Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver

Genome Research

Volumn 26, Issue 12, 2016, Pages 1730-1741

  Li, Xin ^a   Liu, Yun ^a,b   Salz, Tal ^a   Hansen, Kasper D ^a,c   Feinberg, Andrew ^a,c,d  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b FUDAN UNIVERSITY   (China)

^c JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^d Johns Hopkins University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CARCINOGENESIS; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; ENHANCER REGION; ENTEROBACTERIA PHAGE LAMBDA; EPIGENETICS; GENE EXPRESSION; GENE EXPRESSION REGULATION; HISTONE MODIFICATION; HUMAN; HUMAN TISSUE; LIVER TUMOR; LUNG PARENCHYMA; LUNG TUMOR; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; TISSUE DIFFERENTIATION; TRANSCRIPTION TERMINATION; UPREGULATION; WHOLE GENOME SEQUENCING; ANALOGS AND DERIVATIVES; ANTIBODY SPECIFICITY; CHEMISTRY; COMPARATIVE STUDY; GENETIC EPIGENESIS; GENETICS; LIVER; LUNG; NEOPLASM; PATHOLOGY; PROCEDURES;

5 METHYLCYTOSINE; 5-HYDROXYMETHYLCYTOSINE; DNA;

5-METHYLCYTOSINE; CPG ISLANDS; DNA; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; HUMANS; LIVER; LUNG; NEOPLASMS; ORGAN SPECIFICITY; PROMOTER REGIONS, GENETIC; WHOLE GENOME SEQUENCING;

EID: 85002628618     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.211854.116     Document Type: Article

References (42)

1. Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S. 2012. Quantitative sequencing of 5-methylcytosine and 5-hydroxy-methylcytosine at single-base resolution. Science 336: 934-937.
2. Booth MJ, Ost TWB, Beraldi D, Bell NM, Branco MR, Reik W, Balasubramanian S. 2013. Oxidative bisulfite sequencing of 5-methyl-cytosine and 5-hydroxymethylcytosine. Nat Protoc 8: 1841-1851.
3. Cedar H, Bergman Y. 2009. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10: 295-304.
4. Dang L, Jin S, Su SM. 2010. IDH mutations in glioma and acute myeloid leukemia. Trends Mol Med 16: 387-397.
5. Delhommeau F, Dupont S, Valle VD, James C, Trannoy S, Masse A, Kosmider O, Le Couedic J-P, Robert F, Alberdi A. 2009. Mutation in TET2 in myeloid cancers. N Engl J Med 360: 2289-2301.
6. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D. 2011. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43: 768-775.
7. Hansen KD, Langmead B, Irizarry RA. 2012. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol 13: R83.
8. Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. 2014. Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization. Genome Res 24: 177-184.
9. Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S. 2010. Distinct epigenomic landscapes of pluripo-tent and lineage-committed human cells. Cell Stem Cell 6: 479-491.
10. Hon GC, Song C-X, Du T, Jin F, Selvaraj S, Lee AY, Yen CA, Ye Z, Mao S-Q, Wang B-A. 2014. 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Mol Cell 56: 286-297.
11. Hu J, Ge H, Newman M, Liu K. 2012. OSA: a fast and accurate alignment tool for RNA-Seq. Bioinformatics 28: 1933-1934.
12. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M. 2009. The human colon cancer meth-ylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41: 178-186.
13. Jin SG, Jiang Y, Qiu R, Rauch TA, Wang Y, Schackert G, Krex D, Lu Q, Pfeifer GP. 2011a. 5-hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. Cancer Res 71: 7360-7365.
14. Jin SG, Wu X, Li AX, Pfeifer GP. 2011b. Genomic mapping of 5-hydroxyme-thylcytosine in the human brain. Nucleic Acids Res 39: 5015-5024.
15. Jones PA. 2012. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13: 484-492.
16. Kellinger MW, Song C-X, Chong J, Lu X-Y, He C, Wang D. 2012. 5-formyl-cytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription. Nat Struct Mol Biol 19: 831-833.
17. Kowalczyk MS, Hughes JR, Garrick D, Lynch MD, Sharpe JA, Sloane-Stanley JA, McGowan SJ, De Gobbi M, Hosseini M, Vernimmen D. 2012. Intragenic enhancers actas alternative promoters. Mol Cell 45: 447-458.
18. Kudo Y, Tateishi K, Yamamoto K, Yamamoto S, Asaoka Y, Ijichi H, Nagae G, Yoshida H, Aburatani H, Koike K. 2012. Loss of 5-hydroxymethylcyto-sine is accompanied with malignant cellular transformation. Cancer Sci 103: 670-676.
19. Laird A, Thomson JP, Harrison DJ, Meehan RR. 2013. 5-hydroxymethylcy-tosine profiling as an indicator of cellular state. Epigenomics 5: 655-669.
20. Langemeijer SMC, Kuiper RP, Berends M, Knops R, Aslanyan MG, Massop M, Stevens-Linders E, van Hoogen P, van Kessel AG, Raymakers RAP, et al. 2009. Acquired mutationsinTET2 are common inmyelodysplastic syndromes. Nat Genet 41: 838-842.
21. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
22. Lian CG, Xu Y, Ceol C, Wu F, Larson A, Dresser K, Xu W, Tan L, Hu Y, Zhan Q. 2012. Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 150: 1135-1146.
23. Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550.
24. Mellen M, Ayata P, Dewell S, Kriaucionis S, Heintz N. 2012. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 151: 1417-1430.
25. Nestor CE, Ottaviano R, Reddington J, Sproul D, Reinhardt D, Dunican D, Katz E, Dixon JM, Harrison DJ, Meehan R. 2012. Tissue-type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res 22: 467-477.
26. Pastor WA, Aravind L, Rao A. 2013. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol 14: 341-356.
27. Pathiraja TN, Nayak SR, Xi Y, Jiang S, Garee JP, Edwards DP, Lee AV, Chen J, Shea MJ, Santen RJ, et al. 2014. Epigenetic reprogramming of HOXC10 in endocrine-resistant breast cancer. Sci Transl Med 6: 229ra241-229ra241.
28. Pedersen BS, Schwartz DA, Yang IV, Kechris KJ. 2012. Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinformatics 28: 2986-2988.
29. Pfeifer GP, Kadam S, Jin S-G. 2013. 5-hydroxymethylcytosine and its potential roles in development and cancer. Epigenetics Chromatin 6: 1-9.
30. Putiri EL, Tiedemann RL, Thompson JJ, Liu C, Ho T, Choi JH, Robertson KD. 2014. Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells. Genome Biol 15: R81.
31. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, et al. 2015. Integrative analysis of 111 reference human epigenomes. Nature 518: 317-330.
32. Shibata T, Kokubu A, Miyamoto M, Sasajima Y, Yamazaki N. 2011. Mutant IDH1 confers an in vivo growth in a melanoma cell line with BRAF mutation. Am J Pathol 178: 1395-1402.
33. Smith ZD, Meissner A. 2013. DNA methylation: roles in mammalian development. Nat Rev Genet 14: 204-220.
34. Song Q, Smith AD. 2011. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27: 870-871.
35. Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, Li Y, Chen C-H, Zhang W, Jian X, et al. 2011. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotech 29: 68-72.
36. Timp W, Feinberg AP. 2013. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer 13: 497-510.
37. Uribe-Lewis S, Stark R, Carroll T, Dunning M, Bachman M, Ito Y, Stojic L, Halim S, Vowler S, Lynch A, et al. 2015. 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer. Genome Biol 16: 69.
38. Wen L, Li X, Yan L, Tan Y, Li R, Zhao Y, Wang Y, Xie J, Zhang Y, Song C, et al. 2014. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain. Genome Biol 15: R49.
39. Wu H, Zhang Y. 2014. Reversing DNA methylation: mechanisms, geno-mics, and biological functions. Cell 156: 45-68.
40. Yang H, Liu Y, Bai F, Zhang JY, Ma SH, Liu J, Xu ZD, Zhu HG, Ling ZQ, Ye D, et al. 2013. Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene 32: 663-669.
41. Yu M, Hon GC, Szulwach KE, Song C-X, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B. 2012. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149: 1368-1380.
42. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.