#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Nucleosomes Containing Methylated DNA Stabilize DNA Methyltransferases 3A/3B and Ensure Faithful Epigenetic Inheritance


How epigenetic information is propagated during somatic cell divisions is still unclear but is absolutely critical for preserving gene expression patterns and cellular identity. Here we show an unanticipated mechanism for inheritance of DNA methylation patterns where the epigenetic mark not only recruits the catalyzing enzyme but also regulates the protein level, i.e. the enzymatic product (5-methylcytosine) determines the level of the methylase, thus forming a novel homeostatic inheritance system. Nucleosomes containing methylated DNA stabilize de novo DNA methyltransferases, DNMT3A/3B, allowing little free DNMT3A/3B enzymes to exist in the nucleus. Stabilization of DNMT3A/3B on nucleosomes in methylated regions further promotes propagation of DNA methylation. However, reduction of cellular DNA methylation levels creating more potential CpG substrates counter-intuitively results in a dramatic decrease of DNMT3A/3B proteins due to diminished nucleosome binding and subsequent degradation of the unstable free proteins. These data show an unexpected self-regulatory inheritance mechanism that not only ensures somatic propagation of methylated states by DNMT1 and DNMT3A/3B enzymes but also prevents aberrant de novo methylation by causing degradation of free DNMT3A/3B enzymes.


Vyšlo v časopise: Nucleosomes Containing Methylated DNA Stabilize DNA Methyltransferases 3A/3B and Ensure Faithful Epigenetic Inheritance. PLoS Genet 7(2): e32767. doi:10.1371/journal.pgen.1001286
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1001286

Souhrn

How epigenetic information is propagated during somatic cell divisions is still unclear but is absolutely critical for preserving gene expression patterns and cellular identity. Here we show an unanticipated mechanism for inheritance of DNA methylation patterns where the epigenetic mark not only recruits the catalyzing enzyme but also regulates the protein level, i.e. the enzymatic product (5-methylcytosine) determines the level of the methylase, thus forming a novel homeostatic inheritance system. Nucleosomes containing methylated DNA stabilize de novo DNA methyltransferases, DNMT3A/3B, allowing little free DNMT3A/3B enzymes to exist in the nucleus. Stabilization of DNMT3A/3B on nucleosomes in methylated regions further promotes propagation of DNA methylation. However, reduction of cellular DNA methylation levels creating more potential CpG substrates counter-intuitively results in a dramatic decrease of DNMT3A/3B proteins due to diminished nucleosome binding and subsequent degradation of the unstable free proteins. These data show an unexpected self-regulatory inheritance mechanism that not only ensures somatic propagation of methylated states by DNMT1 and DNMT3A/3B enzymes but also prevents aberrant de novo methylation by causing degradation of free DNMT3A/3B enzymes.


Zdroje

1. BirdA

2002 DNA methylation patterns and epigenetic memory. Genes Dev 16 6 21

2. SuzukiMM

BirdA

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

3. JonesPA

BaylinSB

2007 The epigenomics of cancer. Cell 128 683 692

4. SharmaS

KellyTK

JonesPA

2010 Epigenetics in cancer. Carcinogenesis 31 27 36

5. OkanoM

BellDW

HaberDA

LiE

1999 DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99 247 257

6. LawJA

JacobsenSE

Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11 204 220

7. RheeI

BachmanKE

ParkBH

JairKW

YenRW

2002 DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 416 552 556

8. LiangG

ChanMF

TomigaharaY

TsaiYC

GonzalesFA

2002 Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. Mol Cell Biol 22 480 491

9. ChenT

UedaY

DodgeJE

WangZ

LiE

2003 Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol Cell Biol 23 5594 5605

10. RiggsAD

XiongZ

2004 Methylation and epigenetic fidelity. Proc Natl Acad Sci U S A 101 4 5

11. JonesPA

LiangG

2009 Rethinking how DNA methylation patterns are maintained. Nat Rev Genet 10 805 811

12. GowherH

LiebertK

HermannA

XuG

JeltschA

2005 Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J Biol Chem 280 13341 13348

13. OoiSK

QiuC

BernsteinE

LiK

JiaD

2007 DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448 714 717

14. OkitsuCY

HsiehCL

2007 DNA methylation dictates histone H3K4 methylation. Mol Cell Biol 27 2746 2757

15. WeberM

HellmannI

StadlerMB

RamosL

PaaboS

2007 Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39 457 466

16. 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

17. Epsztejn-LitmanS

FeldmanN

Abu-RemailehM

ShufaroY

GersonA

2008 De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat Struct Mol Biol 15 1176 1183

18. SharifJ

MutoM

TakebayashiS

SuetakeI

IwamatsuA

2007 The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450 908 912

19. MeilingerD

FellingerK

BultmannS

RothbauerU

BonapaceIM

2009 Np95 interacts with de novo DNA methyltransferases, Dnmt3a and Dnmt3b, and mediates epigenetic silencing of the viral CMV promoter in embryonic stem cells. EMBO Rep 10 1259 1264

20. AapolaU

KawasakiK

ScottHS

OllilaJ

VihinenM

2000 Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family. Genomics 65 293 298

21. Bourc'hisD

XuGL

LinCS

BollmanB

BestorTH

2001 Dnmt3L and the establishment of maternal genomic imprints. Science 294 2536 2539

22. JeongS

LiangG

SharmaS

LinJC

ChoiSH

2009 Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA. Mol Cell Biol 29 5366 5376

23. LinkPA

GangisettyO

JamesSR

Woloszynska-ReadA

TachibanaM

2009 Distinct roles for histone methyltransferases G9a and GLP in cancer germ-line antigen gene regulation in human cancer cells and murine embryonic stem cells. Mol Cancer Res 7 851 862

24. KondoY

ShenL

AhmedS

BoumberY

SekidoY

2008 Downregulation of histone H3 lysine 9 methyltransferase G9a induces centrosome disruption and chromosome instability in cancer cells. PLoS ONE 3 e2037 doi:10.1371/journal.pone.0002037

25. BachmanKE

RountreeMR

BaylinSB

2001 Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin. J Biol Chem 276 32282 32287

26. SchlesingerY

StraussmanR

KeshetI

FarkashS

HechtM

2007 Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 39 232 236

27. RheeI

JairKW

YenRW

LengauerC

HermanJG

2000 CpG methylation is maintained in human cancer cells lacking DNMT1. Nature 404 1003 1007

28. EggerG

JeongS

EscobarSG

CortezCC

LiTW

2006 Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts suggests an essential role for DNMT1 in cell survival. Proc Natl Acad Sci U S A 103 14080 14085

29. VegaFM

SevillaA

LazoPA

2004 p53 Stabilization and accumulation induced by human vaccinia-related kinase 1. Mol Cell Biol 24 10366 10380

30. WangL

WangJ

SunS

RodriguezM

YueP

2006 A novel DNMT3B subfamily, DeltaDNMT3B, is the predominant form of DNMT3B in non-small cell lung cancer. Int J Oncol 29 201 207

31. JairKW

BachmanKE

SuzukiH

TingAH

RheeI

2006 De novo CpG island methylation in human cancer cells. Cancer Res 66 682 692

32. KimGD

NiJ

KelesogluN

RobertsRJ

PradhanS

2002 Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases. EMBO J 21 4183 4195

33. VilkaitisG

SuetakeI

KlimasauskasS

TajimaS

2005 Processive methylation of hemimethylated CpG sites by mouse Dnmt1 DNA methyltransferase. J Biol Chem 280 64 72

34. Laird PW Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11 191 203

35. JiaD

JurkowskaRZ

ZhangX

JeltschA

ChengX

2007 Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449 248 251

36. LiJY

PuMT

HirasawaR

LiBZ

HuangYN

2007 Synergistic function of DNA methyltransferases Dnmt3a and Dnmt3b in the methylation of Oct4 and Nanog. Mol Cell Biol 27 8748 8759

37. HsiehCL

1999 In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b. Mol Cell Biol 19 8211 8218

38. YokochiT

RobertsonKD

2002 Preferential methylation of unmethylated DNA by Mammalian de novo DNA methyltransferase Dnmt3a. J Biol Chem 277 11735 11745

39. HansenKH

BrackenAP

PasiniD

DietrichN

GehaniSS

2008 A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol 10 1291 1300

40. FelsenfeldG

GroudineM

2003 Controlling the double helix. Nature 421 448 453

41. CollinsRE

NorthropJP

HortonJR

LeeDY

ZhangX

2008 The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nat Struct Mol Biol 15 245 250

42. MargueronR

JustinN

OhnoK

SharpeML

SonJ

2009 Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461 762 767

43. ChodavarapuRK

FengS

BernatavichuteYV

ChenPY

StroudH

Relationship between nucleosome positioning and DNA methylation. Nature

44. MargueronR

ReinbergD

Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 11 285 296

45. OkanoM

XieS

LiE

1998 Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat Genet 19 219 220

46. ShiY

WhetstineJR

2007 Dynamic regulation of histone lysine methylation by demethylases. Mol Cell 25 1 14

47. OtaniJ

NankumoT

AritaK

InamotoS

AriyoshiM

2009 Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. EMBO Rep 10 1235 1241

48. ZilbermanD

Coleman-DerrD

BallingerT

HenikoffS

2008 Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature 456 125 129

49. ZlatanovaJ

CaiafaP

2009 CTCF and its protein partners: divide and rule? J Cell Sci 122 1275 1284

50. WitcherM

EmersonBM

2009 Epigenetic silencing of the p16(INK4a) tumor suppressor is associated with loss of CTCF binding and a chromatin boundary. Mol Cell 34 271 284

51. GraffJR

HermanJG

MyohanenS

BaylinSB

VertinoPM

1997 Mapping patterns of CpG island methylation in normal and neoplastic cells implicates both upstream and downstream regions in de novo methylation. J Biol Chem 272 22322 22329

52. KeshetI

SchlesingerY

FarkashS

RandE

HechtM

2006 Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 38 149 153

53. CoolenMW

StirzakerC

SongJZ

StathamAL

KassirZ

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol 12 235 246

54. HuangTH

PerryMR

LauxDE

1999 Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 8 459 470

55. EggerG

LiangG

AparicioA

JonesPA

2004 Epigenetics in human disease and prospects for epigenetic therapy. Nature 429 457 463

56. OuCY

KimJH

YangCK

StallcupMR

2009 Requirement of cell cycle and apoptosis regulator 1 for target gene activation by Wnt and beta-catenin and for anchorage-independent growth of human colon carcinoma cells. J Biol Chem 284 20629 20637

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2011 Číslo 2
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Získaná hemofilie - Povědomí o nemoci a její diagnostika
nový kurz

Eozinofilní granulomatóza s polyangiitidou
Autori: doc. MUDr. Martina Doubková, Ph.D.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#