2,055
Views
27
CrossRef citations to date
0
Altmetric
Research Paper

DNA methylation variation of human-specific Alu repeats

, , &
Pages 163-173 | Received 24 Sep 2015, Accepted 12 Nov 2015, Published online: 16 Mar 2016

References

  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921; PMID:11237011; http://dx.doi.org/10.1038/35057062
  • Deininger PL, Moran JV, Batzer MA, Kazazian HH, Jr. Mobile elements and mammalian genome evolution. Curr Opin Genet Dev 2003; 13:651-8; PMID:14638329; http://dx.doi.org/10.1016/j.gde.2003.10.013
  • Chu WM, Liu WM, Schmid CW. RNA polymerase III promoter and terminator elements affect Alu RNA expression. Nucleic Acids Res 1995; 23:1750-7; PMID:7540287; http://dx.doi.org/10.1093/nar/23.10.1750
  • Roy-Engel AM, Salem AH, Oyeniran OO, Deininger L, Hedges DJ, Kilroy GE, Batzer MA, Deininger PL. Active Alu element “A-tails”: size does matter. Genome Res 2002; 12:1333-44; PMID:12213770; http://dx.doi.org/10.1101/gr.384802
  • Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat Rev Genet 2002; 3:370-9; PMID:11988762; http://dx.doi.org/10.1038/nrg798
  • Dewannieux M, Heidmann T. Role of poly(A) tail length in Alu retrotransposition. Genomics 2005; 86:378-81; PMID:15993034; http://dx.doi.org/10.1016/j.ygeno.2005.05.009
  • Deininger P.Alu elements: know the SINEs. Genome Biol 2011; 12:236; PMID:22204421; http://dx.doi.org/10.1186/gb-2011-12-12-236
  • Shen MR, Batzer MA, Deininger PL. Evolution of the master Alu gene(s). J Mol Evol 1991; 33:311-20; PMID:1774786; http://dx.doi.org/10.1007/BF02102862
  • Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE. Active Alu retrotransposons in the human genome. Genome Res 2008; 18:1875-83; PMID:18836035; http://dx.doi.org/10.1101/gr.081737.108
  • Carroll ML, Roy-Engel AM, Nguyen SV, Salem AH, Vogel E, Vincent B, Myers J, Ahmad Z, Nguyen L, Sammarco M, et al. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J Mol Biol 2001; 311:17-40; PMID:11469855; http://dx.doi.org/10.1006/jmbi.2001.4847
  • Cordaux R, Hedges DJ, Batzer MA. Retrotransposition of Alu elements: how many sources? Trends Genet 2004; 20:464-7; PMID:15363897; http://dx.doi.org/10.1016/j.tig.2004.07.012
  • Han K, Xing J, Wang H, Hedges DJ, Garber RK, Cordaux R, Batzer MA. Under the genomic radar: the stealth model of Alu amplification. Genome Res 2005; 15:655-64; PMID:15867427; http://dx.doi.org/10.1101/gr.3492605
  • Liu WM, Maraia RJ, Rubin CM, Schmid CW. Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res 1994; 22:1087-95; PMID:7512262; http://dx.doi.org/10.1093/nar/22.6.1087
  • Xing J, Hedges DJ, Han K, Wang H, Cordaux R, Batzer MA. Alu element mutation spectra: molecular clocks and the effect of DNA methylation. J Mol Biol 2004; 344:675-82; PMID:15533437; http://dx.doi.org/10.1016/j.jmb.2004.09.058
  • Schmid CW. Human Alu subfamilies and their methylation revealed by blot hybridization. Nucleic Acids Res 1991; 19:5613-7; PMID:1945838; http://dx.doi.org/10.1093/nar/19.20.5613
  • Hellmann-Blumberg U, Hintz MF, Gatewood JM, Schmid CW. Developmental differences in methylation of human Alu repeats. Mol Cell Biol 1993; 13:4523-30; PMID:8336699; http://dx.doi.org/10.1128/MCB.13.8.4523
  • Kochanek S, Renz D, Doerfler W. DNA methylation in the Alu sequences of diploid and haploid primary human cells. EMBO J 1993; 12:1141-51; PMID:8384552
  • Rodriguez J, Vives L, Jorda M, Morales C, Munoz M, Vendrell E, Peinado MA. Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells. Nucleic Acids Res 2008; 36:770-84; PMID:18084025; http://dx.doi.org/10.1093/nar/gkm1105
  • Xie H, Wang M, Bonaldo M, de F, Smith C, Rajaram V, Goldman S, Tomita T, Soares MB. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res 2009; 37:4331-40; PMID:19458156; http://dx.doi.org/10.1093/nar/gkp393
  • Rubin CM, VandeVoort CA, Teplitz RL, Schmid CW. Alu repeated DNAs are differentially methylated in primate germ cells. Nucleic Acids Res 1994; 22:5121-7; PMID:7800508; http://dx.doi.org/10.1093/nar/22.23.5121
  • Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 2011; 146:1029-41; PMID:21925323; http://dx.doi.org/10.1016/j.cell.2011.08.016
  • Deininger PL, Batzer MA. Alu repeats and human disease. Mol Genet Metab 1999; 67:183-93; PMID:10381326; http://dx.doi.org/10.1006/mgme.1999.2864
  • Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nat Rev Genet 2009; 10:691-703; PMID:19763152; http://dx.doi.org/10.1038/nrg2640
  • Miki Y, Katagiri T, Kasumi F, Yoshimoto T, Nakamura Y. Mutation analysis in the BRCA2 gene in primary breast cancers. Nat Genet 1996; 13:245-7; PMID:8640237; http://dx.doi.org/10.1038/ng0696-245
  • Teugels E, De Brakeleer S, Goelen G, Lissens W, Sermijn E, De Greve J. De novo Alu element insertions targeted to a sequence common to the BRCA1 and BRCA2 genes. Hum Mut 2005; 26:284; PMID:16088935; http://dx.doi.org/10.1002/humu.9366
  • Peixoto A, Pinheiro M, Massena L, Santos C, Pinto P, Rocha P, Pinto C, Teixeira MR. Genomic characterization of two large Alu-mediated rearrangements of the BRCA1 gene. J Hum Genet 2013; 58:78-83; PMID:23223007; http://dx.doi.org/10.1038/jhg.2012.137
  • Park SY, Seo AN, Jung HY, Gwak JM, Jung N, Cho NY, Kang GH. Alu and LINE-1 hypomethylation is associated with HER2 enriched subtype of breast cancer. PLoS One 2014; 9:e100429; PMID:24971511; http://dx.doi.org/10.1371/journal.pone.0100429
  • Bae JM, Shin SH, Kwon HJ, Park SY, Kook MC, Kim YW, Cho NY, Kim N, Kim TY, Kim D, et al. ALU and LINE-1 hypomethylations in multistep gastric carcinogenesis and their prognostic implications. Int J Cancer 2012; 131:1323-31; PMID:22120154; http://dx.doi.org/10.1002/ijc.27369
  • Bollati V, Fabris S, Pegoraro V, Ronchetti D, Mosca L, Deliliers GL, Motta V, Bertazzi PA, Baccarelli A, Neri A. Differential repetitive DNA methylation in multiple myeloma molecular subgroups. Carcinogenesis 2009; 30:1330-5; PMID:19531770; http://dx.doi.org/10.1093/carcin/bgp149
  • Akers SN, Moysich K, Zhang W, Collamat Lai G, Miller A, Lele S, Odunsi K, Karpf AR. LINE1 and Alu repetitive element DNA methylation in tumors and white blood cells from epithelial ovarian cancer patients. Gynecol Oncol 2014; 132:462-7; PMID:24374023; http://dx.doi.org/10.1016/j.ygyno.2013.12.024
  • Rhee YY, Lee TH, Song YS, Wen X, Kim H, Jheon S, Lee CT, Kim J, Cho NY, Chung JH, et al. Prognostic significance of promoter CpG island hypermethylation and repetitive DNA hypomethylation in stage I lung adenocarcinoma. Virchows Arch 2015; 466:675-83; PMID:25772390; http://dx.doi.org/10.1007/s00428-015-1749-0
  • Li J, Huang Q, Zeng F, Li W, He Z, Chen W, Zhu W, Zhang B. The prognostic value of global DNA hypomethylation in cancer: a meta-analysis. PLoS One 2014; 9:e106290; PMID:25184628; http://dx.doi.org/10.1371/journal.pone.0106290
  • Khakpour G, Pooladi A, Izadi P, Noruzinia M, Tavakkoly Bazzaz J. DNA methylation as a promising landscape: A simple blood test for breast cancer prediction. Tumour Biol 2015; 36:4905-12; PMID:26076810; http://dx.doi.org/10.1007/s13277-015-3567-z
  • Ekram MB, Kim J. High-throughput targeted repeat element bisulfite sequencing (HT-TREBS): genome-wide DNA methylation analysis of IAP LTR retrotransposon. PLoS One 2014; 9:e101683; PMID:25003790; http://dx.doi.org/10.1371/journal.pone.0101683
  • Bakshi A, Ekram MB, Kim J. Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-throughput targeted repeat element bisulfite sequencing. Genom Data 2015; 3:87-9; PMID:25554740; http://dx.doi.org/10.1016/j.gdata.2014.11.013
  • McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 2010; 28:495-501; PMID:20436461; http://dx.doi.org/10.1038/nbt.1630
  • Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Sci Acad 2010; 107:21931-6; PMID:21106759; http://dx.doi.org/10.1073/pnas.1016071107
  • Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 2010; 28:817-25; PMID:20657582; http://dx.doi.org/10.1038/nbt.1662
  • Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011; 473:43-9; PMID:21441907; http://dx.doi.org/10.1038/nature09906
  • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009; 462:315-22; PMID:19829295; http://dx.doi.org/10.1038/nature08514
  • Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA, et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 2012; 44:40-6; PMID:22120008; http://dx.doi.org/10.1038/ng.969
  • Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011; 43:768-75; PMID:21706001; http://dx.doi.org/10.1038/ng.865
  • Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell 2011; 44:17-28; PMID:21924933; http://dx.doi.org/10.1016/j.molcel.2011.08.026
  • Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 2012; 22:246-58; PMID:22156296; http://dx.doi.org/10.1101/gr.125872.111
  • Ziller MJ, Gu H, Muller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 2013; 500:477-81; PMID:23925113; http://dx.doi.org/10.1038/nature12433
  • Xiong Z, Laird PW. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 1997; 25:2532-4; PMID:9171110; http://dx.doi.org/10.1093/nar/25.12.2532
  • Weinstein JN, Collisson EA, Mills GB, Shaw KM, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer Analysis Project. Nat Genet 2013; 45:1113-20; PMID:24071849; http://dx.doi.org/10.1038/ng.2764
  • Ueki T, Park JH, Nishidate T, Kijima K, Hirata K, Nakamura Y, Katagiri T. Ubiquitination and downregulation of BRCA1 by ubiquitin-conjugating enzyme E2T overexpression in human breast cancer cells. Cancer Res 2009; 69:8752-60; PMID:19887602; http://dx.doi.org/10.1158/0008-5472.CAN-09-1809
  • Blomquist TM, Brown RD, Crawford EL, de la Serna I, Williams K, Yoon Y, Hernandez DA, Willey JC. CEBPG exhibits allele-specific expression in human bronchial epithelial cells. Gene Regul Syst Biol 2013; 7:125-38; http://dx.doi.org/10.4137/GRSB.S11879
  • Crawford EL, Blomquist T, Mullins DN, Yoon Y, Hernandez DR, Al-Bagdhadi M, Ruiz J, Hammersley J, Willey JC. CEBPG regulates ERCC5/XPG expression in human bronchial epithelial cells and this regulation is modified by E2F1/YY1 interactions. Carcinogenesis 2007; 28:2552-9; PMID:17893230; http://dx.doi.org/10.1093/carcin/bgm214
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357-9; PMID:22388286; http://dx.doi.org/10.1038/nmeth.1923
  • Lutsik P, Feuerbach L, Arand J, Lengauer T, Walter J, Bock C. BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res 2011; 39:W551-6; PMID:21565797; http://dx.doi.org/10.1093/nar/gkr312
  • Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002; 30:207-10; PMID:11752295; http://dx.doi.org/10.1093/nar/30.1.207
  • Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 2005; 21:4067-8; PMID:16141249; http://dx.doi.org/10.1093/bioinformatics/bti652

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.