DNA Methylation and Normal Chromosome Behavior in Neurospora Depend on Five Components of a Histone Methyltransferase Complex, DCDC
Methylation of DNA and of Lysine 9 on histone H3 (H3K9) is associated with gene silencing in many animals, plants, and fungi. In Neurospora crassa, methylation of H3K9 by DIM-5 directs cytosine methylation by recruiting a complex containing Heterochromatin Protein-1 (HP1) and the DIM-2 DNA methyltransferase. We report genetic, proteomic, and biochemical investigations into how DIM-5 is controlled. These studies revealed DCDC, a previously unknown protein complex including DIM-5, DIM-7, DIM-9, CUL4, and DDB1. Components of DCDC are required for H3K9me3, proper chromosome segregation, and DNA methylation. DCDC-defective strains, but not HP1-defective strains, are hypersensitive to MMS, revealing an HP1-independent function of H3K9 methylation. In addition to DDB1, DIM-7, and the WD40 domain protein DIM-9, other presumptive DCAFs (DDB1/CUL4 associated factors) co-purified with CUL4, suggesting that CUL4/DDB1 forms multiple complexes with distinct functions. This conclusion was supported by results of drug sensitivity tests. CUL4, DDB1, and DIM-9 are not required for localization of DIM-5 to incipient heterochromatin domains, indicating that recruitment of DIM-5 to chromatin is not sufficient to direct H3K9me3. DIM-7 is required for DIM-5 localization and mediates interaction of DIM-5 with DDB1/CUL4 through DIM-9. These data support a two-step mechanism for H3K9 methylation in Neurospora.
Vyšlo v časopise:
DNA Methylation and Normal Chromosome Behavior in Neurospora Depend on Five Components of a Histone Methyltransferase Complex, DCDC. PLoS Genet 6(11): e32767. doi:10.1371/journal.pgen.1001196
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1001196
Souhrn
Methylation of DNA and of Lysine 9 on histone H3 (H3K9) is associated with gene silencing in many animals, plants, and fungi. In Neurospora crassa, methylation of H3K9 by DIM-5 directs cytosine methylation by recruiting a complex containing Heterochromatin Protein-1 (HP1) and the DIM-2 DNA methyltransferase. We report genetic, proteomic, and biochemical investigations into how DIM-5 is controlled. These studies revealed DCDC, a previously unknown protein complex including DIM-5, DIM-7, DIM-9, CUL4, and DDB1. Components of DCDC are required for H3K9me3, proper chromosome segregation, and DNA methylation. DCDC-defective strains, but not HP1-defective strains, are hypersensitive to MMS, revealing an HP1-independent function of H3K9 methylation. In addition to DDB1, DIM-7, and the WD40 domain protein DIM-9, other presumptive DCAFs (DDB1/CUL4 associated factors) co-purified with CUL4, suggesting that CUL4/DDB1 forms multiple complexes with distinct functions. This conclusion was supported by results of drug sensitivity tests. CUL4, DDB1, and DIM-9 are not required for localization of DIM-5 to incipient heterochromatin domains, indicating that recruitment of DIM-5 to chromatin is not sufficient to direct H3K9me3. DIM-7 is required for DIM-5 localization and mediates interaction of DIM-5 with DDB1/CUL4 through DIM-9. These data support a two-step mechanism for H3K9 methylation in Neurospora.
Zdroje
1. ReikW
DeanW
WalterJ
2001 Epigenetic reprogramming in mammalian development. Science 293 1089 1093
2. ReikW
WalterJ
2001 Genomic imprinting: parental influence on the genome. Nat Rev Genet 2 21 32
3. MiuraA
YonebayashiS
WatanabeK
ToyamaT
ShimadaH
2001 Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411 212 214
4. HeardE
DistecheCM
2006 Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 20 1848 1867
5. WeberM
SchubelerD
2007 Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr Opin Cell Biol 19 273 280
6. SazeH
ShiraishiA
MiuraA
KakutaniT
2008 Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 319 462 465
7. HondaS
LewisZA
HuarteM
ChoLY
DavidLL
2010 The DMM complex prevents spreading of DNA methylation from transposons to nearby genes in Neurospora crassa. Genes Dev 24 443 454
8. JonesPA
BaylinSB
2007 The epigenomics of cancer. Cell 128 683 692
9. LewisZA
HondaS
KhlafallahTK
JeffressJK
FreitagM
2009 Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res 19 427 437
10. SelkerEU
TountasNA
CrossSH
MargolinBS
MurphyJG
2003 The methylated component of the Neurospora crassa genome. Nature 422 893 897
11. CambareriEB
JensenBC
SchabtachE
SelkerEU
1989 Repeat-induced G-C to A-T mutations in Neurospora. Science 244 1571 1575
12. SelkerEU
1990 Premeiotic instability of repeated sequences in Neurospora crassa. Annu Rev Genet 24 579 613
13. MiaoVP
FreitagM
SelkerEU
2000 Short TpA-rich segments of the zeta-eta region induce DNA methylation in Neurospora crassa. J Mol Biol 300 249 273
14. TamaruH
SelkerEU
2003 Synthesis of Signals for De Novo DNA Methylation in Neurospora crassa. Mol Cell Biol 23 2379 2394
15. KouzminovaEA
SelkerEU
2001 dim-2 encodes a DNA-methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO Journal 20 4309 4323
16. TamaruH
SelkerEU
2001 A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414 277 283
17. FreitagM
HickeyPC
KhlafallahTK
ReadND
SelkerEU
2004 HP1 is essential for DNA methylation in Neurospora. Mol Cell 13 427 434
18. LewisZA
AdhvaryuKK
HondaS
ShiverAL
SelkerEU
2010 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
19. LehnertzB
UedaY
DerijckAA
BraunschweigU
Perez-BurgosL
2003 Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol 13 1192 1200
20. JacksonJP
LindrothAM
CaoX
JacobsenSE
2002 Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416 556 560
21. MalagnacF
BarteeL
BenderJ
2002 An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 21 6842 6852
22. TamaruH
ZhangX
McMillenD
SinghPB
NakayamaJ
2003 Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet 34 75 79
23. HondaS
SelkerEU
2008 Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Mol Cell Biol 28 6044 6055
24. FossHM
RobertsCJ
ClaeysKM
SelkerEU
1993 Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation. Science 262 1737 1741
25. ColotHV
ParkG
TurnerGE
RingelbergC
CrewCM
2006 A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A 103 10352 10357
26. SmithKM
DobosyJR
ReifsnyderJE
RountreeMR
AndersonDC
2010 H2B- and H3-specific histone deacetylases are required for DNA methylation in Neurospora crassa. Genetics(in press)
27. PetroskiMD
DeshaiesRJ
2005 Function and regulation of cullin-RING ubiquitin ligases. Nat Rev Mol Cell Biol 6 9 20
28. HornPJ
BastieJN
PetersonCL
2005 A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev 19 1705 1714
29. JiaS
KobayashiR
GrewalSI
2005 Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat Cell Biol 7 1007 1013
30. HigaLA
WuM
YeT
KobayashiR
SunH
2006 CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat Cell Biol 8 1277 1283
31. HondaS
SelkerEU
2009 Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purification. Genetics 182 11 23
32. HigaLA
ZhangH
2007 Stealing the spotlight: CUL4-DDB1 ubiquitin ligase docks WD40-repeat proteins to destroy. Cell Div 2 5
33. LeeJ
ZhouP
2007 DCAFs, the missing link of the CUL4-DDB1 ubiquitin ligase. Mol Cell 26 775 780
34. ShiuPK
RajuNB
ZicklerD
MetzenbergRL
2001 Meiotic silencing by unpaired DNA. Cell 107 905 916
35. MorrisonDK
2009 The 14-3-3 proteins: integrators of diverse signaling cues that impact cell fate and cancer development. Trends Cell Biol 19 16 23
36. HongEJ
VillenJ
GeraceEL
GygiSP
MoazedD
2005 A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for RNAi-mediated heterochromatin formation. RNA Biol 2 106 111
37. PallML
1993 The use of Ignite (Basta;glufosinate;phosphinothricin) to select transformants of bar-containing plasmids in Neurospora crassa. Fungal Genetics Newsletter 40 58
38. NinomiyaY
SuzukiK
IshiiC
InoueH
2004 Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining. Proc Natl Acad Sci U S A 101 12248 12253
39. VogelMJ
Peric-HupkesD
van SteenselB
2007 Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2 1467 1478
40. ZhaoY
ShenY
YangS
WangJ
HuQ
2010 Ubiquitin ligase components Cullin4 and DDB1 are essential for DNA methylation in Neurospora crassa. J Biol Chem 285 4355 4365
41. KaganskyA
FolcoHD
AlmeidaR
PidouxAL
BoukabaA
2009 Synthetic heterochromatin bypasses RNAi and centromeric repeats to establish functional centromeres. Science 324 1716 1719
42. KellumR
AlbertsBM
1995 Heterochromatin protein 1 is required for correct chromosome segregation in Drosophila embryos. J Cell Sci 108 1419 1431
43. BernardP
MaureJF
PartridgeJF
GenierS
JaverzatJP
2001 Requirement of heterochromatin for cohesion at centromeres. Science 294 2539 2542
44. NonakaN
KitajimaT
YokobayashiS
XiaoG
YamamotoM
2002 Recruitment of cohesin to heterochromatic regions by Swi6/HP1 in fission yeast. Nat Cell Biol 4 89 93
45. PetersAH
O'CarrollD
ScherthanH
MechtlerK
SauerS
2001 Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107 323 337
46. ZhangK
MoschK
FischleW
GrewalSI
2008 Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat Struct Mol Biol 15 381 388
47. BayneEH
WhiteSA
KaganskyA
BijosDA
Sanchez-PulidoL
2010 Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell 140 666 677
48. FreitagM
LeeDW
KotheGO
PrattRJ
AramayoR
2004 DNA methylation is independent of RNA interference in Neurospora. Science 304 1939
49. FritschL
RobinP
MathieuJR
SouidiM
HinauxH
2010 A subset of the histone H3 lysine 9 methyltransferases Suv39h1, G9a, GLP, and SETDB1 participate in a multimeric complex. Mol Cell 37 46 56
50. DavisRH
2000 Neurospora: Contributions of a Model Organism: Oxford Oxford University Press 333
51. MargolinBS
FreitagM
SelkerEU
1997 Improved plasmids for gene targeting at the his-3 locus of Neurospora crassa by electroporation. Fungal Genetics Newsletter 44 34 36
52. PomraningKR
SmithKM
FreitagM
2009 Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47 142 150
53. RountreeMR
SelkerEU
1997 DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev 11 2383 2395
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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