KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

English version České info

Krüppel-associated box domain-zinc finger proteins (KRAB–ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing the study of KRAB–mediated transcriptional regulation at hundreds of different transcriptional units. By targeting a drug-controllable KRAB–containing repressor to gene-trapping lentiviral vectors, we demonstrate that KRAB and its corepressor KAP1 can silence promoters located several tens of kilobases (kb) away from their DNA binding sites, with an efficiency which is generally higher for promoters located within 15 kb or less. Silenced promoters exhibit a loss of histone H3-acetylation, an increase in H3 lysine 9 trimethylation (H3K9me3), and a drop in RNA Pol II recruitment, consistent with a block of transcriptional initiation following the establishment of silencing marks. Furthermore, we reveal that KRAB–mediated repression is established by the long-range spreading of H3K9me3 and heterochromatin protein 1 β (HP1β) between the repressor binding site and the promoter. We confirm the biological relevance of this phenomenon by documenting KAP1–dependent transcriptional repression at an endogenous KRAB–ZFP gene cluster, where KAP1 binds to the 3′ end of genes and mediates propagation of H3K9me3 and HP1β towards their 5′ end. Together, our data support a model in which KRAB/KAP1 recruitment induces long-range repression through the spread of heterochromatin. This finding not only suggests auto-regulatory mechanisms in the control of KRAB–ZFP gene clusters, but also provides important cues for interpreting future genome-wide DNA binding data of KRAB–ZFPs and KAP1.

Vyšlo v časopise: KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading. PLoS Genet 6(3): e32767. doi:10.1371/journal.pgen.1000869
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1000869

Souhrn

Zdroje

1. DingG

LorenzP

KreutzerM

LiY

ThiesenHJ

2009 SysZNF: the C2H2 zinc finger gene database. Nucleic Acids Res 37 D267 273

2. EmersonRO

ThomasJH

2009 Adaptive evolution in zinc finger transcription factors. PLoS Genet 5 e1000325 doi:10.1371/journal.pgen.1000325

3. HuntleyS

BaggottDM

HamiltonAT

Tran-GyamfiM

YangS

2006 A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res 16 669 677

4. TadepallyHD

BurgerG

AubryM

2008 Evolution of C2H2-zinc finger genes and subfamilies in mammals: species-specific duplication and loss of clusters, genes and effector domains. BMC Evol Biol 8 176

5. UrrutiaR

2003 KRAB-containing zinc-finger repressor proteins. Genome Biol 4 231

6. VaquerizasJM

KummerfeldSK

TeichmannSA

LuscombeNM

2009 A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10 252 263

7. HamiltonAT

HuntleyS

Tran-GyamfiM

BaggottDM

GordonL

2006 Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Res 16 584 594

8. CammasF

HerzogM

LerougeT

ChambonP

LossonR

2004 Association of the transcriptional corepressor TIF1beta with heterochromatin protein 1 (HP1): an essential role for progression through differentiation. Genes Dev 18 2147 2160

9. CammasF

MarkM

DolleP

DierichA

ChambonP

2000 Mice lacking the transcriptional corepressor TIF1beta are defective in early postimplantation development. Development 127 2955 2963

10. HuG

KimJ

XuQ

LengY

OrkinSH

2009 A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev 23 837 848

11. JakobssonJ

CorderoMI

BisazR

GronerAC

BusskampV

2008 KAP1-mediated epigenetic repression in the forebrain modulates behavioral vulnerability to stress. Neuron 60 818 831

12. LiX

ItoM

ZhouF

YoungsonN

ZuoX

2008 A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev Cell 15 547 557

13. TianC

XingG

XieP

LuK

NieJ

2009 KRAB-type zinc-finger protein Apak specifically regulates p53-dependent apoptosis. Nat Cell Biol 11 580 591

14. ZhengL

PanH

LiS

Flesken-NikitinA

ChenPL

2000 Sequence-specific transcriptional corepressor function for BRCA1 through a novel zinc finger protein, ZBRK1. Mol Cell 6 757 768

15. RoweHM

JakobssonJ

MesnardD

RougemontJ

ReynardS

KAP1 controls endogenous retroviruses in embryonic stem cells. Nature 463 237 240

16. AbrinkM

OrtizJA

MarkC

SanchezC

LoomanC

2001 Conserved interaction between distinct Kruppel-associated box domains and the transcriptional intermediary factor 1 beta. Proc Natl Acad Sci U S A 98 1422 1426

17. FriedmanJR

FredericksWJ

JensenDE

SpeicherDW

HuangXP

1996 KAP-1, a novel corepressor for the highly conserved KRAB repression domain. Genes Dev 10 2067 2078

18. Le DouarinB

NielsenAL

GarnierJM

IchinoseH

JeanmouginF

1996 A possible involvement of TIF1 alpha and TIF1 beta in the epigenetic control of transcription by nuclear receptors. Embo J 15 6701 6715

19. MoosmannP

GeorgievO

Le DouarinB

BourquinJP

SchaffnerW

1996 Transcriptional repression by RING finger protein TIF1 beta that interacts with the KRAB repressor domain of KOX1. Nucleic Acids Res 24 4859 4867

20. LechnerMS

BeggGE

SpeicherDW

RauscherFJ3rd

2000 Molecular determinants for targeting heterochromatin protein 1-mediated gene silencing: direct chromoshadow domain-KAP-1 corepressor interaction is essential. Mol Cell Biol 20 6449 6465

21. NielsenAL

OrtizJA

YouJ

Oulad-AbdelghaniM

KhechumianR

1999 Interaction with members of the heterochromatin protein 1 (HP1) family and histone deacetylation are differentially involved in transcriptional silencing by members of the TIF1 family. Embo J 18 6385 6395

22. RyanRF

SchultzDC

AyyanathanK

SinghPB

FriedmanJR

1999 KAP-1 corepressor protein interacts and colocalizes with heterochromatic and euchromatic HP1 proteins: a potential role for Kruppel-associated box-zinc finger proteins in heterochromatin-mediated gene silencing. Mol Cell Biol 19 4366 4378

23. SchultzDC

FriedmanJR

RauscherFJ3rd

2001 Targeting histone deacetylase complexes via KRAB-zinc finger proteins: the PHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2alpha subunit of NuRD. Genes Dev 15 428 443

24. SchultzDC

AyyanathanK

NegorevD

MaulGG

RauscherFJ3rd

2002 SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev 16 919 932

25. SripathySP

StevensJ

SchultzDC

2006 The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression. Mol Cell Biol 26 8623 8638

26. UnderhillC

QutobMS

YeeSP

TorchiaJ

2000 A novel nuclear receptor corepressor complex, N-CoR, contains components of the mammalian SWI/SNF complex and the corepressor KAP-1. J Biol Chem 275 40463 40470

27. WiznerowiczM

JakobssonJ

SzulcJ

LiaoS

QuazzolaA

2007 The Kruppel-associated box repressor domain can trigger de novo promoter methylation during mouse early embryogenesis. J Biol Chem 282 34535 34541

28. DialynasGK

VitaliniMW

WallrathLL

2008 Linking Heterochromatin Protein 1 (HP1) to cancer progression. Mutat Res 647 13 20

29. NielsenAL

Oulad-AbdelghaniM

OrtizJA

RemboutsikaE

ChambonP

2001 Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins. Mol Cell 7 729 739

30. PlateroJS

HartnettT

EissenbergJC

1995 Functional analysis of the chromo domain of HP1. Embo J 14 3977 3986

31. ThiruA

NietlispachD

MottHR

OkuwakiM

LyonD

2004 Structural basis of HP1/PXVXL motif peptide interactions and HP1 localisation to heterochromatin. Embo J 23 489 499

32. KwonSH

WorkmanJL

2008 The heterochromatin protein 1 (HP1) family: put away a bias toward HP1. Mol Cells 26 217 227

33. AagaardL

LaibleG

SelenkoP

SchmidM

DornR

1999 Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. Embo J 18 1923 1938

34. BannisterAJ

ZegermanP

PartridgeJF

MiskaEA

ThomasJO

2001 Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410 120 124

35. LachnerM

O'CarrollD

ReaS

MechtlerK

JenuweinT

2001 Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410 116 120

36. NakayamaJ

RiceJC

StrahlBD

AllisCD

GrewalSI

2001 Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292 110 113

37. AyyanathanK

LechnerMS

BellP

MaulGG

SchultzDC

2003 Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. Genes Dev 17 1855 1869

38. O'GeenH

SquazzoSL

IyengarS

BlahnikK

RinnJL

2007 Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet 3 e89 doi:10.1371/journal.pgen.0030089

39. VogelMJ

GuelenL

de WitE

Peric-HupkesD

LodenM

2006 Human heterochromatin proteins form large domains containing KRAB-ZNF genes. Genome Res 16 1493 1504

40. DeuschleU

MeyerWK

ThiesenHJ

1995 Tetracycline-reversible silencing of eukaryotic promoters. Mol Cell Biol 15 1907 1914

41. MoosmannP

GeorgievO

ThiesenHJ

HagmannM

SchaffnerW

1997 Silencing of RNA polymerases II and III-dependent transcription by the KRAB protein domain of KOX1, a Kruppel-type zinc finger factor. Biol Chem 378 669 677

42. MitchellRS

BeitzelBF

SchroderAR

ShinnP

ChenH

2004 Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol 2 e234 doi:10.1371/journal.pbio.0020234

43. WuX

LiY

CriseB

BurgessSM

2003 Transcription start regions in the human genome are favored targets for MLV integration. Science 300 1749 1751

44. SchroderAR

ShinnP

ChenH

BerryC

EckerJR

2002 HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110 521 529

45. WangGP

CiuffiA

LeipzigJ

BerryCC

BushmanFD

2007 HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res 17 1186 1194

46. BrasherSV

SmithBO

FoghRH

NietlispachD

ThiruA

2000 The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer. Embo J 19 1587 1597

47. MurzinaN

VerreaultA

LaueE

StillmanB

1999 Heterochromatin dynamics in mouse cells: interaction between chromatin assembly factor 1 and HP1 proteins. Mol Cell 4 529 540

48. CammasF

JanoshaziA

LerougeT

LossonR

2007 Dynamic and selective interactions of the transcriptional corepressor TIF1 beta with the heterochromatin protein HP1 isotypes during cell differentiation. Differentiation 75 627 637

49. FrietzeS

LanX

JinVX

FarnhamPJ

2009 Genomic targets of the KRAB and scan domain-containing zinc finger protein 263 (ZNF263). J Biol Chem

50. GrewalSI

JiaS

2007 Heterochromatin revisited. Nat Rev Genet 8 35 46

51. StewartMD

LiJ

WongJ

2005 Relationship between histone H3 lysine 9 methylation, transcription repression, and heterochromatin protein 1 recruitment. Mol Cell Biol 25 2525 2538

52. RicletR

ChendebM

VoneschJL

KoczanD

ThiesenHJ

2009 Disruption of the interaction between transcriptional intermediary factor 1{beta} and heterochromatin protein 1 leads to a switch from DNA hyper- to hypomethylation and H3K9 to H3K27 trimethylation on the MEST promoter correlating with gene reactivation. Mol Biol Cell 20 296 305

53. TalbertPB

HenikoffS

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

54. de WitE

GreilF

van SteenselB

2007 High-resolution mapping reveals links of HP1 with active and inactive chromatin components. PLoS Genet 3 e38 doi:10.1371/journal.pgen.0030038

55. JohanssonAM

StenbergP

PetterssonF

LarssonJ

2007 POF and HP1 bind expressed exons, suggesting a balancing mechanism for gene regulation. PLoS Genet 3 e209 doi:10.1371/journal.pgen.0030209

56. BurkeSJ

CollierJJ

ScottDK

2009 cAMP prevents glucose-mediated modifications of histone H3 and recruitment of the RNA polymerase II holoenzyme to the L-PK gene promoter. J Mol Biol 392 578 588

57. CloosPA

ChristensenJ

AggerK

HelinK

2008 Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev 22 1115 1140

58. LohYH

ZhangW

ChenX

GeorgeJ

NgHH

2007 Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. Genes Dev 21 2545 2557

59. LomvardasS

ThanosD

2001 Nucleosome sliding via TBP DNA binding in vivo. Cell 106 685 696

60. AntoniouM

HarlandL

MustoeT

WilliamsS

HoldstockJ

2003 Transgenes encompassing dual-promoter CpG islands from the human TBP and HNRPA2B1 loci are resistant to heterochromatin-mediated silencing. Genomics 82 269 279

61. Lindahl AllenM

AntoniouM

2007 Correlation of DNA methylation with histone modifications across the HNRPA2B1-CBX3 ubiquitously-acting chromatin open element (UCOE). Epigenetics 2 227 236

62. ClarkSJ

2007 Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis. Hum Mol Genet 16 Spec No 1 R88 95

63. BeerDG

KardiaSL

HuangCC

GiordanoTJ

LevinAM

2002 Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 8 816 824

64. BhattacharjeeA

RichardsWG

StauntonJ

LiC

MontiS

2001 Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A 98 13790 13795

65. De PalmaM

MontiniE

Santoni de SioFR

BenedicentiF

GentileA

2005 Promoter trapping reveals significant differences in integration site selection between MLV and HIV vectors in primary hematopoietic cells. Blood 105 2307 2315

66. WiznerowiczM

TronoD

2003 Conditional suppression of cellular genes: lentivirus vector-mediated drug-inducible RNA interference. J Virol 77 8957 8961

67. ZuffereyR

NagyD

MandelRJ

NaldiniL

TronoD

1997 Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo. Nat Biotechnol 15 871 875

68. ChenWV

SorianoP

2003 Gene trap mutagenesis in embryonic stem cells. Methods Enzymol 365 367 386

69. EwingB

HillierL

WendlMC

GreenP

1998 Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8 175 185

70. KentWJ

2002 BLAT–the BLAST-like alignment tool. Genome Res 12 656 664

71. VandesompeleJ

De PreterK

PattynF

PoppeB

Van RoyN

2002 Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3 RESEARCH0034

72. IseliC

AmbrosiniG

BucherP

JongeneelCV

2007 Indexing strategies for rapid searches of short words in genome sequences. PLoS One 2 e579 doi:10.1371/journal.pone.0000579

73. LiH

RauchT

ChenZX

SzaboPE

RiggsAD

2006 The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. J Biol Chem 281 19489 19500