Temple S: The development of neural stem cells. Nature. 2001, 414: 112-117. 10.1038/35102174.
Article
CAS
PubMed
Google Scholar
Sauvageot CM, Stiles CD: Molecular mechanisms controlling cortical gliogenesis. Curr Opin Neurobiol. 2002, 12: 244-249. 10.1016/S0959-4388(02)00322-7.
Article
CAS
PubMed
Google Scholar
Miller FD, Gauthier AS: Timing is everything: making neurons versus glia in the developing cortex. Neuron. 2007, 54: 357-369. 10.1016/j.neuron.2007.04.019.
Article
CAS
PubMed
Google Scholar
Mason S, Piper M, Gronostajski RM, Richards LJ: Nuclear factor one transcription factors in CNS development. Mol Neurobiol. 2009, 39: 10-23. 10.1007/s12035-008-8048-6.
Article
CAS
PubMed
Google Scholar
das Neves L, Duchala CS, Tolentino-Silva F, Haxhiu MA, Colmenares C, Macklin WB, Campbell CE, Butz KG, Gronostajski RM, Godinho F: Disruption of the murine nuclear factor I-A gene (Nfia) results in perinatal lethality, hydrocephalus, and agenesis of the corpus callosum. Proc Natl Acad Sci USA. 1999, 96: 11946-11951. 10.1073/pnas.96.21.11946.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang W, Yi MJ, Chen X, Cole F, Krauss RS, Kang JS: Cortical thinning and hydrocephalus in mice lacking the immunoglobulin superfamily member CDO. Mol Cell Biol. 2006, 26: 3764-3772. 10.1128/MCB.26.10.3764-3772.2006.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yagi S, Hirabayashi K, Sato S, Li W, Takahashi Y, Hirakawa T, Wu G, Hattori N, Hattori N, Ohgane J, Tanaka S, Liu XS, Shiota K: DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res. 2008, 18: 1969-1978. 10.1101/gr.074070.107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kremenskoy M, Kremenska Y, Ohgane J, Hattori N, Tanaka S, Hashizume K, Shiota K: Genome-wide analysis of DNA methylation status of CpG islands in embryoid bodies, teratomas, and fetuses. Biochem Biophys Res Commun. 2003, 311: 884-890. 10.1016/j.bbrc.2003.10.078.
Article
CAS
PubMed
Google Scholar
Hattori N, Nishino K, Ko Y, Ohgane J, Tanaka S, Shiota K: Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. J Biol Chem. 2004, 279: 17063-17069. 10.1074/jbc.M309002200.
Article
CAS
PubMed
Google Scholar
Nishino K, Hattori N, Tanaka S, Shiota K: DNA methylation-mediated control of Sry gene expression in mouse gonadal development. J Biol Chem. 2004, 279: 22306-22313. 10.1074/jbc.M309513200.
Article
CAS
PubMed
Google Scholar
Hattori N, Imao Y, Nishino K, Ohgane J, Yagi S, Tanaka S, Shiota K: Epigenetic regulation of Nanog gene in embryonic stem and trophoblast stem cells. Genes Cells. 2007, 12: 387-396. 10.1111/j.1365-2443.2007.01058.x.
Article
CAS
PubMed
Google Scholar
Sakamoto H, Kogo Y, Ohgane J, Hattori N, Yagi S, Tanaka S, Shiota K: Sequential changes in genome-wide DNA methylation status during adipocyte differentiation. Biochem Biophys Res Commun. 2008, 366: 360-366. 10.1016/j.bbrc.2007.11.137.
Article
CAS
PubMed
Google Scholar
Maeda C, Sato S, Hattori N, Tanaka S, Yagi S, Shiota K: DNA hypomethylation circuit of the mouse oocyte-specific histone H1foo gene in female germ cell lineage. Biol Reprod. 2008, 78: 816-821. 10.1095/biolreprod.107.066522.
Article
CAS
PubMed
Google Scholar
Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM: Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006, 16: 1046-1055. 10.1101/gr.5273806.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res. 2008, 18: 1518-1529. 10.1101/gr.077479.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hatada I, Namihira M, Morita S, Kimura M, Horii T, Nakashima K: Astrocyte-specific genes are generally demethylated in neural precursor cells prior to astrocytic differentiation. PLoS One. 2008, 3: e3189-10.1371/journal.pone.0003189.
Article
PubMed Central
PubMed
Google Scholar
Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schübeler D: Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell. 2008, 30: 755-766. 10.1016/j.molcel.2008.05.007.
Article
CAS
PubMed
Google Scholar
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES: Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008, 454: 766-770.
PubMed Central
CAS
PubMed
Google Scholar
Hirabayashi Y, Gotoh Y: Epigenetic control of neural precursor cell fate during development. Nat Rev Neurosci. 2010, 11: 377-388. 10.1038/nrn2810.
Article
CAS
PubMed
Google Scholar
Sato S, Yagi S, Arai Y, Hirabayashi K, Hattori N, Iwatani M, Okita K, Ohgane J, Tanaka S, Wakayama T, Yamanaka S, Shiota K: Genome-wide DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) residing in mouse pluripotent stem cells. Genes Cells. 2010, 15: 607-618. 10.1111/j.1365-2443.2010.01404.x.
Article
CAS
PubMed
Google Scholar
Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS: Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA. 2006, 103: 12457-12462. 10.1073/pnas.0601180103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shiota K: DNA methylation profiles of CpG islands for cellular differentiation and development in mammals. Cytogenet Gennome Res. 2004, 105: 325-334. 10.1159/000078205.
Article
CAS
Google Scholar
Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP: The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009, 41: 178-186. 10.1038/ng.298.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fazzari MJ, Greally JM: Epigenomics: beyond CpG islands. Nat Rev Genet. 2004, 5: 446-455. 10.1038/nrg1349.
Article
CAS
PubMed
Google Scholar
Yagi S, Hirosawa M, Shiota K: DNA methylation profile: a composer-, conductor-, and player-orchestrated Mammalian genome consisting of genes and transposable genetic elements. J Reprod Dev. 2012, 58: 265-273. 10.1262/jrd.2011-030.
Article
CAS
PubMed
Google Scholar
Hutnick LK, Golshani P, Namihira M, Xue Z, Matynia A, Yang XW, Silva AJ, Schweizer FE, Fan G: DNA hypomethylation restricted to the murine forebrain induces cortical degeneration and impairs postnatal neuronal maturation. Hum Mol Genet. 2009, 18: 2875-2888. 10.1093/hmg/ddp222.
Article
PubMed Central
CAS
PubMed
Google Scholar
Xu GL, Bestor TH, Bourc’his D, Hsieh CL, Tommerup N, Bugge M, Hulten M, Qu X, Russo JJ, Viegas-Péquignot E: Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature. 1999, 402: 187-191. 10.1038/46052.
Article
CAS
PubMed
Google Scholar
Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY: Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet. 1999, 23: 185-188. 10.1038/13810.
Article
CAS
PubMed
Google Scholar
O’Driscoll M, Cerosaletti KM, Girard PM, Dai Y, Stumm M, Kysela B, Hirsch B, Gennery A, Palmer SE, Seidel J, Gatti RA, Varon R, Oettinger MA, Neitzel H, Jeggo PA, Concannon P: DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency. Mol Cell. 2001, 8: 1175-1185. 10.1016/S1097-2765(01)00408-7.
Article
PubMed
Google Scholar
Lu W, Quintero-Rivera F, Fan Y, Alkuraya FS, Donovan DJ, Xi Q, Turbe-Doan A, Li QG, Campbell CG, Shanske AL, Sherr EH, Ahmad A, Peters R, Rilliet B, Parvex P, Bassuk AG, Harris DJ, Ferguson H, Kelly C, Walsh CA, Gronostajski RM, Devriendt K, Higgins A, Ligon AH, Quade BJ, Morton CC, Gusella JF, Maas RL: NFIA haploinsufficiency is associated with a CNS malformation syndrome and urinary tract defects. PLoS Genet. 2007, 3: e80-10.1371/journal.pgen.0030080.
Article
PubMed Central
PubMed
Google Scholar
Frank KM, Sharpless NE, Gao Y, Sekiguchi JM, Ferguson DO, Zhu C, Manis JP, Horner J, DePinho RA, Alt FW: DNA ligase IV deficiency in mice leads to defective neurogenesis and embryonic lethality via the p53 pathway. Mol Cell. 2000, 5: 993-1002. 10.1016/S1097-2765(00)80264-6.
Article
CAS
PubMed
Google Scholar
Deuel TA, Liu JS, Corbo JC, Yoo SY, Rorke-Adams LB, Walsh CA: Genetic interactions between doublecortin and doublecortin-like kinase in neuronal migration and axon outgrowth. Neuron. 2006, 49: 41-53. 10.1016/j.neuron.2005.10.038.
Article
CAS
PubMed
Google Scholar
Demyanenko GP, Riday TT, Tran TS, Dalal J, Darnell EP, Brennaman LH, Sakurai T, Grumet M, Philpot BD, Maness PF: NrCAM deletion causes topographic mistargeting of thalamocortical axons to the visual cortex and disrupts visual acuity. J Neurosci. 2011, 31: 1545-1558. 10.1523/JNEUROSCI.4467-10.2011.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ohgane J, Wakayama T, Kogo Y, Senda S, Hattori N, Tanaka S, Yanagimachi R, Shiota K: DNA methylation variation in cloned mice. Genesis. 2001, 30: 45-50. 10.1002/gene.1031.
Article
CAS
PubMed
Google Scholar
Arai Y, Ohgane J, Yagi S, Ito R, Iwasaki Y, Saito K, Akutsu K, Takatori S, Ishii R, Hayashi R, Izumi S, Sugino N, Kondo F, Horie M, Nakazawa H, Makino T, Shiota K: Epigenetic assessment of environmental chemicals detected in maternal peripheral and cord blood samples. J Reprod Dev. 2011, 57: 507-517. 10.1262/jrd.11-034A.
Article
CAS
PubMed
Google Scholar
Maekawa R, Yagi S, Ohgane J, Yamagata Y, Asada H, Tamura I, Sugino N, Shiota K: Disease-dependent differently methylated regions (D-DMRs) of DNA are enriched on the X chromosome in uterine leiomyoma. J Reprod Dev. 2011, 57: 604-612. 10.1262/jrd.11-035A.
Article
CAS
PubMed
Google Scholar
Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM: Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenet Genome Res. 2006, 114: 1-15. 10.1159/000091922.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jones PA, Baylin SB: The epigenomics of cancer. Cell. 2007, 128: 683-692. 10.1016/j.cell.2007.01.029.
Article
PubMed Central
CAS
PubMed
Google Scholar
Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A: BioMart–biological queries made easy. BMC Genomics. 2009, 10: 22-10.1186/1471-2164-10-22.
Article
PubMed Central
PubMed
Google Scholar
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A: Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005, 15: 1451-1455. 10.1101/gr.4086505.
Article
PubMed Central
CAS
PubMed
Google Scholar
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J: TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003, 34: 374-378.
CAS
PubMed
Google Scholar
Huang Da W, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, Lempicki RA: DAVID bioinformatics resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007, 35 (Web Server issue): W169-W175.
Article
PubMed
Google Scholar
Sim FJ, McClain CR, Schanz SJ, Protack TL, Windrem MS, Goldman SA: CD140a identifies a population of highly myelinogenic, migration-competent and efficiently engrafting human oligodendrocyte progenitor cells. Nat Biotechnol. 2011, 29: 934-941. 10.1038/nbt.1972.
Article
PubMed Central
CAS
PubMed
Google Scholar