CTCF-Dependent Chromatin Bias Constitutes Transient Epigenetic Memory of the Mother at the Imprinting Control Region in Prospermatogonia

1. Ferguson-SmithAC

SuraniMA

2001 Imprinting and the epigenetic asymmetry between parental genomes. Science 293 1086 1089

2. ReikW

WalterJ

2001 Genomic imprinting: parental influence on the genome. Nat Rev Genet 2 21 32

3. MannJR

SzabóPE

ReedMR

Singer-SamJ

2000 Methylated DNA sequences in genomic imprinting. Crit Rev Eukaryot Gene Expr 10 241 257

4. WutzA

SmrzkaOW

SchweiferN

SchellanderK

WagnerEF

1997 Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389 745 749

5. ThorvaldsenJL

BartolomeiMS

2000 Molecular biology. Mothers setting boundaries. Science 288 2145 2146

6. FitzpatrickGV

SolowayPD

HigginsMJ

2002 Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat Genet 32 426 431

7. Ferguson-SmithA

LinSP

TsaiCE

YoungsonN

TevendaleM

2003 Genomic imprinting—insights from studies in mice. Semin Cell Dev Biol 14 43 49

8. WilliamsonCM

TurnerMD

BallST

NottinghamWT

GlenisterP

2006 Identification of an imprinting control region affecting the expression of all transcripts in the Gnas cluster. Nat Genet 38 350 355

9. HataK

OkanoM

LeiH

LiE

2002 Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development 129 1983 1993

10. LiE

BeardC

JaenischR

1993 Role for DNA methylation in genomic imprinting. Nature 366 362 365

11. Bourc'hisD

XuGL

LinCS

BollmanB

BestorTH

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

12. KanedaM

OkanoM

HataK

SadoT

TsujimotoN

2004 Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 429 900 903

13. BrannanCI

BartolomeiMS

1999 Mechanisms of genomic imprinting. Curr Opin Genet Dev 9 164 170

14. KafferCR

GrinbergA

PfeiferK

2001 Regulatory mechanisms at the mouse Igf2/H19 locus. Mol Cell Biol 21 8189 8196

15. LeightonPA

SaamJR

IngramRS

StewartCL

TilghmanSM

1995 An enhancer deletion affects both H19 and Igf2 expression. Genes Dev 9 2079 2089

16. BartolomeiMS

WebberAL

BrunkowME

TilghmanSM

1993 Epigenetic mechanisms underlying the imprinting of the mouse H19 gene. Genes Dev 7 1663 1673

17. TremblayKD

DuranKL

BartolomeiMS

1997 A 5′ 2-kilobase-pair region of the imprinted mouse H19 gene exhibits exclusive paternal methylation throughout development. Mol Cell Biol 17 4322 4329

18. TremblayKD

SaamJR

IngramRS

TilghmanSM

BartolomeiMS

1995 A paternal-specific methylation imprint marks the alleles of the mouse H19 gene. Nat Genet 9 407 413

19. LeightonPA

IngramRS

EggenschwilerJ

EfstratiadisA

TilghmanSM

1995 Disruption of imprinting caused by deletion of the H19 gene region in mice. Nature 375 34 39

20. RipocheMA

KressC

PoirierF

DandoloL

1997 Deletion of the H19 transcription unit reveals the existence of a putative imprinting control element. Genes Dev 11 1596 1604

21. ThorvaldsenJL

DuranKL

BartolomeiMS

1998 Deletion of the H19 differentially methylated domain results in loss of imprinted expression of H19 and Igf2. Genes Dev 12 3693 3702

22. SrivastavaM

HsiehS

GrinbergA

Williams-SimonsL

HuangSP

2000 H19 and Igf2 monoallelic expression is regulated in two distinct ways by a shared cis acting regulatory region upstream of H19. Genes Dev 14 1186 1195

23. BellAC

FelsenfeldG

2000 Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405 482 485

24. HarkAT

SchoenherrCJ

KatzDJ

IngramRS

LevorseJM

2000 CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405 486 489

25. KafferCR

SrivastavaM

ParkKY

IvesE

HsiehS

2000 A transcriptional insulator at the imprinted H19/Igf2 locus. Genes Dev 14 1908 1919

26. KanduriC

PantV

LoukinovD

PugachevaE

QiCF

2000 Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive. Curr Biol 10 853 856

27. SzabóP

TangSH

RentsendorjA

PfeiferGP

MannJR

2000 Maternal-specific footprints at putative CTCF sites in the H19 imprinting control region give evidence for insulator function. Curr Biol 10 607 610

28. BellAC

WestAG

FelsenfeldG

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

29. MoonH

FilippovaG

LoukinovD

PugachevaE

ChenQ

2005 CTCF is conserved from Drosophila to humans and confers enhancer blocking of the Fab-8 insulator. EMBO Rep 6 165 170

30. FilippovaGN

FagerlieS

KlenovaEM

MyersC

DehnerY

1996 An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol Cell Biol 16 2802 2813

31. SzabóPE

TangSH

SilvaFJ

TsarkWM

MannJR

2004 Role of CTCF binding sites in the Igf2/H19 imprinting control region. Mol Cell Biol 24 4791 4800

32. SchoenherrCJ

LevorseJM

TilghmanSM

2003 CTCF maintains differential methylation at the Igf2/H19 locus. Nat Genet 33 66 69

33. PantV

MarianoP

KanduriC

MattssonA

LobanenkovV

2003 The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains. Genes Dev 17 586 590

34. HanL

LeeDH

SzabóPE

2008 CTCF is the master organizer of domain-wide allele-specific chromatin at the H19/Igf2 imprinted region. Mol Cell Biol 28 1124 1135

35. LiT

HuJF

QiuX

LingJ

ChenH

2008 CTCF regulates allelic expression of Igf2 by orchestrating a promoter-polycomb repressive complex 2 intrachromosomal loop. Mol Cell Biol 28 6473 6482

36. SinghP

HanL

RivasGE

LeeDH

NicholsonTB

2010 Allele-specific H3K79 Di- versus trimethylation distinguishes opposite parental alleles at imprinted regions. Mol Cell Biol 30 2693 2707

37. DavisTL

YangGJ

McCarreyJR

BartolomeiMS

2000 The H19 methylation imprint is erased and re-established differentially on the parental alleles during male germ cell development. Hum Mol Genet 9 2885 2894

38. LiJY

Lees-MurdockDJ

XuGL

WalshCP

2004 Timing of establishment of paternal methylation imprints in the mouse. Genomics 84 952 960

39. UedaT

AbeK

MiuraA

YuzurihaM

ZubairM

2000 The paternal methylation imprint of the mouse H19 locus is acquired in the gonocyte stage during foetal testis development. Genes Cells 5 649 659

40. HajkovaP

ErhardtS

LaneN

HaafT

El-MaarriO

2002 Epigenetic reprogramming in mouse primordial germ cells. Mech Dev 117 15 23

41. KatoY

KanedaM

HataK

KumakiK

HisanoM

2007 Role of the Dnmt3 family in de novo methylation of imprinted and repetitive sequences during male germ cell development in the mouse. Hum Mol Genet 16 2272 2280

42. DavisTL

TraslerJM

MossSB

YangGJ

BartolomeiMS

1999 Acquisition of the H19 methylation imprint occurs differentially on the parental alleles during spermatogenesis. Genomics 58 18 28

43. SzabóPE

HubnerK

ScholerH

MannJR

2002 Allele-specific expression of imprinted genes in mouse migratory primordial germ cells. Mech Dev 115 157 160

44. SzabóPE

MannJR

1995 Biallelic expression of imprinted genes in the mouse germ line: implications for erasure, establishment, and mechanisms of genomic imprinting. Genes Dev 9 1857 1868

45. CicconeDN

SuH

HeviS

GayF

LeiH

2009 KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. Nature 461 415 418

46. HajkovaP

AncelinK

WaldmannT

LacosteN

LangeUC

2008 Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 452 877 881

47. SekiY

HayashiK

ItohK

MizugakiM

SaitouM

2005 Extensive and orderly reprogramming of genome-wide chromatin modifications associated with specification and early development of germ cells in mice. Dev Biol 278 440 458

48. SekiY

YamajiM

YabutaY

SanoM

ShigetaM

2007 Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development 134 2627 2638

49. YatsukiH

JohK

HigashimotoK

SoejimaH

AraiY

2002 Domain regulation of imprinting cluster in Kip2/Lit1 subdomain on mouse chromosome 7F4/F5: large-scale DNA methylation analysis reveals that DMR-Lit1 is a putative imprinting control region. Genome Res 12 1860 1870

50. HiuraH

ObataY

KomiyamaJ

ShiraiM

KonoT

2006 Oocyte growth-dependent progression of maternal imprinting in mice. Genes Cells 11 353 361

51. OlekA

OswaldJ

WalterJ

1996 A modified and improved method for bisulphite based cytosine methylation analysis. Nucleic Acids Res 24 5064 5066

52. JurinkeC

DenissenkoMF

OethP

EhrichM

van den BoomD

2005 A single nucleotide polymorphism based approach for the identification and characterization of gene expression modulation using MassARRAY. Mutat Res 573 83 95

53. LoukinovDI

PugachevaE

VatolinS

PackSD

MoonH

2002 BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma. Proc Natl Acad Sci U S A 99 6806 6811

54. JelinicP

StehleJC

ShawP

2006 The testis-specific factor CTCFL cooperates with the protein methyltransferase PRMT7 in H19 imprinting control region methylation. PLoS Biol 4 e355 doi:10.1371/journal.pbio.0040355

55. FarrarD

RaiS

ChernukhinI

JagodicM

ItoY

2010 Mutational analysis of the poly(ADP-ribosyl)ation sites of the transcription factor CTCF provides an insight into the mechanism of its regulation by poly(ADP-ribosyl)ation. Mol Cell Biol 30 1199 1216

56. LefevreP

WithamJ

LacroixCE

CockerillPN

BoniferC

2008 The LPS-induced transcriptional upregulation of the chicken lysozyme locus involves CTCF eviction and noncoding RNA transcription. Mol Cell 32 129 139

57. DelavalK

GovinJ

CerqueiraF

RousseauxS

KhochbinS

2007 Differential histone modifications mark mouse imprinting control regions during spermatogenesis. Embo J 26 720 729

58. KriaucionisS

HeintzN

2009 The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324 929 930

59. TahilianiM

KohKP

ShenY

PastorWA

BandukwalaH

2009 Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324 930 935

60. JinSG

KadamS

PfeiferGP

2010 Examination of the specificity of DNA methylation profiling techniques toward 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res 38 e125

61. TamaruH

SelkerEU

2001 A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414 277 283

62. 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

63. JacksonJP

JohnsonL

JasencakovaZ

ZhangX

PerezBurgosL

2004 Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112 308 315

64. JacksonJP

LindrothAM

CaoX

JacobsenSE

2002 Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416 556 560

65. 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

66. La SalleS

MertineitC

TaketoT

MoensPB

BestorTH

2004 Windows for sex-specific methylation marked by DNA methyltransferase expression profiles in mouse germ cells. Dev Biol 268 403 415

67. Lees-MurdockDJ

ShovlinTC

GardinerT

De FeliciM

WalshCP

2005 DNA methyltransferase expression in the mouse germ line during periods of de novo methylation. Dev Dyn 232 992 1002

68. LefevreC

MannJR

2008 RNA expression microarray analysis in mouse prospermatogonia: identification of candidate epigenetic modifiers. Dev Dyn 237 1082 1089

69. SakaiY

SuetakeI

ShinozakiF

YamashinaS

TajimaS

2004 Co-expression of de novo DNA methyltransferases Dnmt3a2 and Dnmt3L in gonocytes of mouse embryos. Gene Expr Patterns 5 231 237

70. ChedinF

LieberMR

HsiehCL

2002 The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci U S A 99 16916 16921

71. 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

72. LuciferoD

MannMR

BartolomeiMS

TraslerJM

2004 Gene-specific timing and epigenetic memory in oocyte imprinting. Hum Mol Genet 13 839 849

73. BuehrM

McLarenA

1993 Isolation and culture of primordial germ cells. Methods Enzymol 225 58 77

74. WoodMJ

WittinghamDG

RallWF

1987 The low temperature preservation of mouse oocytes and embryos, Mammalian Development: A Practical Approach (ed. M. Monk) pp 255–280.;

MonkM

Oxford IRL Press 255 280