metazoans is important for assembling facultative, or temporary, heterochromatin which maintains cell type-specific or
environmentally specific gene repression
(Simon and Kingston 2013; Lewis 2017). In
animals, plants, and some fungi, facultative heterochromatin is demarcated by the presence of
histone H3 containing trimethylated lysine 27
(H3K27me3). In N. crassa, both dimethylated
and trimethylated H3K27 are found together
covering ~7% of the Neurospora genome.
These regions typically have high gene content,
in contrast to constitutive heterochromatin,
and are located near the telomeres of all the
seven chromosomes (Smith et al. 2008; Jamieson et al. 2013). Subtelomeric H3K27me2/3associated domains are highly enriched for
genes that are present only in fungi and are
less conserved with other eukaryotes, though a
few of these repressed and lowly expressed
genes have known functions (Jamieson et al.
2013).
1. Assembly of Facultative Heterochromatin by
Polycomb Repressive Complex-2
Recent efforts have focused on elucidating the
mechanisms that control methylation of H3
lysine 27 and assembly of facultative domains.
H3K27me2/3 is catalyzed by the Polycomb
Repressive Complex 2 (PRC2), a four-member
complex comprised of the histone methyltransferase SET-7/KMT6 (NCU07496) and three
additional members: EED (NCU05300), SUZ12
(NCU05460), and P55/CAC-3 (Neurospora p55/
chromatin assembly complex-3; NCU06679)
(Borkovich et al. 2004; Jamieson et al. 2013).
Neurospora PRC2 members are conserved with
related fungal species and with higher eukaryotes (Jamieson et al. 2013); however, genes
encoding members of the H3K27me2/3 reader
complex PRC1, found in Drosophila, mammals,
and plants, are not encoded in Neurospora
(Jamieson et al. 2013; Lewis 2017), leading to
the question of how the facultative heterochromatin mark is read and interpreted. Loss of
PRC2 in Neurospora does not confer any
noticeable growth defect (Jamieson et al.
2013), in contrast to other closely related fungal
species (Connolly et al. 2013; Studt et al. 2016).
Depending on the target locus, placement
of the H3K27me2/3 mark within chromosomal
domains can occur in a position-dependent or
position-independent manner (Fig. 1.2c)
(Jamieson et al. 2018). Analysis of H3K27me2/
3 in translocation strains revealed that new
telomere creation as a result of chromosome
rearrangement leads to establishment of a new
facultative heterochromatin domain adjacent to
the new chromosome end (Jamieson et al.
16
A. J. Courtney et al.