Lee HC, Chang S-S, Choudhary S, Aalto AP, Maiti M,
Bamford DH, Liu Y (2009) qiRNA, a new type of
small interfering RNA induced by DNA damage.
Nature 459:274–277
Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC,
Liu Y (2010) Diverse pathways generate
microRNA-like RNAs and dicer-independent
small interfering RNAs in fungi. Mol Cell
38:803–814
Lin YL, Ma LT, Lee YR, Lin SS, Wang SY, Chang TT,
Shaw JF, Li WH, Chu FH (2015) MicroRNA-like
small RNAs prediction in the development of
Antrodia cinnamomea. PLoS One 10:e0123245
Liu Y, Lee HC, Aalto AP, Yang Q, Chang SS, Huang G,
Fisher D, Cha J, Poranen MM, Bamford DH (2010)
The DNA/RNA-dependent RNA polymerase QDE1 generates aberrant RNA and dsRNA for RNAi in
a process requiring replication protein a and a
DNA helicase. PLoS Biol 8:e1000496
Lo ´pez-Camarillo C, Marchat LA (2013) MicroRNAs in
cancer. Annu Rev Pathol 9:287–314
Lu WT, Hawley BR, Skalka GL, Baldock RA, Smith EM,
Bader AS, Malewicz M, Watts FZ, Wilczynska A,
Bushell M (2018) Drosha drives the formation of
DNA:RNA hybrids around DNA break sites to
facilitate DNA repair. Nat Commun 9:532
Martienssen R, Moazed D (2015) RNAi and heterochromatin. Cold Spring Harb Perspect Biol 7:a019323
Meussen BJ, De Graaff LH, Sanders JPM, Weusthuis RA
(2012) Metabolic engineering of Rhizopus oryzae
for the production of platform chemicals. Appl
Microbiol Biotechnol 94:875–886
Michalik KM, Bo ¨ttcher R, Fo ¨rstemann K (2012) A small
RNA response at DNA ends in Drosophila. Nucleic
Acids Res 40:9596–9603
Michielse CB, Salim K, Ragas P, Ram AFJ, Kudla B,
Jarry B, Punt PJ, Van Den Hondel CAMJJ (2004)
Development of a system for integrative and stable
transformation of the zygomycete Rhizopus oryzae
by agrobacterium-mediated DNA transfer. Mol
Gen Genomics 271:499–510
Mochama P, Jadhav P, Neupane A, Marzano SYL (2018)
Mycoviruses as triggers and targets of RNA silencing in white mold fungus Sclerotinia sclerotiorum.
Viruses 10:214
Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska
M, Ginalski K (2017) Cut-and-paste transposons
in fungi with diverse lifestyles. Genome Biol Evol
9:3463–3477
Nakayashiki H, Kadotani N, Mayama S (2006) Evolution and diversification of RNA silencing proteins
in fungi. J Mol Evol 63:127–135
Napoli C, Lemieux C, Jorgensen R (1990) Introduction
of a chimeric chalcone synthase gene into Petunia
results in reversible co-suppression of homologous genes in trans. Plant Cell 2:279–289
Nevers A, Doyen A, Malabat C, Ne ´ron B, Kergrohen T,
Jacquier A, Badis G (2018) Antisense transcriptional interference mediates condition-specific
gene repression in budding yeast. Nucleic Acids
Res 46:6009–6025
Nicola ´s FE, Torres-Martı ´nez S, Ruiz-Va ´zquez RM
(2003) Two classes of small antisense RNAs in
fungal RNA silencing triggered by non-integrative
transgenes. EMBO J 22:3983–3991
Nicola ´s FE, de Haro JP, Torres-Martı ´nez S, Ruiz-Va ´zquez RM (2007) Mutants defective in a Mucor
circinelloides dicer-like gene are not compromised
in siRNA silencing but display developmental
defects. Fungal Genet Biol 44:504–516
Nicolas FE, Moxon S, de Haro JP, Calo S, Grigoriev IV,
Torres-Martı ´nez S, Moulton V, Ruiz-Va ´zquez
RM, Dalmay T (2010) Endogenous short RNAs
generated by dicer 2 and RNA-dependent RNA
polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Res
38:5535–5541
Nicola ´s FE, Torres-Martı ´nez S, Ruiz-Va ´zquez RM
(2013) Loss and retention of RNA interference in
fungi and parasites. PLoS Pathog 9:e1003089
Nicola ´s FE, Vila A, Moxon S, Cascales MD, TorresMartı ´nez S, Ruiz-Va ´zquez RM, Garre V (2015)
The RNAi machinery controls distinct responses
to environmental signals in the basal fungus
Mucor circinelloides. BMC Genomics 16:237
Noble LM, Holland LM, McLauchlan AJ, Andrianopoulos A (2016) A plastic vegetative growth threshold
governs reproductive capacity in Aspergillus nidulans. Genetics 204:1161–1175
Nolan T, Braccini L, Azzalin G, De Toni A, Macino G,
Cogoni C (2005) The post-transcriptional gene
silencing machinery functions independently of
DNA methylation to repress a LINE1-like retrotransposon in Neurospora crassa. Nucleic Acids
Res 33:1564–1573
Nowara D, Gay A, Lacomme C, Shaw J, Ridout C,
Douchkov D, Hensel G, Kumlehn J, Schweizer P
(2010) HIGS: host-induced gene silencing in the
obligate biotrophic fungal pathogen Blumeria graminis. Plant Cell 22:3130–3141
Nunes CC, Dean RA (2012) Host-induced gene silencing: a tool for understanding fungal host interaction and for developing novel disease control
strategies. Mol Plant Pathol 13:519–529
Panwar V, McCallum B, Bakkeren G (2013) Hostinduced gene silencing of wheat leaf rust fungus
Puccinia triticina pathogenicity genes mediated by
the barley stripe mosaic virus. Plant Mol Biol
81:595–608
Papp T, Csernetics A ´ , Nagy G, Bencsik O, Iturriaga EA,
Eslava AP, Va ´gvo ¨lgyi C (2013) Canthaxanthin production with modified Mucor circinelloides strains.
Appl Microbiol Biotechnol 97:4937–4950
Peres da Silva R, Puccia R, Rodrigues ML, Oliveira DL,
Joffe LS, Ce ´sar GV, Nimrichter L, Goldenberg S,
Alves LR (2015) Extracellular vesicle-mediated
export of fungal RNA. Sci Rep 5:7763
120
F. E. Nicola ´s et al.
Bamford DH, Liu Y (2009) qiRNA, a new type of
small interfering RNA induced by DNA damage.
Nature 459:274–277
Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC,
Liu Y (2010) Diverse pathways generate
microRNA-like RNAs and dicer-independent
small interfering RNAs in fungi. Mol Cell
38:803–814
Lin YL, Ma LT, Lee YR, Lin SS, Wang SY, Chang TT,
Shaw JF, Li WH, Chu FH (2015) MicroRNA-like
small RNAs prediction in the development of
Antrodia cinnamomea. PLoS One 10:e0123245
Liu Y, Lee HC, Aalto AP, Yang Q, Chang SS, Huang G,
Fisher D, Cha J, Poranen MM, Bamford DH (2010)
The DNA/RNA-dependent RNA polymerase QDE1 generates aberrant RNA and dsRNA for RNAi in
a process requiring replication protein a and a
DNA helicase. PLoS Biol 8:e1000496
Lo ´pez-Camarillo C, Marchat LA (2013) MicroRNAs in
cancer. Annu Rev Pathol 9:287–314
Lu WT, Hawley BR, Skalka GL, Baldock RA, Smith EM,
Bader AS, Malewicz M, Watts FZ, Wilczynska A,
Bushell M (2018) Drosha drives the formation of
DNA:RNA hybrids around DNA break sites to
facilitate DNA repair. Nat Commun 9:532
Martienssen R, Moazed D (2015) RNAi and heterochromatin. Cold Spring Harb Perspect Biol 7:a019323
Meussen BJ, De Graaff LH, Sanders JPM, Weusthuis RA
(2012) Metabolic engineering of Rhizopus oryzae
for the production of platform chemicals. Appl
Microbiol Biotechnol 94:875–886
Michalik KM, Bo ¨ttcher R, Fo ¨rstemann K (2012) A small
RNA response at DNA ends in Drosophila. Nucleic
Acids Res 40:9596–9603
Michielse CB, Salim K, Ragas P, Ram AFJ, Kudla B,
Jarry B, Punt PJ, Van Den Hondel CAMJJ (2004)
Development of a system for integrative and stable
transformation of the zygomycete Rhizopus oryzae
by agrobacterium-mediated DNA transfer. Mol
Gen Genomics 271:499–510
Mochama P, Jadhav P, Neupane A, Marzano SYL (2018)
Mycoviruses as triggers and targets of RNA silencing in white mold fungus Sclerotinia sclerotiorum.
Viruses 10:214
Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska
M, Ginalski K (2017) Cut-and-paste transposons
in fungi with diverse lifestyles. Genome Biol Evol
9:3463–3477
Nakayashiki H, Kadotani N, Mayama S (2006) Evolution and diversification of RNA silencing proteins
in fungi. J Mol Evol 63:127–135
Napoli C, Lemieux C, Jorgensen R (1990) Introduction
of a chimeric chalcone synthase gene into Petunia
results in reversible co-suppression of homologous genes in trans. Plant Cell 2:279–289
Nevers A, Doyen A, Malabat C, Ne ´ron B, Kergrohen T,
Jacquier A, Badis G (2018) Antisense transcriptional interference mediates condition-specific
gene repression in budding yeast. Nucleic Acids
Res 46:6009–6025
Nicola ´s FE, Torres-Martı ´nez S, Ruiz-Va ´zquez RM
(2003) Two classes of small antisense RNAs in
fungal RNA silencing triggered by non-integrative
transgenes. EMBO J 22:3983–3991
Nicola ´s FE, de Haro JP, Torres-Martı ´nez S, Ruiz-Va ´zquez RM (2007) Mutants defective in a Mucor
circinelloides dicer-like gene are not compromised
in siRNA silencing but display developmental
defects. Fungal Genet Biol 44:504–516
Nicolas FE, Moxon S, de Haro JP, Calo S, Grigoriev IV,
Torres-Martı ´nez S, Moulton V, Ruiz-Va ´zquez
RM, Dalmay T (2010) Endogenous short RNAs
generated by dicer 2 and RNA-dependent RNA
polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Res
38:5535–5541
Nicola ´s FE, Torres-Martı ´nez S, Ruiz-Va ´zquez RM
(2013) Loss and retention of RNA interference in
fungi and parasites. PLoS Pathog 9:e1003089
Nicola ´s FE, Vila A, Moxon S, Cascales MD, TorresMartı ´nez S, Ruiz-Va ´zquez RM, Garre V (2015)
The RNAi machinery controls distinct responses
to environmental signals in the basal fungus
Mucor circinelloides. BMC Genomics 16:237
Noble LM, Holland LM, McLauchlan AJ, Andrianopoulos A (2016) A plastic vegetative growth threshold
governs reproductive capacity in Aspergillus nidulans. Genetics 204:1161–1175
Nolan T, Braccini L, Azzalin G, De Toni A, Macino G,
Cogoni C (2005) The post-transcriptional gene
silencing machinery functions independently of
DNA methylation to repress a LINE1-like retrotransposon in Neurospora crassa. Nucleic Acids
Res 33:1564–1573
Nowara D, Gay A, Lacomme C, Shaw J, Ridout C,
Douchkov D, Hensel G, Kumlehn J, Schweizer P
(2010) HIGS: host-induced gene silencing in the
obligate biotrophic fungal pathogen Blumeria graminis. Plant Cell 22:3130–3141
Nunes CC, Dean RA (2012) Host-induced gene silencing: a tool for understanding fungal host interaction and for developing novel disease control
strategies. Mol Plant Pathol 13:519–529
Panwar V, McCallum B, Bakkeren G (2013) Hostinduced gene silencing of wheat leaf rust fungus
Puccinia triticina pathogenicity genes mediated by
the barley stripe mosaic virus. Plant Mol Biol
81:595–608
Papp T, Csernetics A ´ , Nagy G, Bencsik O, Iturriaga EA,
Eslava AP, Va ´gvo ¨lgyi C (2013) Canthaxanthin production with modified Mucor circinelloides strains.
Appl Microbiol Biotechnol 97:4937–4950
Peres da Silva R, Puccia R, Rodrigues ML, Oliveira DL,
Joffe LS, Ce ´sar GV, Nimrichter L, Goldenberg S,
Alves LR (2015) Extracellular vesicle-mediated
export of fungal RNA. Sci Rep 5:7763
120
F. E. Nicola ´s et al.