tion in fkbA locus (Calo et al. 2014). An unanswered question is why the accumulation of
sRNAs from the fkbA locus is induced in
response to the drug. One possible explanation
is based on the high level of expression of fkbA
that might lead to the formation of aRNA, triggering the silencing as it has been observed in
plants (Gazzani et al. 2008).
The isolation of M. circinelloides epimutants exhibiting resistance to 5-fluoroorotic
acid (5-FOA) has revealed that RNAi-dependent epimutation plays a broad role enabling
rapid and reversible responses of this fungus
(Chang et al. 2019). The distribution of RNAirelated mechanisms involved in the phenotypic
plasticity in other fungi is unknown and
requires further studies, but it is very
promising that one of such mechanism could
operate in response to multiple environments
in N. crassa (Kronholm et al. 2016).
D. Small RNAs Associated with Antisense
Transcripts
Noncoding RNAs that overlap with proteincoding regions as a consequence of convergent
transcription, named natural antisense transcripts (NATs), have been identified in a high
number in animals and plants (Faghihi and
Wahlestedt 2009) and in a lesser extent in phylogenetically diverse fungi (Donaldson and
Saville 2012). These NATs use different
mechanisms to control gene expression, including transcriptional interference, chromatin
remodeling, and dsRNA formation. The
dsRNA can be a substrate of the RNAi machinery to produce nat-siRNAs, which has been
observed only in S. pombe within the fungal
kingdom (Donaldson and Saville 2012). In several fungi, the presence of NATs is not associated with the formation of nat-siRNAs,
although NATs regulates gene expression and
cellular processes (Nevers et al. 2018; Shao et al.
2017), including pathogenesis (Donaldson and
Saville 2013).
The biogenesis of disiRNAs in N. crassa is
related to nat-siRNAs because they derive from
genes in which convergent transcription causes
stalling of RNA polymerase II (Dang et al.
2016). The slow progression of polymerase II
allows binding of the exonuclease ERI-1
(Table 5.2) to nascent mRNA provoking the
generation of disiRNAs, although the precise
role ERI-1 in disiRNA biogenesis is unknown
(Dang et al. 2016). Like siRNAs, disiRNAs map
to both strands of the genome and are bound to
Argonaute protein QDE-2 (Lee et al. 2010).
Interestingly, disiRNA loci are associated with
DNA methylation and K3K9me3 (Dang et al.
2013), which are dependent on ERI-1 binding
on mRNA and antisense transcription, whereas
disiRNAs only contribute to these epigenetic
modifications (Dang et al. 2016). The role of
disiRNA in QDE-2-mediated DNA methylation
is not clear, although a mechanism similar to
siRNA-mediated heterochromatin formation in
S. pombe by recognizing the nascent RNA and
recruiting histone-modifying enzymes has been
suggested (Dang et al. 2016).
E. Cross-Kingdom Regulation
Recent pieces of evidence have shown that
sRNAs can move between interacting organisms to silence the gene expression in trans in
the non-related species, a phenomenon called
cross-kingdom or trans-kingdom RNAi (Kuan
et al. 2016; Weiberg and Jin 2015; Weiberg et al.
2015). In fungi, it was observed for the first time
in the aggressive plant pathogen Botrytis
cinerea, which can transfer siRNAs during the
infection to the plant host that hijack components of the plant RNAi pathway, suppressing
the expression of host immunity genes (Weiberg et al. 2013). These sRNAs are derived from
long-terminal repeat (LTR) retrotransposons
and require the two Dicer-like enzymes of B.
cinerea for their production. Consequently,
deletion of both dicer genes leads to reduced
virulence in plants (Weiberg et al. 2013). B.
cinerea sRNAs are translocated by an unknown
mechanism to the plant cell where they bind to
one of the plant Ago proteins (AGO1 in Arabidopsis thaliana) to silence genes involved in
plant immunity (Weiberg et al. 2013). Interestingly, the A. thaliana mutant in AGO1 is also
resistant to another plant fungal pathogen, Verticillium dahlia (Ellendorff et al. 2009), and V.
116
F. E. Nicola ´s et al.
sRNAs from the fkbA locus is induced in
response to the drug. One possible explanation
is based on the high level of expression of fkbA
that might lead to the formation of aRNA, triggering the silencing as it has been observed in
plants (Gazzani et al. 2008).
The isolation of M. circinelloides epimutants exhibiting resistance to 5-fluoroorotic
acid (5-FOA) has revealed that RNAi-dependent epimutation plays a broad role enabling
rapid and reversible responses of this fungus
(Chang et al. 2019). The distribution of RNAirelated mechanisms involved in the phenotypic
plasticity in other fungi is unknown and
requires further studies, but it is very
promising that one of such mechanism could
operate in response to multiple environments
in N. crassa (Kronholm et al. 2016).
D. Small RNAs Associated with Antisense
Transcripts
Noncoding RNAs that overlap with proteincoding regions as a consequence of convergent
transcription, named natural antisense transcripts (NATs), have been identified in a high
number in animals and plants (Faghihi and
Wahlestedt 2009) and in a lesser extent in phylogenetically diverse fungi (Donaldson and
Saville 2012). These NATs use different
mechanisms to control gene expression, including transcriptional interference, chromatin
remodeling, and dsRNA formation. The
dsRNA can be a substrate of the RNAi machinery to produce nat-siRNAs, which has been
observed only in S. pombe within the fungal
kingdom (Donaldson and Saville 2012). In several fungi, the presence of NATs is not associated with the formation of nat-siRNAs,
although NATs regulates gene expression and
cellular processes (Nevers et al. 2018; Shao et al.
2017), including pathogenesis (Donaldson and
Saville 2013).
The biogenesis of disiRNAs in N. crassa is
related to nat-siRNAs because they derive from
genes in which convergent transcription causes
stalling of RNA polymerase II (Dang et al.
2016). The slow progression of polymerase II
allows binding of the exonuclease ERI-1
(Table 5.2) to nascent mRNA provoking the
generation of disiRNAs, although the precise
role ERI-1 in disiRNA biogenesis is unknown
(Dang et al. 2016). Like siRNAs, disiRNAs map
to both strands of the genome and are bound to
Argonaute protein QDE-2 (Lee et al. 2010).
Interestingly, disiRNA loci are associated with
DNA methylation and K3K9me3 (Dang et al.
2013), which are dependent on ERI-1 binding
on mRNA and antisense transcription, whereas
disiRNAs only contribute to these epigenetic
modifications (Dang et al. 2016). The role of
disiRNA in QDE-2-mediated DNA methylation
is not clear, although a mechanism similar to
siRNA-mediated heterochromatin formation in
S. pombe by recognizing the nascent RNA and
recruiting histone-modifying enzymes has been
suggested (Dang et al. 2016).
E. Cross-Kingdom Regulation
Recent pieces of evidence have shown that
sRNAs can move between interacting organisms to silence the gene expression in trans in
the non-related species, a phenomenon called
cross-kingdom or trans-kingdom RNAi (Kuan
et al. 2016; Weiberg and Jin 2015; Weiberg et al.
2015). In fungi, it was observed for the first time
in the aggressive plant pathogen Botrytis
cinerea, which can transfer siRNAs during the
infection to the plant host that hijack components of the plant RNAi pathway, suppressing
the expression of host immunity genes (Weiberg et al. 2013). These sRNAs are derived from
long-terminal repeat (LTR) retrotransposons
and require the two Dicer-like enzymes of B.
cinerea for their production. Consequently,
deletion of both dicer genes leads to reduced
virulence in plants (Weiberg et al. 2013). B.
cinerea sRNAs are translocated by an unknown
mechanism to the plant cell where they bind to
one of the plant Ago proteins (AGO1 in Arabidopsis thaliana) to silence genes involved in
plant immunity (Weiberg et al. 2013). Interestingly, the A. thaliana mutant in AGO1 is also
resistant to another plant fungal pathogen, Verticillium dahlia (Ellendorff et al. 2009), and V.
116
F. E. Nicola ´s et al.