VEZF1 Elements Mediate Protection from DNA Methylation


There is growing consensus that genome organization and long-range gene regulation involves partitioning of the genome into domains of distinct epigenetic chromatin states. Chromatin insulator or barrier elements are key components of these processes as they can establish boundaries between chromatin states. The ability of elements such as the paradigm β-globin HS4 insulator to block the range of enhancers or the spread of repressive histone modifications is well established. Here we have addressed the hypothesis that a barrier element in vertebrates should be capable of defending a gene from silencing by DNA methylation. Using an established stable reporter gene system, we find that HS4 acts specifically to protect a gene promoter from de novo DNA methylation. Notably, protection from methylation can occur in the absence of histone acetylation or transcription. There is a division of labor at HS4; the sequences that mediate protection from methylation are separable from those that mediate CTCF-dependent enhancer blocking and USF-dependent histone modification recruitment. The zinc finger protein VEZF1 was purified as the factor that specifically interacts with the methylation protection elements. VEZF1 is a candidate CpG island protection factor as the G-rich sequences bound by VEZF1 are frequently found at CpG island promoters. Indeed, we show that VEZF1 elements are sufficient to mediate demethylation and protection of the APRT CpG island promoter from DNA methylation. We propose that many barrier elements in vertebrates will prevent DNA methylation in addition to blocking the propagation of repressive histone modifications, as either process is sufficient to direct the establishment of an epigenetically stable silent chromatin state.


Vyšlo v časopise: VEZF1 Elements Mediate Protection from DNA Methylation. PLoS Genet 6(1): e32767. doi:10.1371/journal.pgen.1000804
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1000804

Souhrn

There is growing consensus that genome organization and long-range gene regulation involves partitioning of the genome into domains of distinct epigenetic chromatin states. Chromatin insulator or barrier elements are key components of these processes as they can establish boundaries between chromatin states. The ability of elements such as the paradigm β-globin HS4 insulator to block the range of enhancers or the spread of repressive histone modifications is well established. Here we have addressed the hypothesis that a barrier element in vertebrates should be capable of defending a gene from silencing by DNA methylation. Using an established stable reporter gene system, we find that HS4 acts specifically to protect a gene promoter from de novo DNA methylation. Notably, protection from methylation can occur in the absence of histone acetylation or transcription. There is a division of labor at HS4; the sequences that mediate protection from methylation are separable from those that mediate CTCF-dependent enhancer blocking and USF-dependent histone modification recruitment. The zinc finger protein VEZF1 was purified as the factor that specifically interacts with the methylation protection elements. VEZF1 is a candidate CpG island protection factor as the G-rich sequences bound by VEZF1 are frequently found at CpG island promoters. Indeed, we show that VEZF1 elements are sufficient to mediate demethylation and protection of the APRT CpG island promoter from DNA methylation. We propose that many barrier elements in vertebrates will prevent DNA methylation in addition to blocking the propagation of repressive histone modifications, as either process is sufficient to direct the establishment of an epigenetically stable silent chromatin state.


Zdroje

1. KellumR

SchedlP

1991 A position-effect assay for boundaries of higher order chromosomal domains. Cell 64 941 950

2. StalderJ

LarsenA

EngelJD

DolanM

GroudineM

1980 Tissue-specific DNA cleavages in the globin chromatin domain introduced by DNAase I. Cell 20 451 460

3. GasznerM

FelsenfeldG

2006 Insulators: exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet 7 703 713

4. ValenzuelaL

KamakakaRT

2006 Chromatin insulators. Annu Rev Genet 40 107 138

5. WallaceJA

FelsenfeldG

2007 We gather together: insulators and genome organization. Curr Opin Genet Dev 17 400 407

6. WestAG

FraserP

2005 Remote control of gene transcription. Hum Mol Genet 14 Spec No 1 R101 111

7. WestAG

GasznerM

FelsenfeldG

2002 Insulators: many functions, many mechanisms. Genes Dev 16 271 288

8. ChungJH

WhiteleyM

FelsenfeldG

1993 A 5′ element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell 74 505 514

9. BellAC

WestAG

FelsenfeldG

1999 The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 98 387 396

10. PikaartMJ

Recillas-TargaF

FelsenfeldG

1998 Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulators. Genes Dev 12 2852 2862

11. ChungJH

BellAC

FelsenfeldG

1997 Characterization of the chicken beta-globin insulator. Proc Natl Acad Sci U S A 94 575 580

12. Recillas-TargaF

PikaartMJ

Burgess-BeusseB

BellAC

LittMD

2002 Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities. Proc Natl Acad Sci U S A 99 6883 6888

13. YaoS

OsborneCS

BharadwajRR

PasceriP

SukonnikT

2003 Retrovirus silencer blocking by the cHS4 insulator is CTCF independent. Nucleic Acids Res 31 5317 5323

14. WestAG

HuangS

GasznerM

LittMD

FelsenfeldG

2004 Recruitment of histone modifications by USF proteins at a vertebrate barrier element. Molecular Cell 16 453 463

15. HuangS

LiX

YusufzaiTM

QiuY

FelsenfeldG

2007 USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier. Mol Cell Biol 27 7991 8002

16. MutskovVJ

FarrellCM

WadePA

WolffeAP

FelsenfeldG

2002 The barrier function of an insulator couples high histone acetylation levels with specific protection of promoter DNA from methylation. Genes Dev 16 1540 1554

17. LiCL

EmeryDW

2008 The cHS4 chromatin insulator reduces gammaretroviral vector silencing by epigenetic modifications of integrated provirus. Gene Ther 15 49 53

18. MutskovV

FelsenfeldG

2004 Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9. Embo J 23 138 149

19. AitsebaomoJ

Kingsley-KallesenML

WuY

QuertermousT

PattersonC

2001 Vezf1/DB1 is an endothelial cell-specific transcription factor that regulates expression of the endothelin-1 promoter. J Biol Chem 276 39197 39205

20. Koyano-NakagawaN

NishidaJ

BaldwinD

AraiK

YokotaT

1994 Molecular cloning of a novel human cDNA encoding a zinc finger protein that binds to the interleukin-3 promoter. Mol Cell Biol 14 5099 5107

21. LewisCD

ClarkSP

FelsenfeldG

GouldH

1988 An erythrocyte-specific protein that binds to the poly(dG) region of the chicken beta-globin gene promoter. Genes Dev 2 863 873

22. BartonMC

MadaniN

EmersonBM

1993 The erythroid protein cGATA-1 functions with a stage-specific factor to activate transcription of chromatin-assembled beta-globin genes. Genes Dev 7 1796 1809

23. BuckleR

BalmerM

YenidunyaA

AllanJ

1991 The promoter and enhancer of the inactive chicken beta-globin gene contains precisely positioned nucleosomes. Nucleic Acids Res 19 1219 1226

24. JacksonPD

EvansT

NickolJM

FelsenfeldG

1989 Developmental modulation of protein binding to beta-globin gene regulatory sites within chicken erythrocyte nuclei. Genes Dev 3 1860 1873

25. ClarkSP

LewisCD

FelsenfeldG

1990 Properties of BGP1, a poly(dG)-binding protein from chicken erythrocytes. Nucleic Acids Res 18 5119 5126

26. WendtKS

YoshidaK

ItohT

BandoM

KochB

2008 Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451 796 801

27. GowherH

StuhlmannH

FelsenfeldG

2008 Vezf1 regulates genomic DNA methylation through its effects on expression of DNA methyltransferase Dnmt3b. Genes Dev 22 2075 2084

28. BrandeisM

FrankD

KeshetI

SiegfriedZ

MendelsohnM

1994 Sp1 elements protect a CpG island from de novo methylation. Nature 371 435 438

29. MacleodD

CharltonJ

MullinsJ

BirdAP

1994 Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev 8 2282 2292

30. MarinM

KarisA

VisserP

GrosveldF

PhilipsenS

1997 Transcription factor Sp1 is essential for early embryonic development but dispensable for cell growth and differentiation. Cell 89 619 628

31. TalbertPB

HenikoffS

2006 Spreading of silent chromatin: inaction at a distance. Nat Rev Genet 7 793 803

32. IssaJP

2004 CpG island methylator phenotype in cancer. Nat Rev Cancer 4 988 993

33. TurkerMS

2002 Gene silencing in mammalian cells and the spread of DNA methylation. Oncogene 21 5388 5393

34. HuangS

LittM

FelsenfeldG

2005 Methylation of histone H4 by arginine methyltransferase PRMT1 is essential in vivo for many subsequent histone modifications. Genes Dev 19 1885 1893

35. PrioleauMN

NonyP

SimpsonM

FelsenfeldG

1999 An insulator element and condensed chromatin region separate the chicken beta-globin locus from an independently regulated erythroid-specific folate receptor gene. Embo J 18 4035 4048

36. PrioleauMN

GendronMC

HyrienO

2003 Replication of the chicken beta-globin locus: early-firing origins at the 5′ HS4 insulator and the rho- and betaA-globin genes show opposite epigenetic modifications. Mol Cell Biol 23 3536 3549

37. SzaboPE

TangSH

ReedMR

SilvaFJ

TsarkWM

2002 The chicken beta-globin insulator element conveys chromatin boundary activity but not imprinting at the mouse Igf2/H19 domain. Development 129 897 904

38. LinIG

HsiehCL

2001 Chromosomal DNA demethylation specified by protein binding. EMBO Rep 2 108 112

39. AntequeraF

BirdA

1993 Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci U S A 90 11995 11999

40. RakyanVK

DownTA

ThorneNP

FlicekP

KuleshaE

2008 An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 18 1518 1529

41. StraussmanR

NejmanD

RobertsD

SteinfeldI

BlumB

2009 Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 16 564 571

42. SuzukiMM

BirdA

2008 DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9 465 476

43. JonesPA

BaylinSB

2007 The epigenomics of cancer. Cell 128 683 692

44. FanS

FangF

ZhangX

ZhangMQ

2007 Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome. PLoS ONE 2 e1184

45. OkiM

ValenzuelaL

ChibaT

ItoT

KamakakaRT

2004 Barrier proteins remodel and modify chromatin to restrict silenced domains. Mol Cell Biol 24 1956 1967

46. HashimshonyT

ZhangJ

KeshetI

BustinM

CedarH

2003 The role of DNA methylation in setting up chromatin structure during development. Nat Genet 34 187 192

47. JaenischR

BirdA

2003 Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 Suppl 245 254

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Genetika Reprodukčná medicína

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PLOS Genetics


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