Variant Histone H2afv reprograms DNA methylation during early zebrafish development

References

• 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(7271):315-22. doi:10.1038/nature08514. PMID:19829295
   PubMed Web of Science ®Google Scholar
• Long HK, King HW, Patient RK, Odom DT, Klose RJ. Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved. Nucleic Acids Res. 2016;44(14):6693-706. doi:10.1093/nar/gkw258. PMID:27084945
   PubMed Web of Science ®Google Scholar
• Zhang C, Hoshida Y, Sadler KC. Comparative epigenomic profiling of the DNA methylome in mouse and zebrafish uncovers high interspecies divergence. Front Genet. 2016;7:110. doi:10.3389/fgene.2016.00110. PMID:27379160
   PubMed Web of Science ®Google Scholar
• Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, et al. Dynamic changes in the human methylome during differentiation. Genome Res. 2010;20(3):320-31. doi:10.1101/gr.101907.109. PMID:20133333
   PubMed Web of Science ®Google Scholar
• Lee HJ, Lowdon RF, Maricque B, Zhang B, Stevens M, Li D, Johnson SL, Wang T. Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. Nat Commun. 2015;6:6315. doi:10.1038/ncomms7315. PMID:25697895
   PubMed Web of Science ®Google Scholar
• Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA, Gehrke C. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res. 1982;10(8):2709-21. doi:10.1093/nar/10.8.2709. PMID:7079182
   PubMed Web of Science ®Google Scholar
• Branco MR, King M, Perez-Garcia V, Bogutz AB, Caley M, Fineberg E, Lefebvre L, Cook SJ, Dean W, Hemberger M, et al. Maternal DNA methylation regulates early trophoblast development. Dev Cell. 2016;36(2):152-63. doi:10.1016/j.devcel.2015.12.027. PMID:26812015
   PubMed Web of Science ®Google Scholar
• Schubeler D. Function and information content of DNA methylation. Nature. 2015;517(7534):321-6. doi:10.1038/nature14192. PMID:25592537
   PubMed Web of Science ®Google Scholar
• Smith ZD, Meissner A. DNA methylation: Roles in mammalian development. Nat Rev Genet. 2013;14(3):204-20. doi:10.1038/nrg3354. PMID:23400093
   PubMed Web of Science ®Google Scholar
• Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA. Epigenetic reprogramming in mouse primordial germ cells. Mech Dev. 2002;117(1-2):15-23. doi:10.1016/S0925-4773(02)00181-8. PMID:12204247
   PubMed Web of Science ®Google Scholar
• Mayer W, Fundele R, Haaf T. Spatial separation of parental genomes during mouse interspecific (Mus musculus x M. spretus) spermiogenesis. Chromosome Res. 2000;8(6):555-8. doi:10.1023/A:1009227924235. PMID:11032324
   PubMed Web of Science ®Google Scholar
• Mhanni AA, McGowan RA. Global changes in genomic methylation levels during early development of the zebrafish embryo. Dev Genes Evol. 2004;214(8):412-7. doi:10.1007/s00427-004-0418-0. PMID:15309635
   PubMed Web of Science ®Google Scholar
• Sanz LA, Kota SK, Feil R. Genome-wide DNA demethylation in mammals. Genome Biol. 2010;11(3):110. doi:10.1186/gb-2010-11-3-110. PMID:20236475
   PubMed Web of Science ®Google Scholar
• Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010;463(7284):1101-5. doi:10.1038/nature08829. PMID:20098412
   PubMed Web of Science ®Google Scholar
• Siklenka K, Erkek S, Godmann M, Lambrot R, McGraw S, Lafleur C, Cohen T, Xia J, Suderman M, Hallett M, et al. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science. 2015;350(6261):aab2006. doi:10.1126/science.aab2006. PMID:26449473
   PubMed Web of Science ®Google Scholar
• Rodgers AB, Morgan CP, Leu NA, Bale TL. Transgenerational epigenetic programming via sperm microRNA recapitulates effects of paternal stress. Proc Natl Acad Sci U S A. 2015;112(44):13699-704. doi:10.1073/pnas.1508347112. PMID:26483456
   PubMed Web of Science ®Google Scholar
• Chen Q, Yan M, Cao Z, Li X, Zhang Y, Shi J, Feng GH, Peng H, Zhang X, Zhang Y, et al. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science. 2016;351(6271):397-400. doi:10.1126/science.aad7977. PMID:26721680
   PubMed Web of Science ®Google Scholar
• Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, Belleannee C, Kucukural A, Serra RW, Sun F, et al. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science. 2016;351(6271):391-6. doi:10.1126/science.aad6780. PMID:26721685
   PubMed Web of Science ®Google Scholar
• Du J, Johnson LM, Jacobsen SE, Patel DJ. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol. 2015;16(9):519-32. doi:10.1038/nrm4043. PMID:26296162
   PubMed Web of Science ®Google Scholar
• Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008;133(3):523-36. doi:10.1016/j.cell.2008.03.029. PMID:18423832
   PubMed Web of Science ®Google Scholar
• Rea M, Zheng W, Chen M, Braud C, Bhangu D, Rognan TN, Xiao W. Histone H1 affects gene imprinting and DNA methylation in Arabidopsis. Plant J. 2012;71(5):776-86. doi:10.1111/j.1365-313X.2012.05028.x. PMID:22519754
   PubMed Web of Science ®Google Scholar
• Saze H, Tsugane K, Kanno T, Nishimura T. DNA methylation in plants: Relationship to small RNAs and histone modifications, and functions in transposon inactivation. Plant Cell Physiol. 2012;53(5):766-84. doi:10.1093/pcp/pcs008. PMID:22302712
   PubMed Web of Science ®Google Scholar
• Wollmann H, Stroud H, Yelagandula R, Tarutani Y, Jiang D, Jing L, Jamge B, Takeuchi H, Holec S, Nie X, et al. The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana. Genome Biol. 2017;18(1):94. doi:10.1186/s13059-017-1221-3. PMID:28521766
   PubMedGoogle Scholar
• Zemach A, Grafi G. Methyl-CpG-binding domain proteins in plants: Interpreters of DNA methylation. Trends Plant Sci. 2007;12(2):80-5. doi:10.1016/j.tplants.2006.12.004. PMID:17208509
   PubMed Web of Science ®Google Scholar
• Nekrasov M, Amrichova J, Parker BJ, Soboleva TA, Jack C, Williams R, Huttley GA, Tremethick DJ. Histone H2A.Z inheritance during the cell cycle and its impact on promoter organization and dynamics. Nat Struct Mol Biol. 2012;19(11):1076-83. doi:10.1038/nsmb.2424. PMID:23085713
   PubMed Web of Science ®Google Scholar
• Raisner RM, Hartley PD, Meneghini MD, Bao MZ, Liu CL, Schreiber SL, Rando OJ, Madhani HD. Histone variant H2A.Z Marks the 5′ ends of both active and inactive genes in euchromatin. Cell. 2005;123(2):233-48. doi:10.1016/j.cell.2005.10.002. PMID:16239142
   PubMed Web of Science ®Google Scholar
• Soboleva TA, Nekrasov M, Ryan DP, Tremethick DJ. Histone variants at the transcription start-site. Trends Genet. 2014;30(5):199-209. doi:10.1016/j.tig.2014.03.002. PMID:24768041
   PubMed Web of Science ®Google Scholar
• Nashun B, Yukawa M, Liu H, Akiyama T, Aoki F. Changes in the nuclear deposition of histone H2A variants during pre-implantation development in mice. Development. 2010;137(22):3785-94. doi:10.1242/dev.051805. PMID:20943707
   PubMed Web of Science ®Google Scholar
• Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 2008;456(7218):125-9. doi:10.1038/nature07324. PMID:18815594
   PubMed Web of Science ®Google Scholar
• Kobor MS, Lorincz MC. H2A.Z and DNA methylation: Irreconcilable differences. Trends Biochem Sci. 2009;34(4):158-61. doi:10.1016/j.tibs.2008.12.006. PMID:19282182
   PubMed Web of Science ®Google Scholar
• Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 2010;328(5980):916-9. doi:10.1126/science.1186366. PMID:20395474
   PubMed Web of Science ®Google Scholar
• Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Curr Biol. 2010;20(17):R780-5. doi:10.1016/j.cub.2010.07.007. PMID:20833323
   PubMed Web of Science ®Google Scholar
• Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet. 2012;8(10):e1002988. doi:10.1371/journal.pgen.1002988. PMID:23071449
   PubMed Web of Science ®Google Scholar
• Yang X, Noushmehr H, Han H, Andreu-Vieyra C, Liang G, Jones PA. Gene reactivation by 5-aza-2'-deoxycytidine-induced demethylation requires SRCAP-mediated H2A.Z insertion to establish nucleosome depleted regions. PLoS Genet. 2012;8(3):e1002604. doi:10.1371/journal.pgen.1002604. PMID:22479200
   PubMed Web of Science ®Google Scholar
• Zeybel M, Hardy T, Wong YK, Mathers JC, Fox CR, Gackowska A, Oakley F, Burt AD, Wilson CL, Anstee QM, et al. Multigenerational epigenetic adaptation of the hepatic wound-healing response. Nat Med. 2012;18(9):1369-77. doi:10.1038/nm.2893. PMID:22941276
   PubMed Web of Science ®Google Scholar
• Jiang L, Zhang J, Wang JJ, Wang L, Zhang L, Li G, Yang X, Ma X, Sun X, Cai J, et al. Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos. Cell. 2013;153(4):773-84. doi:10.1016/j.cell.2013.04.041. PMID:23663777
   PubMed Web of Science ®Google Scholar
• Potok ME, Nix DA, Parnell TJ, Cairns BR. Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell. 2013;153(4):759-72. doi:10.1016/j.cell.2013.04.030. PMID:23663776
   PubMed Web of Science ®Google Scholar
• Lindeman LC, Winata CL, Aanes H, Mathavan S, Alestrom P, Collas P. Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos. Int J Dev Biol. 2010;54(5):803-13. doi:10.1387/ijdb.103081ll. PMID:20336603
   PubMed Web of Science ®Google Scholar
• Andersen IS, Reiner AH, Aanes H, Alestrom P, Collas P. Developmental features of DNA methylation during activation of the embryonic zebrafish genome. Genome Biol. 2012;13(7):R65. doi:10.1186/gb-2012-13-7-r65. PMID:22830626
   PubMed Web of Science ®Google Scholar
• Bogdanovic O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I, et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016;48(4):417-26. doi:10.1038/ng.3522. PMID:26928226
   PubMed Web of Science ®Google Scholar
• Kobayashi H, Sakurai T, Imai M, Takahashi N, Fukuda A, Yayoi O, Sato S, Nakabayashi K, Hata K, Sotomaru Y, et al. Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet. 2012;8(1):e1002440. doi:10.1371/journal.pgen.1002440. PMID:22242016
   PubMed Web of Science ®Google Scholar
• Kobayashi H, Sakurai T, Miura F, Imai M, Mochiduki K, Yanagisawa E, Sakashita A, Wakai T, Suzuki Y, Ito T, et al. High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res. 2013;23(4):616-27. doi:10.1101/gr.148023.112. PMID:23410886
   PubMed Web of Science ®Google Scholar
• Lee HJ, Lowdon RF, Maricque B, Zhang B, Stevens M, Li D, Johnson SL, Wang T. Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. Nat Commun. 2015;6:6315. doi:10.1038/ncomms7315. PMID:25697895
   PubMed Web of Science ®Google Scholar
• Martin CC, Laforest L, Akimenko MA, Ekker M. A role for DNA methylation in gastrulation and somite patterning. Dev Biol. 1999;206(2):189-205. doi:10.1006/dbio.1998.9105. PMID:9986732
   PubMed Web of Science ®Google Scholar
• Rai K, Jafri IF, Chidester S, James SR, Karpf AR, Cairns BR, Jones DA. Dnmt3 and G9a cooperate for tissue-specific development in zebrafish. J Biol Chem. 2010;285(6):4110-21. doi:10.1074/jbc.M109.073676. PMID:19946145
   PubMed Web of Science ®Google Scholar
• Hajkova P, Ancelin K, Waldmann T, Lacoste N, Lange UC, Cesari F, Lee C, Almouzni G, Schneider R, Surani MA. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature. 2008;452(7189):877-81. doi:10.1038/nature06714. PMID:18354397
   PubMed Web of Science ®Google Scholar
• Sivasubbu S, Balciunas D, Davidson AE, Pickart MA, Hermanson SB, Wangensteen KJ, Wolbrink DC, Ekker SC. Gene-breaking transposon mutagenesis reveals an essential role for histone H2afza in zebrafish larval development. Mech Dev. 2006;123(7):513-29. doi:10.1016/j.mod.2006.06.002. PMID:16859902
   PubMed Web of Science ®Google Scholar
• Pauls S, Geldmacher-Voss B, Campos-Ortega JA. A zebrafish histone variant H2A.F/Z and a transgenic H2A.F/Z:GFP fusion protein for in vivo studies of embryonic development. Dev Genes Evol. 2001;211(12):603-10. doi:10.1007/s00427-001-0196-x. PMID:11819118
   PubMed Web of Science ®Google Scholar
• Faast R, Thonglairoam V, Schulz TC, Beall J, Wells JRE, Taylor H, Matthaei K, Rathjen PD, Tremethick DJ, Lyons I. Histone variant H2A.Z is required for early mammalian development. Curr Biol. 2001;11(15):1183-7. doi:10.1016/S0960-9822(01)00329-3. PMID:11516949
   PubMed Web of Science ®Google Scholar
• Percival SM, Parant JM. Observing mitotic division and dynamics in a live zebrafish embryo. J Vis Exp. 2016;(113). PMID:27501381.
   PubMed Web of Science ®Google Scholar
• Robu ME, Larson JD, Nasevicius A, Beiraghi S, Brenner C, Farber SA, Ekker SC. p53 activation by knockdown technologies. PLoS Genetics. 2007;3(5):e78. doi:10.1371/journal.pgen.0030078. PMID:17530925
   PubMed Web of Science ®Google Scholar
• Fang X, Corrales J, Thornton C, Scheffler BE, Willett KL. Global and gene specific DNA methylation changes during zebrafish development. Comp Biochem Physiol B Biochem Mol Biol. 2013;166(1):99-108. doi:10.1016/j.cbpb.2013.07.007. PMID:23876386
   PubMed Web of Science ®Google Scholar
• Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A. 2006;103(5):1412-7. doi:10.1073/pnas.0510310103. PMID:16432200
   PubMed Web of Science ®Google Scholar
• Deaton AM, Bird A. CpG islands and the regulation of transcription. Genes Dev. 2011;25(10):1010-22. doi:10.1101/gad.2037511. PMID:21576262
   PubMed Web of Science ®Google Scholar
• Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129(4):823-37. doi:10.1016/j.cell.2007.05.009. PMID:17512414
   PubMed Web of Science ®Google Scholar
• Bruce K, Myers FA, Mantouvalou E, Lefevre P, Greaves I, Bonifer C, Tremethick DJ, Thorne AW, Crane-Robinson C. The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken. Nucleic Acids Res. 2005;33(17):5633-9. doi:10.1093/nar/gki874. PMID:16204459
   PubMed Web of Science ®Google Scholar
• Thambirajah AA, Dryhurst D, Ishibashi T, Li A, Maffey AH, Ausio J. H2A.Z stabilizes chromatin in a way that is dependent on core histone acetylation. J Biol Chem. 2006;281(29):20036-44. doi:10.1074/jbc.M601975200. PMID:16707487
   PubMed Web of Science ®Google Scholar
• Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid RF, Anand S, et al. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res. 2013;23(11):1938-50. doi:10.1101/gr.153692.112. PMID:24002785
   PubMed Web of Science ®Google Scholar
• Wu SF, Zhang H, Hammoud SS, Potok M, Nix DA, Jones DA, Cairns BR. DNA methylation profiling in zebrafish. Methods Cell Biol. 2011;104:327-39. doi:10.1016/B978-0-12-374814-0.00018-5. PMID:21924171
   PubMed Web of Science ®Google Scholar
• Wu S-F. Epigenomes of zebrafish mature sperm and early embryos. ProQuest: The University of Utah; 2013.
   Google Scholar
• Jones PA, Liang G. Rethinking how DNA methylation patterns are maintained. Nat Rev Genet. 2009;10(11):805-11. doi:10.1038/nrg2651. PMID:19789556
   PubMed Web of Science ®Google Scholar
• Kent B, Magnani E, Walsh MJ, Sadler KC. UHRF1 regulation of Dnmt1 is required for pre-gastrula zebrafish development. Dev Biol. 2016;412(1):99-113. doi:10.1016/j.ydbio.2016.01.036. PMID:26851214
   PubMed Web of Science ®Google Scholar
• Ridgway P, Brown KD, Rangasamy D, Svensson U, Tremethick DJ. Unique Residues on the H2A.Z containing nucleosome surface are important for xenopus laevis development. J Biol Chem. 2004;279(42):43815-20. doi:10.1074/jbc.M408409200. PMID:15299007
   PubMed Web of Science ®Google Scholar
• Conerly ML, Teves SS, Diolaiti D, Ulrich M, Eisenman RN, Henikoff S. Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis. Genome Res. 2010;20(10):1383-90. doi:10.1101/gr.106542.110. PMID:20709945
   PubMed Web of Science ®Google Scholar
• Boyes J, Bird A. Repression of genes by DNA methylation depends on CpG density and promoter strength: Evidence for involvement of a methyl-CpG binding protein. EMBO J. 1992;11(1):327-33. PMID:1310933
   PubMed Web of Science ®Google Scholar
• Klose RJ, Bird AP. Genomic DNA methylation: The mark and its mediators. Trends Biochem Sci. 2006;31(2):89-97. doi:10.1016/j.tibs.2005.12.008. PMID:16403636
   PubMed Web of Science ®Google Scholar
• Okitsu CY, Hsieh C-L. DNA methylation dictates histone H3K4 methylation. Mol Cell Biol. 2007;27(7):2746-57. doi:10.1128/MCB.02291-06. PMID:17242185
   PubMed Web of Science ®Google Scholar
• Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008;454(7205):766-70. doi:10.1038/nature07107. PMID:18600261
   PubMed Web of Science ®Google Scholar
• Ke XS, Qu Y, Cheng Y, Li WC, Rotter V, Oyan AM, Kalland KH. Global profiling of histone and DNA methylation reveals epigenetic-based regulation of gene expression during epithelial to mesenchymal transition in prostate cells. BMC Genomics. 2010;11:669. doi:10.1186/1471-2164-11-669. PMID:21108828
   PubMed Web of Science ®Google Scholar
• Yang X, Noushmehr H, Han H, Andreu-Vieyra C, Liang G, Jones PA. Gene reactivation by 5-Aza-2′-Deoxycytidine–induced demethylation requires SRCAP–Mediated H2A.Z insertion to establish nucleosome depleted regions. PLoS Genetics. 2012;8(3):e1002604. doi:10.1371/journal.pgen.1002604. PMID:22479200
   PubMed Web of Science ®Google Scholar
• Abbott DW, Ivanova VS, Wang X, Bonner WM, Ausió J. Characterization of the stability and folding of H2A.Z chromatin particles: Implications for transcriptional activation. J Biol Chem. 2001;276(45):41945-9. doi:10.1074/jbc.M108217200. PMID:11551971
   PubMed Web of Science ®Google Scholar
• Bestor TH, Edwards JR, Boulard M. Notes on the role of dynamic DNA methylation in mammalian development. Proc Natl Acad Sci U S A. 2014. PMID:25368180.
   PubMed Web of Science ®Google Scholar
• Jacob V, Chernyavskaya Y, Chen X, Tan PS, Kent B, Hoshida Y, Sadler KC. DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos. Development. 2015;142(3):510-21. doi:10.1242/dev.115980. PMID:25564650
   PubMed Web of Science ®Google Scholar
• Chernyavskaya Y, M R, Tokarz D, Jacob V, Gopinath S, Zhang C, Sun X, Wang S, Magnani E, Madakashira BP, et al. Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger an antiviral response. Development. 2017 (in press); doi:10.1242/dev.147629. PMID:28698226
   PubMed Web of Science ®Google Scholar
• Mudbhary R, Hoshida Y, Chernyavskaya Y, Jacob V, Villanueva A, Fiel MI, Chen X, Kojima K, Thung S, Bronson Roderick T, et al. UHRF1 overexpression drives DNA hypomethylation and hepatocellular carcinoma. Cancer Cell. 2014;25(2):196-209. doi:10.1016/j.ccr.2014.01.003. PMID:24486181
   PubMed Web of Science ®Google Scholar
• Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. methylKit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012;13(10):R87. doi:10.1186/gb-2012-13-10-r87. PMID:23034086
   PubMed Web of Science ®Google Scholar
• Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, To BL, Lewis ID, Brown AL, D'Andrea RJ, Melnick A, et al. An optimized algorithm for detecting and annotating regional differential methylation. BMC Bioinformatics. 2013;14 Suppl 5:S10. doi:10.1186/1471-2105-14-S5-S10. PMID:23735126
   PubMed Web of Science ®Google Scholar