RESEARCH ARTICLE

Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain

  • Junjie U. GUO 1,2,3 ,
  • Keith E. SZULWACH 4 ,
  • Yijing SU 1,3 ,
  • Yujing LI 4 ,
  • Bing YAO 4 ,
  • Zihui XU 4 ,
  • Joo Heon SHIN 5 ,
  • Bing XIE 5 ,
  • Yuan GAO 1,5 ,
  • Guo-li MING 1,2,3 ,
  • Peng JIN , 4 ,
  • Hongjun SONG , 1,2,3
Expand
  • 1. Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
  • 2. The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
  • 3. Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
  • 4. Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
  • 5. Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA

Received date: 09 Jan 2014

Accepted date: 11 Jan 2014

Published date: 01 Feb 2014

Copyright

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg

Abstract

Mounting evidence points to critical roles for DNA modifications, including 5-methylcytosine (5mC) and its oxidized forms, in the development, plasticity and disorders of the mammalian nervous system. The novel DNA base 5-hydroxymethylcytosine (5hmC) is known to be capable of initiating passive or active DNA demethylation, but whether and how extensively 5hmC functions in shaping the post-mitotic neuronal DNA methylome is unclear. Here we report the genome-wide distribution of 5hmC in dentate granule neurons from adult mouse hippocampus in vivo. 5hmC in the neuronal genome is highly enriched in gene bodies, especially in exons, and correlates with gene expression. Direct genome-wide comparison of 5hmC distribution between embryonic stem cells and neurons reveals extensive differences, reflecting the functional disparity between these two cell types. Importantly, integrative analysis of 5hmC, overall DNA methylation and gene expression profiles of dentate granule neurons in vivo reveals the genome-wide antagonism between these two states of cytosine modifications, supporting a role for 5hmC in shaping the neuronal DNA methylome by promoting active DNA demethylation.

Cite this article

Junjie U. GUO , Keith E. SZULWACH , Yijing SU , Yujing LI , Bing YAO , Zihui XU , Joo Heon SHIN , Bing XIE , Yuan GAO , Guo-li MING , Peng JIN , Hongjun SONG . Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain[J]. Frontiers in Biology, 2014 , 9(1) : 66 -74 . DOI: 10.1007/s11515-014-1295-1

Acknowledgments

We thank Cheryl Strauss and Kimberley Christian for critical reading of the manuscript. This study was supported in part by the National Institutes of Health (NS051630 and MH076090 to P.J.; NS047344, MH087874, ES021957 to H.S., HD0679184 and NS048271 to G.L.M.), the Emory Genetics Discovery Fund (P.J.), the Simons Foundation Autism Research Initiative (P.J. and H.S.), Dr. Miriam & Sheldon G. Adelson Medical Research Foundation (G.L.M.), Maryland Stem Cell Research Foundation (G.L.M.), and John Hopkins Brain Science Institute (G.L.M.). J.U.G. is a Damon Runyon fellow supported by the Damon Runyon Cancer Research Foundation. Y.S. was supported by a postdoctoral fellowship from Maryland Stem Cell Research Foundation.
1
BhutaniN, BurnsD M, BlauH M (2011). DNA demethylation dynamics. Cell, 146(6): 866–872

DOI PMID

2
BirdA (2002). DNA methylation patterns and epigenetic memory. Genes Dev, 16(1): 6–21

DOI PMID

3
BoothM J, BrancoM R, FiczG, OxleyD, KruegerF, ReikW, BalasubramanianS (2012). Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science, 336(6083): 934–937

DOI PMID

4
BrancoM R, FiczG, ReikW (2012). Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet, 13(1): 7–13

PMID

5
DawlatyM M, BreilingA, LeT, RaddatzG, BarrasaM I, ChengA W, GaoQ, PowellB E, LiZ, XuM, FaullK F, LykoF, JaenischR (2013). Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development. Dev Cell, 24(3): 310–323

DOI PMID

6
FengJ, ChangH, LiE, FanG (2005). Dynamic expression of de novo DNA methyltransferases Dnmt3a and Dnmt3b in the central nervous system. J Neurosci Res, 79(6): 734–746

DOI PMID

7
FengJ, ZhouY, CampbellS L, LeT, LiE, SweattJ D, SilvaA J, FanG (2010). Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci, 13(4): 423–430

DOI PMID

8
FrauerC, HoffmannT, BultmannS, CasaV, CardosoM C, AntesI, LeonhardtH (2011). Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS ONE, 6(6): e21306

DOI PMID

9
GlobischD, MünzelM, MüllerM, MichalakisS, WagnerM, KochS, BrücklT, BielM, CarellT (2010). Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE, 5(12): e15367

DOI PMID

10
GollM G, BestorT H (2005). Eukaryotic cytosine methyltransferases. Annu Rev Biochem, 74(1): 481–514

DOI PMID

11
GotoK, NumataM, KomuraJ I, OnoT, BestorT H, KondoH (1994). Expression of DNA methyltransferase gene in mature and immature neurons as well as proliferating cells in mice. Differentiation, 56(1–2): 39–44

DOI PMID

12
GuT P, GuoF, YangH, WuH P, XuG F, LiuW, XieZ G, ShiL, HeX, JinS G, IqbalK, ShiY G, DengZ, SzabóP E, PfeiferG P, LiJ, XuG L (2011). The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature, 477(7366): 606–610

DOI PMID

13
GuoJ U, MaD K, MoH, BallM P, JangM H, BonaguidiM A, BalazerJ A, EavesH L, XieB, FordE, ZhangK, MingG L, GaoY, SongH (2011a). Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci, 14(10): 1345–1351

DOI PMID

14
GuoJ U, SuY, ShinJ H, ShinJ, LiH, XieB, ZhongC, HuS, LeT, FanG, ZhuH, ChangQ, GaoY, MingG L, SongH (2013). Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat Neurosci, doi: 10.1038/nn.3607

PMID

15
GuoJ U, SuY, ZhongC, MingG L, SongH (2011b). Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond. Cell Cycle, 10(16): 2662–2668

DOI PMID

16
GuoJ U, SuY, ZhongC, MingG L, SongH (2011c). Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell, 145(3): 423–434

DOI PMID

54
HahnM A, QiuR, WuX, LiA X, ZhangH, WangJ, JuiJ, JinS G, JiangY, PfeiferG P, LuQ (2013). Dynamics of 5-hydroxymethylcytosine and chromatin marks in Mammalian neurogenesis. Cell Rep, 3: 291–300

17
HeY F, LiB Z, LiZ, LiuP, WangY, TangQ, DingJ, JiaY, ChenZ, LiL, SunY, LiX, DaiQ, SongC X, ZhangK, HeC, XuG L (2011). Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science, 333(6047): 1303–1307

DOI PMID

18
InoueA, ZhangY (2011). Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science, 334(6053): 194

DOI PMID

19
ItoS, D’AlessioA C, TaranovaO V, HongK, SowersL C, ZhangY (2010). Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature, 466(7310): 1129–1133

DOI PMID

20
ItoS, ShenL, DaiQ, WuS C, CollinsL B, SwenbergJ A, HeC, ZhangY (2011). Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science, 333(6047): 1300–1303

DOI PMID

21
KaasG A, ZhongC, EasonD E, RossD L, VachhaniR V, MingG L, KingJ R, SongH, SweattJ D (2013). TET1 controls CNS 5-methylcytosine hydroxylation, active DNA demethylation, gene transcription, and memory formation. Neuron, 79(6): 1086–1093

DOI PMID

22
KimT K, HembergM, GrayJ M, CostaA M, BearD M, WuJ, HarminD A, LaptewiczM, Barbara-HaleyK, KuerstenS, Markenscoff-PapadimitriouE, KuhlD, BitoH, WorleyP F, KreimanG, GreenbergM E (2010). Widespread transcription at neuronal activity-regulated enhancers. Nature, 465(7295): 182–187

DOI PMID

23
KohliR M, ZhangY (2013). TET enzymes, TDG and the dynamics of DNA demethylation. Nature, 502(7472): 472–479

DOI PMID

24
KriaucionisS, HeintzN (2009). The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science, 324(5929): 929–930

DOI PMID

25
LienertF, WirbelauerC, SomI, DeanA, MohnF, SchóbelerD (2011). Identification of genetic elements that autonomously determine DNA methylation states. Nat Genet, 43(11): 1091–1097

DOI PMID

26
ListerR, PelizzolaM, DowenR H, HawkinsR D, HonG, Tonti-FilippiniJ, NeryJ R, LeeL, YeZ, NgoQ M, EdsallL, Antosiewicz-BourgetJ, StewartR, RuottiV, MillarA H, ThomsonJ A, RenB, EckerJ R (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462(7271): 315–322

DOI PMID

27
MaD K, GuoJ U, MingG L, SongH (2009a). DNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation. Cell Cycle, 8(10): 1526–1531

DOI PMID

28
MaD K, PonnusamyK, SongM R, MingG L, SongH (2009b). Molecular genetic analysis of FGFR1 signalling reveals distinct roles of MAPK and PLCgamma1 activation for self-renewal of adult neural stem cells. Mol Brain, 2(1): 16

DOI PMID

29
MeissnerA, MikkelsenT S, GuH, WernigM, HannaJ, SivachenkoA, ZhangX, BernsteinB E, NusbaumC, JaffeD B, GnirkeA, JaenischR, LanderE S (2008). Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature, 454(7205): 766–770

PMID

30
MellénM, AyataP, DewellS, KriaucionisS, HeintzN (2012). MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell, 151(7): 1417–1430

DOI PMID

31
MillerC A, SweattJ D (2007). Covalent modification of DNA regulates memory formation. Neuron, 53(6): 857–869

DOI PMID

32
PastorW A, AravindL, RaoA (2013). TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol, 14(6): 341–356

DOI PMID

33
PastorW A, PapeU J, HuangY, HendersonH R, ListerR, KoM, McLoughlinE M, BrudnoY, MahapatraS, KapranovP, TahilianiM, DaleyG Q, LiuX S, EckerJ R, MilosP M, AgarwalS, RaoA (2011). Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature, 473(7347): 394–397

DOI PMID

34
RudenkoA, DawlatyM M, SeoJ, ChengA W, MengJ, LeT, FaullK F, JaenischR, TsaiL H (2013). Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Neuron, 79(6): 1109–1122

DOI PMID

35
ShuklaS, KavakE, GregoryM, ImashimizuM, ShutinoskiB, KashlevM, OberdoerfferP, SandbergR, OberdoerfferS (2011). CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature, 479(7371): 74–79

DOI PMID

36
SongC X, SzulwachK E, DaiQ, FuY, MaoS Q, LinL, StreetC, LiY, PoidevinM, WuH, GaoJ, LiuP, LiL, XuG L, JinP, HeC (2013). Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell, 153(3): 678–691

DOI PMID

37
SongC X, SzulwachK E, FuY, DaiQ, YiC, LiX, LiY, ChenC H, ZhangW, JianX, WangJ, ZhangL, LooneyT J, ZhangB, GodleyL A, HicksL M, LahnB T, JinP, HeC (2011). Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol, 29(1): 68–72

DOI PMID

38
SpruijtC G, GnerlichF, SmitsA H, PfaffenederT, JansenP W, BauerC, MünzelM, WagnerM, MüllerM, KhanF, EberlH C, MensingaA, BrinkmanA B, LephikovK, MüllerU, WalterJ, BoelensR, van IngenH, LeonhardtH, CarellT, VermeulenM (2013). Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell, 152(5): 1146–1159

DOI PMID

39
StadlerM B, MurrR, BurgerL, IvanekR, LienertF, SchölerA, van NimwegenE, WirbelauerC, OakeleyE J, GaidatzisD, TiwariV K, SchübelerD (2011a). DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, 480(7378): 490–495

PMID

40
StadlerM B, MurrR, BurgerL, IvanekR, LienertF, SchölerA, van NimwegenE, WirbelauerC, OakeleyE J, GaidatzisD, TiwariV K, SchübelerD (2011b). DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, 480(7378): 490–495

PMID

41
SzulwachK E, LiX, LiY, SongC X, HanJ W, KimS, NamburiS, HermetzK, KimJ J, RuddM K, YoonY S, RenB, HeC, JinP (2011a). Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet, 7(6): e1002154

DOI PMID

42
SzulwachK E, LiX, LiY, SongC X, WuH, DaiQ, IrierH, UpadhyayA K, GearingM, LeveyA I, VasanthakumarA, GodleyL A, ChangQ, ChengX, HeC, JinP (2011b). 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci, 14(12): 1607–1616

DOI PMID

43
TahilianiM, KohK P, ShenY, PastorW A, BandukwalaH, BrudnoY, AgarwalS, IyerL M, LiuD R, AravindL, RaoA (2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science, 324(5929): 930–935

DOI PMID

44
ValinluckV, SowersL C (2007). Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res, 67(3): 946–950

DOI PMID

45
WangF, YangY, LinX, WangJ Q, WuY S, XieW, WangD, ZhuS, LiaoY Q, SunQ, YangY G, LuoH R, GuoC, HanC, TangT S (2013). Genome-wide loss of 5-hmC is a novel epigenetic feature of Huntington’s disease. Hum Mol Genet, 22(18): 3641–3653

DOI PMID

46
WuS C, ZhangY (2010). Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol, 11(9): 607–620

DOI PMID

47
XuY, WuF, TanL, KongL, XiongL, DengJ, BarberaA J, ZhengL, ZhangH, HuangS, MinJ, NicholsonT, ChenT, XuG, ShiY, ZhangK, ShiY G (2011). Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell, 42(4): 451–464

DOI PMID

48
YamaguchiS, ShenL, LiuY, SendlerD, ZhangY (2013). Role of Tet1 in erasure of genomic imprinting. Nature, 504(7480): 460–464

DOI PMID

49
YaoB, LinL, StreetR C, ZalewskiZ A, GallowayJ N, WuH, NelsonD L, JinP (2013). Genome-wide alteration of 5-hydroxymethylcytosine in a mouse model of fragile X-associated tremor/ataxia syndrome. Hum Mol Genet, (Oct): 20 (Epub ahead of print)

PMID

50
YuM, HonG C, SzulwachK E, SongC X, ZhangL, KimA, LiX, DaiQ, ShenY, ParkB, MinJ H, JinP, RenB, HeC (2012). Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell, 149(6): 1368–1380

DOI PMID

51
ZhangH, ZhangX, ClarkE, MulcaheyM, HuangS, ShiY G (2010). TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine. Cell Res, 20(12): 1390–1393

DOI PMID

52
ZhangR R, CuiQ Y, MuraiK, LimY C, SmithZ D, JinS, YeP, RosaL, LeeY K, WuH P, LiuW, XuZ M, YangL, DingY Q, TangF, MeissnerA, DingC, ShiY, XuG L (2013). Tet1 regulates adult hippocampal neurogenesis and cognition. Cell Stem Cell, 13(2): 237–245

DOI PMID

53
ZhuJ K (2009). Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet, 43(1): 143–166

DOI PMID

Outlines

/