Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice

BMC Genomics

Reid S Alisch³  Stephen T Warren⁴  Thaddeus G Golos⁵  Patrick H Roseboom³  Mark A Garthwaite¹  Ryan M Brown³  Andrea Hatch³  Andrew T J White³  Ligia A Papale³  Pankaj Chopra² 

[1] Obstetrics & Gynecology, University of Wisconsin – Madison, 1223 Capitol Court, Madison, Wisconsin 53715, USA;Departments of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA;Department of Psychiatry, University of Wisconsin–Madison, 6001 Research Park Blvd., Madison, Wisconsin 53719, USA;Departments of Pediatrics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA;Departments of Wisconsin National Primate Research Center, University of Wisconsin – Madison, 1223 Capitol Court, Madison, Wisconsin 53715, USA

关键词: Evolution;    5-hydroxymethylcytosine (5-hmC);    DNA methylation;    Epigenetics;   

Others  :  1217874
DOI  :  10.1186/1471-2164-15-131

 received in 2013-09-17, accepted in 2014-02-05,  发布年份 2014

【 摘 要 】

Background

Methylation on the fifth position of cytosine (5-mC) is an essential epigenetic mark that is linked to both normal neurodevelopment and neurological diseases. The recent identification of another modified form of cytosine, 5-hydroxymethylcytosine (5-hmC), in both stem cells and post-mitotic neurons, raises new questions as to the role of this base in mediating epigenetic effects. Genomic studies of these marks using model systems are limited, particularly with array-based tools, because the standard method of detecting DNA methylation cannot distinguish between 5-mC and 5-hmC and most methods have been developed to only survey the human genome.

Results

We show that non-human data generated using the optimization of a widely used human DNA methylation array, designed only to detect 5-mC, reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R² > 0.99). Genome-wide methylation analysis, using this approach, reveals 6,102 differentially methylated loci between rhesus placental and fetal tissues with pathways analysis significantly overrepresented for developmental processes. Restricting the analysis to oncogenes and tumor suppressor genes finds 76 differentially methylated loci, suggesting that rhesus placental tissue carries a cancer epigenetic signature. Similarly, adapting the assay to detect 5-hmC finds highly reproducible 5-hmC levels within human, rhesus, and mouse brain tissue that is species-specific with a hierarchical abundance among the three species (human > rhesus >> mouse). Annotation of 5-hmC with respect to gene structure reveals a significant prevalence in the 3'UTR and an association with chromatin-related ontological terms, suggesting an epigenetic feedback loop mechanism for 5-hmC.

Conclusions

Together, these data show that this array-based methylation assay is generalizable to all mammals for the detection of both 5-mC and 5-hmC, greatly improving the utility of mammalian model systems to study the role of epigenetics in human health, disease, and evolution.

【 授权许可】

   
2014 Chopra et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

【 参考文献 】

• [1]Jaenisch R, Bird A: Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003, 33(Suppl):245-254.
• [2]Feinberg AP, Vogelstein B: Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 1983, 301:89-92.
• [3]Moulton T, Crenshaw T, Hao Y, Moosikasuwan J, Lin N, Dembitzer F, Hensle T, Weiss L, McMorrow L, Loew T, et al.: Epigenetic lesions at the H19 locus in Wilms’ tumour patients. Nat Genet 1994, 7:440-447.
• [4]Steenman MJ, Rainier S, Dobry CJ, Grundy P, Horon IL, Feinberg AP: Loss of imprinting of IGF2 is linked to reduced expression and abnormal methylation of H19 in Wilms’ tumour. Nat Genet 1994, 7:433-439.
• [5]Sutcliffe JS, Nakao M, Christian S, Orstavik KH, Tommerup N, Ledbetter DH, Beaudet AL: Deletions of a differentially methylated CpG island at the SNRPN gene define a putative imprinting control region. Nat Genet 1994, 8:52-58.
• [6]Arima T, Drewell RA, Arney KL, Inoue J, Makita Y, Hata A, Oshimura M, Wake N, Surani MA: A conserved imprinting control region at the HYMAI/ZAC domain is implicated in transient neonatal diabetes mellitus. Hum Mol Genet 2001, 10:1475-1483.
• [7]Orr HT, Zoghbi HY: Trinucleotide repeat disorders. Annu Rev Neurosci 2007, 30:575-621.
• [8]Szulwach KE, Li X, Li Y, Song CX, Wu H, Dai Q, Irier H, Upadhyay AK, Gearing M, Levey AI, et al.: 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci 2011, 14:1607-1616.
• [9]Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL: A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 1992, 89:1827-1831.
• [10]Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S: Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 2012, 336:934-937.
• [11]Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, et al.: Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 2012, 149:1368-1380.
• [12]Bork S, Pfister S, Witt H, Horn P, Korn B, Ho AD, Wagner W: DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells. Aging Cell 2010, 9:54-63.
• [13]Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, Campan M, Noushmehr H, Bell CG, Maxwell AP, et al.: Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 2010, 20:440-446.
• [14]Chen YA, Choufani S, Ferreira JC, Grafodatskaya D, Butcher DT, Weksberg R: Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray. Genomics 2011, 97:214-222.
• [15]Koch CM, Suschek CV, Lin Q, Bork S, Goergens M, Joussen S, Pallua N, Ho AD, Zenke M, Wagner W: Specific age-associated DNA methylation changes in human dermal fibroblasts. PLoS One 2011, 6:e16679.
• [16]Alisch RS, Barwick BG, Chopra P, Myrick LK, Satten GA, Conneely KN, Warren ST: Age-associated DNA methylation in pediatric populations. Genome Res 2012, 22:623-632.
• [17]Nazor KL, Altun G, Lynch C, Tran H, Harness JV, Slavin I, Garitaonandia I, Muller FJ, Wang YC, Boscolo FS, et al.: Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives. Cell Stem Cell 2012, 10:620-634.
• [18]Bischof P, Meisser A, Campana A: Biochemistry and molecular biology of trophoblast invasion. Ann N Y Acad Sci 2001, 943:157-162.
• [19]Janneau JL, Maldonado-Estrada J, Tachdjian G, Miran I, Motte N, Saulnier P, Sabourin JC, Cote JF, Simon B, Frydman R, et al.: Transcriptional expression of genes involved in cell invasion and migration by normal and tumoral trophoblast cells. J Clin Endocrinol Metab 2002, 87:5336-5339.
• [20]Zhou Y, Genbacev O, Fisher SJ: The human placenta remodels the uterus by using a combination of molecules that govern vasculogenesis or leukocyte extravasation. Ann N Y Acad Sci 2003, 995:73-83.
• [21]Ohlsson R: Growth factors, protooncogenes and human placental development. Cell Differ Dev 1989, 28:1-15.
• [22]Strickland S, Richards WG: Invasion of the trophoblasts. Cell 1992, 71:355-357.
• [23]Chiu RW, Chim SS, Wong IH, Wong CS, Lee WS, To KF, Tong JH, Yuen RK, Shum AS, Chan JK, et al.: Hypermethylation of RASSF1A in human and rhesus placentas. Am J Pathol 2007, 170:941-950.
• [24]Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y: Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 2010, 466:1129-1133.
• [25]Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S, Reik W: Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 2011, 473:398-402.
• [26]Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, Rappsilber J, Helin K: TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011, 473:343-348.
• [27]Wu H, Zhang Y: Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev 2011, 25:2436-2452.
• [28]Wang T, Wu H, Li Y, Szulwach KE, Lin L, Li X, Chen IP, Goldlust IS, Chamberlain SJ, Dodd A, et al.: Subtelomeric hotspots of aberrant 5-hydroxymethylcytosine-mediated epigenetic modifications during reprogramming to pluripotency. Nat Cell Biol 2013, 15:700-711.
• [29]Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, et al.: The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009, 41:178-186.
• [30]Szulwach KE, Li X, Li Y, Song CX, Han JW, Kim S, Namburi S, Hermetz K, Kim JJ, Rudd MK, et al.: Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet 2011, 7:e1002154.
• [31]Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, et al.: Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011, 473:394-397.
• [32]Wong NC, Ng J, Hall NE, Lunke S, Salmanidis M, Brumatti G, Ekert PG, Craig JM, Saffery R: Exploring the utility of human DNA methylation arrays for profiling mouse genomic DNA. Genomics 2013, 102:38-46.
• [33]Xue WC, Chan KY, Feng HC, Chiu PM, Ngan HY, Tsao SW, Cheung AN: Promoter hypermethylation of multiple genes in hydatidiform mole and choriocarcinoma. J Mol Diagn 2004, 6:326-334.
• [34]Khare T, Pai S, Koncevicius K, Pal M, Kriukiene E, Liutkeviciute Z, Irimia M, Jia P, Ptak C, Xia M, et al.: 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nat Struct Mol Biol 2012, 19:1037-1043.