required for DNA methylation in Neurospora
crassa. Mol Cell Biol 28:6044–6055
Hurley J, Loros JJ, Dunlap JC (2015) Dissecting the
mechanisms of the clock in Neurospora. Methods
Enzymol 551:29–52
Iyer V, Struhl K (1995) Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its
intrinsic DNA structure. EMBO J 14:2570–2579
Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002)
Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature
416:556–560
Jamieson K, McNaught KJ, Ormsby T et al (2018) Telomere repeats induce domains of H3K27 methylation in Neurospora. elife 7:e31216. https://doi.org/
10.7554/eLife.31216
Jamieson K, Rountree MR, Lewis ZA et al (2013)
Regional control of histone H3 lysine 27 methylation in Neurospora. Proc Natl Acad Sci U S A
110:6027–6032
Jamieson K, Wiles ET, McNaught KJ et al (2016) Loss of
HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at
constitutive heterochromatin. Genome Res
26:97–107
Janevska S, Baumann L, Sieber CMK et al (2018) Elucidation of the two H3K36me3 histone methyltransferases Set2 and Ash1 in Fusarium fujikuroi
unravels their different chromosomal targets and
a major impact of Ash1 on genome stability.
Genetics 208:153–171
Janssen A, Colmenares SU, Karpen GH (2018) Heterochromatin: guardian of the genome. Annu Rev Cell
Dev Biol 34:265–288
Jiao L, Liu X (2015) Structural basis of histone H3K27
trimethylation by an active polycomb repressive
complex 2. Science 350:aac4383
Joshi AA, Struhl K (2005) Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to pol II elongation. Mol Cell 20:971–978
Keogh M-C, Kurdistani SK, Morris SA et al (2005)
Cotranscriptional set2 methylation of histone H3
lysine 36 recruits a repressive Rpd3 complex. Cell
123:593–605
Kizer KO, Phatnani HP, Shibata Y et al (2005) A novel
domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation
with transcript elongation. Mol Cell Biol 25:3305–
3316
Klocko AD, Ormsby T, Galazka JM et al (2016) Normal
chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora
crassa. Proc Natl Acad Sci U S A 113:15048–15053
Klocko AD, Rountree MR, Grisafi PL et al (2015) Neurospora importin a is required for normal heterochromatic formation and DNA methylation. PLoS
Genet 11:e1005083
Klocko AD, Uesaka M, Ormsby T et al (2019) Nucleosome positioning by an evolutionarily conserved
chromatin remodeler prevents aberrant DNA
methylation in. Genetics 211:563–578
Kornberg RD (1974) Chromatin structure: a repeating
unit of histones and DNA. Science 184:868–871
Kouzminova E, Selker EU (2001) Dim-2 encodes a DNA
methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J 20:4309–
4323
Krietenstein N, Wal M, Watanabe S et al (2016) Genomic nucleosome organization reconstituted with
pure proteins. Cell 167:709–721.e12
Krogan NJ, Kim M, Tong A et al (2003) Methylation of
histone H3 by Set2 in Saccharomyces cerevisiae is
linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 23:4207–4218
Lai WKM, Pugh BF (2017) Understanding nucleosome
dynamics and their links to gene expression and
DNA replication. Nat Rev Mol Cell Biol 18:548–562
Lan H, Wu L, Sun R et al (2019) The HosA histone
deacetylase regulates alatoxin biosynthesis
through direct regulation of aflatoxin cluster
genes. Mol Plant-Microbe Interact 32(9):1210–
1228. MPMI01190033R
Lee H-C, Li L, Gu W et al (2010) Diverse pathways
generate microRNA-like RNAs and dicerindependent small interfering RNAs in fungi. Mol
Cell 38:803–814
Lewis ZA (2017) Polycomb Group Systems in Fungi:
new models for understanding Polycomb repressive complex 2. Trends Genet 33:220–231
Lewis ZA, Adhvaryu KK, Honda S et al (2010a) DNA
methylation and normal chromosome behavior in
Neurospora depend on five components of a histone methyltransferase complex, DCDC. PLoS
Genet 6:e1001196
Lewis ZA, Adhvaryu KK, Honda S et al (2010b) Identification of DIM-7, a protein required to target the
DIM-5 H3 methyltransferase to chromatin. Proc
Natl Acad Sci U S A 107:8310–8315
Lewis ZA, Honda S, Khlafallah TK et al (2009) Relics of
repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome
Res 19:427–437
Lieberman-Aiden E, van Berkum NL, Williams L et al
(2009) Comprehensive mapping of long-range
interactions reveals folding principles of the
human genome. Science 326:289–293
Liu X, Dang Y, Matsu-Ura T et al (2017) DNA replication is required for circadian clock function by
regulating rhythmic nucleosome composition.
Mol Cell 67:203–213.e4
Liu CL, Kaplan T, Kim M et al (2005) Singlenucleosome mapping of histone modifications in
S. cerevisiae. PLoS Biol 3:e328
Lombardi LM, Ellahi A, Rine J (2011) Direct regulation
of nucleosome density by the conserved AAAATPase Yta7. Proc Natl Acad Sci U S A 108:
E1302–E1311
Luger K, Ma ¨der AW, Richmond RK et al (1997) Crystal
structure of the nucleosome core particle at 2.8 a
resolution. Nature 389:251–260
Maeda K, Izawa M, Nakajima Y et al (2017) Increased
metabolite production by deletion of an HDA122
A. J. Courtney et al.
crassa. Mol Cell Biol 28:6044–6055
Hurley J, Loros JJ, Dunlap JC (2015) Dissecting the
mechanisms of the clock in Neurospora. Methods
Enzymol 551:29–52
Iyer V, Struhl K (1995) Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its
intrinsic DNA structure. EMBO J 14:2570–2579
Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002)
Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature
416:556–560
Jamieson K, McNaught KJ, Ormsby T et al (2018) Telomere repeats induce domains of H3K27 methylation in Neurospora. elife 7:e31216. https://doi.org/
10.7554/eLife.31216
Jamieson K, Rountree MR, Lewis ZA et al (2013)
Regional control of histone H3 lysine 27 methylation in Neurospora. Proc Natl Acad Sci U S A
110:6027–6032
Jamieson K, Wiles ET, McNaught KJ et al (2016) Loss of
HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at
constitutive heterochromatin. Genome Res
26:97–107
Janevska S, Baumann L, Sieber CMK et al (2018) Elucidation of the two H3K36me3 histone methyltransferases Set2 and Ash1 in Fusarium fujikuroi
unravels their different chromosomal targets and
a major impact of Ash1 on genome stability.
Genetics 208:153–171
Janssen A, Colmenares SU, Karpen GH (2018) Heterochromatin: guardian of the genome. Annu Rev Cell
Dev Biol 34:265–288
Jiao L, Liu X (2015) Structural basis of histone H3K27
trimethylation by an active polycomb repressive
complex 2. Science 350:aac4383
Joshi AA, Struhl K (2005) Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to pol II elongation. Mol Cell 20:971–978
Keogh M-C, Kurdistani SK, Morris SA et al (2005)
Cotranscriptional set2 methylation of histone H3
lysine 36 recruits a repressive Rpd3 complex. Cell
123:593–605
Kizer KO, Phatnani HP, Shibata Y et al (2005) A novel
domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation
with transcript elongation. Mol Cell Biol 25:3305–
3316
Klocko AD, Ormsby T, Galazka JM et al (2016) Normal
chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora
crassa. Proc Natl Acad Sci U S A 113:15048–15053
Klocko AD, Rountree MR, Grisafi PL et al (2015) Neurospora importin a is required for normal heterochromatic formation and DNA methylation. PLoS
Genet 11:e1005083
Klocko AD, Uesaka M, Ormsby T et al (2019) Nucleosome positioning by an evolutionarily conserved
chromatin remodeler prevents aberrant DNA
methylation in. Genetics 211:563–578
Kornberg RD (1974) Chromatin structure: a repeating
unit of histones and DNA. Science 184:868–871
Kouzminova E, Selker EU (2001) Dim-2 encodes a DNA
methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J 20:4309–
4323
Krietenstein N, Wal M, Watanabe S et al (2016) Genomic nucleosome organization reconstituted with
pure proteins. Cell 167:709–721.e12
Krogan NJ, Kim M, Tong A et al (2003) Methylation of
histone H3 by Set2 in Saccharomyces cerevisiae is
linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 23:4207–4218
Lai WKM, Pugh BF (2017) Understanding nucleosome
dynamics and their links to gene expression and
DNA replication. Nat Rev Mol Cell Biol 18:548–562
Lan H, Wu L, Sun R et al (2019) The HosA histone
deacetylase regulates alatoxin biosynthesis
through direct regulation of aflatoxin cluster
genes. Mol Plant-Microbe Interact 32(9):1210–
1228. MPMI01190033R
Lee H-C, Li L, Gu W et al (2010) Diverse pathways
generate microRNA-like RNAs and dicerindependent small interfering RNAs in fungi. Mol
Cell 38:803–814
Lewis ZA (2017) Polycomb Group Systems in Fungi:
new models for understanding Polycomb repressive complex 2. Trends Genet 33:220–231
Lewis ZA, Adhvaryu KK, Honda S et al (2010a) DNA
methylation and normal chromosome behavior in
Neurospora depend on five components of a histone methyltransferase complex, DCDC. PLoS
Genet 6:e1001196
Lewis ZA, Adhvaryu KK, Honda S et al (2010b) Identification of DIM-7, a protein required to target the
DIM-5 H3 methyltransferase to chromatin. Proc
Natl Acad Sci U S A 107:8310–8315
Lewis ZA, Honda S, Khlafallah TK et al (2009) Relics of
repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome
Res 19:427–437
Lieberman-Aiden E, van Berkum NL, Williams L et al
(2009) Comprehensive mapping of long-range
interactions reveals folding principles of the
human genome. Science 326:289–293
Liu X, Dang Y, Matsu-Ura T et al (2017) DNA replication is required for circadian clock function by
regulating rhythmic nucleosome composition.
Mol Cell 67:203–213.e4
Liu CL, Kaplan T, Kim M et al (2005) Singlenucleosome mapping of histone modifications in
S. cerevisiae. PLoS Biol 3:e328
Lombardi LM, Ellahi A, Rine J (2011) Direct regulation
of nucleosome density by the conserved AAAATPase Yta7. Proc Natl Acad Sci U S A 108:
E1302–E1311
Luger K, Ma ¨der AW, Richmond RK et al (1997) Crystal
structure of the nucleosome core particle at 2.8 a
resolution. Nature 389:251–260
Maeda K, Izawa M, Nakajima Y et al (2017) Increased
metabolite production by deletion of an HDA122
A. J. Courtney et al.