B. Small-Interfering RNAs in Chromosome
Function
In previous sections, we have described several
mechanisms that use siRNAs to protect the
genome from TEs. These protective mechanisms seem to be adopted by eukaryotic cells
during evolution to play other relevant functions in the cells. This might be the case for the
formation of heterochromatin in different
regions of the chromosomes, particularly in
regional centromeres, where siRNAs play an
essential role (Pidoux and Allshire 2005; Volpe
and Martienssen 2011). Regional centromeres,
contrary to point centromeres, are long ranging
from few kilobases to megabases and made of
repetitive DNA that consists of either arrays of
satellite DNA or TEs or both (Roy and Sanyal
2011). TEs are proposed to play a more significant role in the evolution of this type of centromeres, and their domestication may have
given rise to the dh/dg and a-satellite repeats
present in the centromeres of fission yeast
(Schizosaccharomyces pombe) and humans,
respectively (Gao et al. 2015; Wong and Choo
2004).
In fission yeast, RNAi plays a critical role in
heterochromatin formation, which it is
required for normal centromere function leading to chromosome segregation (Pidoux and
Allshire 2005). Dicer-independent sRNAs,
named primal RNAs or priRNAs (Table 5.1),
are the main effectors in the initiation of heterochromatin formation (Halic and Moazed
2010). The priRNAs are generated from ssRNAs
to later form a complex with Ago1 that targets
long non-coding centromeric transcripts. This
complex recruits the RdRP to synthesize
dsRNA, which is subsequently processed by
Dicer into secondary siRNAs. These secondary
siRNAs are loaded onto the RNA-induced transcriptional silencing complex (RITS), which
includes Ago1. The binding of siRNAcontaining RITS to the nascent transcripts in
the centromeric regions recruits the Clr4
methyltransferase complex, which deposits the
H3K9me mark and HP1 family proteins leading
to heterochromatin formation (Martienssen
and Moazed 2015; Ugolini and Halic 2018).
In addition to the establishment of heterochromatin formation in the centromeres, RNAi
also seems to play an essential function in centromere evolution in species belonging to the
phylum Basidiomycota. Here, RNAi and cytosine methylation are proposed to maintain
repetitive transposon-rich centromeres, since
RNAi-deficient species or mutants from RNAiproficient species have shorter centromeres
(Yadav et al. 2018). This agrees with the fact
that fungi with RNAi systems have more total
DNA corresponding to TEs than RNAideficient species, although fewer elements are
functional, reflecting stringent control over
transposition (Muszewska et al. 2017).
III. Small RNAs in the Regulation of
Gene Expression
Soon after the discovery of RNAi, the focus on
its defensive role gave way to a whole new
research field based on the endogenous regulatory functions of sRNAs. It was initiated when
miRNAs, previously identified and studied in
Caenorhabditis elegans (Lee et al. 1993), were
found to be conserved in most plants and animals. These discoveries opened an extensive
period in which the regulatory roles of RNAi
and endogenous sRNAs (esRNAs) were the hot
topic in molecular biology for several years.
Hundreds of miRNAs were found creating a
regulatory network that might involve more
than 60% of total genes in humans (Friedman
et al. 2009) and regulate most of the complex
biological processes in living cells such as
development, differentiation, maintenance,
cell death, and diseases associated with the misregulation of these molecules (Esteller 2011;
Lo ´pez-Camarillo and Marchat 2013; Stefani
and Slack 2008). During this time, miRNAs
and other regulatory esRNAs were considered
to be absent in fungi, until molecules similar to
miRNAs and regulatory esRNAs were discovered in Neurospora crassa and Mucor circinelloides, respectively (Lee et al. 2010; Nicolas et al.
2010). However, the regulatory role of esRNAs
has been scarcely studied in fungi because few
112
F. E. Nicola ´s et al.
Function
In previous sections, we have described several
mechanisms that use siRNAs to protect the
genome from TEs. These protective mechanisms seem to be adopted by eukaryotic cells
during evolution to play other relevant functions in the cells. This might be the case for the
formation of heterochromatin in different
regions of the chromosomes, particularly in
regional centromeres, where siRNAs play an
essential role (Pidoux and Allshire 2005; Volpe
and Martienssen 2011). Regional centromeres,
contrary to point centromeres, are long ranging
from few kilobases to megabases and made of
repetitive DNA that consists of either arrays of
satellite DNA or TEs or both (Roy and Sanyal
2011). TEs are proposed to play a more significant role in the evolution of this type of centromeres, and their domestication may have
given rise to the dh/dg and a-satellite repeats
present in the centromeres of fission yeast
(Schizosaccharomyces pombe) and humans,
respectively (Gao et al. 2015; Wong and Choo
2004).
In fission yeast, RNAi plays a critical role in
heterochromatin formation, which it is
required for normal centromere function leading to chromosome segregation (Pidoux and
Allshire 2005). Dicer-independent sRNAs,
named primal RNAs or priRNAs (Table 5.1),
are the main effectors in the initiation of heterochromatin formation (Halic and Moazed
2010). The priRNAs are generated from ssRNAs
to later form a complex with Ago1 that targets
long non-coding centromeric transcripts. This
complex recruits the RdRP to synthesize
dsRNA, which is subsequently processed by
Dicer into secondary siRNAs. These secondary
siRNAs are loaded onto the RNA-induced transcriptional silencing complex (RITS), which
includes Ago1. The binding of siRNAcontaining RITS to the nascent transcripts in
the centromeric regions recruits the Clr4
methyltransferase complex, which deposits the
H3K9me mark and HP1 family proteins leading
to heterochromatin formation (Martienssen
and Moazed 2015; Ugolini and Halic 2018).
In addition to the establishment of heterochromatin formation in the centromeres, RNAi
also seems to play an essential function in centromere evolution in species belonging to the
phylum Basidiomycota. Here, RNAi and cytosine methylation are proposed to maintain
repetitive transposon-rich centromeres, since
RNAi-deficient species or mutants from RNAiproficient species have shorter centromeres
(Yadav et al. 2018). This agrees with the fact
that fungi with RNAi systems have more total
DNA corresponding to TEs than RNAideficient species, although fewer elements are
functional, reflecting stringent control over
transposition (Muszewska et al. 2017).
III. Small RNAs in the Regulation of
Gene Expression
Soon after the discovery of RNAi, the focus on
its defensive role gave way to a whole new
research field based on the endogenous regulatory functions of sRNAs. It was initiated when
miRNAs, previously identified and studied in
Caenorhabditis elegans (Lee et al. 1993), were
found to be conserved in most plants and animals. These discoveries opened an extensive
period in which the regulatory roles of RNAi
and endogenous sRNAs (esRNAs) were the hot
topic in molecular biology for several years.
Hundreds of miRNAs were found creating a
regulatory network that might involve more
than 60% of total genes in humans (Friedman
et al. 2009) and regulate most of the complex
biological processes in living cells such as
development, differentiation, maintenance,
cell death, and diseases associated with the misregulation of these molecules (Esteller 2011;
Lo ´pez-Camarillo and Marchat 2013; Stefani
and Slack 2008). During this time, miRNAs
and other regulatory esRNAs were considered
to be absent in fungi, until molecules similar to
miRNAs and regulatory esRNAs were discovered in Neurospora crassa and Mucor circinelloides, respectively (Lee et al. 2010; Nicolas et al.
2010). However, the regulatory role of esRNAs
has been scarcely studied in fungi because few
112
F. E. Nicola ´s et al.