to drive open chromatin at certain genome
sites. A study of WCC and another transcription factor necessary for induction of a subset
of light-inducible genes, SUB-1, revealed that
WCC was needed to create open chromatin in
response to light (Sancar et al. 2015). On the
other hand, open chromatin at SUB-1
(NCU01154) binding sites did not depend on
SUB-1 (Sancar et al. 2015). Thus, some transcription factors play critical roles in opening
chromatin, which could in turn allow for additional transcription factors to subsequently
bind promoters at an adjacent sequence motif,
thereby enabling combinatorial regulation of
gene expression by multiple transcription factors. Interestingly, interactions of WCC with
SWI/SNF are required for circadian activation
of frq expression in the dark, but not for its
light-induced activation (Wang et al. 2014).
Together, these results indicate that WCC may
promote chromatin accessibility through multiple mechanisms. More broadly, these data are
consistent with a model in which a subset of N.
crassa transcription factors, such as the WCC,
function as master or “pioneer” transcription
factors.
In addition to their elevated accessibility
compared to the rest of the genome, promoters
can be distinguished from coding sequences
and heterochromatin by additional structural
features. N. crassa histones can be acetylated
at a number of residues (Xiong et al. 2010),
and many promoters are highly enriched for
histones with acetylated lysines (Anderson
et al. 2010; Smith et al. 2010; Bicocca et al.
2018). Mutation of the ngf (NCU10847) gene
encoding a homolog of the highly conserved
GCN5 lysine acetyltransferase or a key lysine
residue in histone H3 (NCU01635) causes
defects in WCC-dependent activation of the
light-induced gene albino-3 (NCU01427) (Grimaldi et al. 2006; Brenna et al. 2012), demonstrating that histone lysine acetylation
positively regulates transcription in N. crassa
similar to other organisms. Unmodified lysines
in the histone tails are proposed to create a
relatively inaccessible chromatin structure that
is refractory to transcription due to strong
interactions between positively charged lysines
in the histone tail with adjacent nucleosomes
and the negatively charged DNA backbone
(Verdone et al. 2005). Thus, histone lysine acetylation may promote transcription in two ways:
(1) Acetylation neutralizes the positive charge
of lysines in the histone tail, which is proposed
to weaken histone-DNA interactions, increase
the accessibility of the underlying DNA, and
lower the energetic barrier to transcription.
(2) Acetylated lysines can be recognized and
bound by specific chromatin-binding proteins
(e.g., see Gong et al. 2016), facilitating transcription factor recruitment to promoters for
enhancing transcription. Additional work is
needed to elucidate the complex role(s) of acetylation in N. crassa promoters, but hyperacetylated lysines of promoter histones are
strongly correlated with active transcription
(Smith et al. 2010; Bicocca et al. 2018).
Finally, a common feature of N. crassa promoters is the histone variant, H2A.Z
(NCU05347). This histone variant is highly
conserved from yeast to humans and is commonly enriched in promoter nucleosomes
(Talbert and Henikoff 2010). Despite extensive
study in multiple organisms, however, the
function of H2A.Z has remained mysterious.
Genetic studies implicate H2A.Z in transcriptional activation, transcription repression, and
DNA repair, yet how this histone variant performs different functions in different genomic
contexts is poorly understood (Talbert and
Henikoff 2010). Two published studies of N.
crassa H2A.Z suggest that it may repress transcription (Liu et al. 2017; Dong et al. 2018), but
RNA-seq analysis suggests that H2A.Z is
required for repression of some genes and activation of others (A.J. Courtney and Z.A. Lewis,
unpublished). The paradoxical functions of
H2A.Z likely depend on posttranslational modifications of H2A.Z as well as other promoter
features that co-localize with H2A.Z. Hierarchical clustering of transcriptional start sites
in N. crassa was performed based on multiple
chromatin features including H2A.Z. This
approach resolved at least five distinct promoter structures present in this fungus (A.J.
Courtney and Z.A. Lewis, unpublished)
(Fig. 1.1b). The recruitment of unidentified
H2A.Z binding proteins may also impact
these transcriptional effects.
1 Chromatin Structure and Function in Neurospora crassa
7
sites. A study of WCC and another transcription factor necessary for induction of a subset
of light-inducible genes, SUB-1, revealed that
WCC was needed to create open chromatin in
response to light (Sancar et al. 2015). On the
other hand, open chromatin at SUB-1
(NCU01154) binding sites did not depend on
SUB-1 (Sancar et al. 2015). Thus, some transcription factors play critical roles in opening
chromatin, which could in turn allow for additional transcription factors to subsequently
bind promoters at an adjacent sequence motif,
thereby enabling combinatorial regulation of
gene expression by multiple transcription factors. Interestingly, interactions of WCC with
SWI/SNF are required for circadian activation
of frq expression in the dark, but not for its
light-induced activation (Wang et al. 2014).
Together, these results indicate that WCC may
promote chromatin accessibility through multiple mechanisms. More broadly, these data are
consistent with a model in which a subset of N.
crassa transcription factors, such as the WCC,
function as master or “pioneer” transcription
factors.
In addition to their elevated accessibility
compared to the rest of the genome, promoters
can be distinguished from coding sequences
and heterochromatin by additional structural
features. N. crassa histones can be acetylated
at a number of residues (Xiong et al. 2010),
and many promoters are highly enriched for
histones with acetylated lysines (Anderson
et al. 2010; Smith et al. 2010; Bicocca et al.
2018). Mutation of the ngf (NCU10847) gene
encoding a homolog of the highly conserved
GCN5 lysine acetyltransferase or a key lysine
residue in histone H3 (NCU01635) causes
defects in WCC-dependent activation of the
light-induced gene albino-3 (NCU01427) (Grimaldi et al. 2006; Brenna et al. 2012), demonstrating that histone lysine acetylation
positively regulates transcription in N. crassa
similar to other organisms. Unmodified lysines
in the histone tails are proposed to create a
relatively inaccessible chromatin structure that
is refractory to transcription due to strong
interactions between positively charged lysines
in the histone tail with adjacent nucleosomes
and the negatively charged DNA backbone
(Verdone et al. 2005). Thus, histone lysine acetylation may promote transcription in two ways:
(1) Acetylation neutralizes the positive charge
of lysines in the histone tail, which is proposed
to weaken histone-DNA interactions, increase
the accessibility of the underlying DNA, and
lower the energetic barrier to transcription.
(2) Acetylated lysines can be recognized and
bound by specific chromatin-binding proteins
(e.g., see Gong et al. 2016), facilitating transcription factor recruitment to promoters for
enhancing transcription. Additional work is
needed to elucidate the complex role(s) of acetylation in N. crassa promoters, but hyperacetylated lysines of promoter histones are
strongly correlated with active transcription
(Smith et al. 2010; Bicocca et al. 2018).
Finally, a common feature of N. crassa promoters is the histone variant, H2A.Z
(NCU05347). This histone variant is highly
conserved from yeast to humans and is commonly enriched in promoter nucleosomes
(Talbert and Henikoff 2010). Despite extensive
study in multiple organisms, however, the
function of H2A.Z has remained mysterious.
Genetic studies implicate H2A.Z in transcriptional activation, transcription repression, and
DNA repair, yet how this histone variant performs different functions in different genomic
contexts is poorly understood (Talbert and
Henikoff 2010). Two published studies of N.
crassa H2A.Z suggest that it may repress transcription (Liu et al. 2017; Dong et al. 2018), but
RNA-seq analysis suggests that H2A.Z is
required for repression of some genes and activation of others (A.J. Courtney and Z.A. Lewis,
unpublished). The paradoxical functions of
H2A.Z likely depend on posttranslational modifications of H2A.Z as well as other promoter
features that co-localize with H2A.Z. Hierarchical clustering of transcriptional start sites
in N. crassa was performed based on multiple
chromatin features including H2A.Z. This
approach resolved at least five distinct promoter structures present in this fungus (A.J.
Courtney and Z.A. Lewis, unpublished)
(Fig. 1.1b). The recruitment of unidentified
H2A.Z binding proteins may also impact
these transcriptional effects.
1 Chromatin Structure and Function in Neurospora crassa
7