Adkins, M. W., S. R. Howar and J. K. Tyler. 2004. Chromatin disassembly mediated by histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol. Cell 14: 657–666.
PubMed Link
Agger, K. and 9 others. 2007. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449: 731–734.
PubMed Link
Aksan, I. and C. R. Goding. 1998. Targeting the microphthalmia basic helix-loop-helix-leucine zipper transcription factor to a subset of E-box elements in vitro and in vivo. Mol. Cell Biol. 18: 6930–6938.
PubMed Link
Andersen, F. G., J. Jensen, R. S. Heller, H. V. Petersen, L.-I. Larsson, O. D. Madsen and P. Serup. 1999. Pax6 and Pdx1 form a functional complex on the rat somatostatin gene upstream enhancer. FEBS Lett. 445: 315–320.
PubMed Link
Angier, N. 1992. A first step in putting genes into action: Bend the DNA. New York Times, August 4, pp. C1, C7.
Aravin, A. A. and 8 others. 2003. The small RNA profile during Drosophila melanogaster development. Dev. Cell. 5: 337–350.
PubMed Link
Ashworth, D. and 10 others. 1998. DNA satellite analysis of Dolly. Nature 394: 329.
PubMed Link
Bagga, S. J. Bracht, S. Hunter, K. Massirer, J. Holtz, R. Eachus and A. E. Pasquinelli. 2005. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122: 553–563.
PubMed Link
Baird, M. L. and 7 others. 1981. A nucleotide change at a splice junction in the human β-globin gene is associated with b0-thalassemia. Proc. Natl. Acad. Sci. USA 78: 4218–4221.
PubMed Link
Barash, Y. and 7 others. 2010. Deciphering the splicing code. Nature 465: 53–59.
PubMed Link
Barbosa-Morais, N. L. and 16 others. 2012. The evolutionary landscape of alternative splicing in vertebrate species. Science 338: 1587–1593.
PubMed Link
Barrangou, R. and 7 others. 2007. CRISPR provides acquired resisistance against viruses in prokaryotes. Science 315: 1709–1712.
PubMed Link
Bartel, D. P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function.Cell 116: 281–297.
PubMed Link
Bartke, T., M. Vermeulen, B. Xhemalce, S. C. Robson, M. Mann and T. Kouzarides. 2010. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143: 470–484.
PubMed Link
Bartolomei, M. S., A. L. Webber, M. E. Brunkow and S. M. Tilghman. 1993. Epigenetic mechanisms underlying the imprinting of the mouse H19 gene. Genes Dev. 7: 1663–1673.
PubMed Link
Bassett, A. R., C. Tibbit, C. P. Ponting and J. L. Liu. 2013. Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep. 4: 220–228.
PubMed Link
Bazzini, A. A., M. T. Lee and A. J. Giraldez. 2012. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336: 233–237.
PubMed Link
Beermann, W. 1952. Chromomerenkonstanz und spezifische Modifikationen der Chromosomenstruktur in der Entwicklung und Organdifferenzierung von Chironomus tentans. Chromosoma 5: 139–198.
Bell, A. C. and G. Felsenfeld. 2000. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405: 482–485.
PubMed Link
Bentley, N. J., T. Eisen and C. R. Goding. 1994. Melanocyte-specific expression of the human tyrosinase promoter: Activation by the microphthalmia gene product and the role of the initiator. Mol. Cell. Biol. 14: 7996–8006.
PubMed Link
Berezikov, E. and R. H. Plasterk. 2005. Camels and zebrafish, viruses and cancer: A microRNA update. Hum. Mol. Genet. 14; spec. no. 2: R183–R190.
PubMed Link
Berkes, C. A., D. A. Bergstrom, B. H.Penn, K. J. Seaver, P. S. Knoepfler and S. J. Tapscott. 2004. Pbx marks genes for activation by MyoD indicating a role for a homeodomain protein in establishing myogenic potential. Mol. Cell 14: 465–477.
PubMed Link
Bird, A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev. 16: 6–21.
PubMed Link
Black, D. L. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72: 291–336.
PubMed Link
Bottardi, S., L. Mavoungou and E. Milot E. 2015. IKAROS: a multifunctional regulator of the polymerase II transcription cycle. Trends Genet. 31: 500–508.
PubMed Link
Boveri, T. 1904. Ergebnisse uber die Konstitution der chromatischen Substanz des Zellkerns. Fischer, Jena.
Briggs, R. and T. J. King. 1952. Transplantation of living nuclei from blastula cells into enucleated frogs' eggs. Proc. Natl. Acad. Sci. USA 38: 455–463.
PubMed Link
Burdge, G. C., J. Slater-Jefferies, C. Torrens, E. S. Phillips, M. A. Hanson and K. A. Lillycrop. 2007. Dietary protein restriction of pregnant rats in the F0 generation induces altered methylation of hepatic gene promoters in the adult male offspring in the F1 and F2 generations. Brit. J. Nutrit. 97: 435–439.
PubMed Link
Cacace, F., P. Paci, V. Cusimano, A. Germani and L. Farina. 2012. Stochastic modeling of expression kinetics identifies messenger half-lives and reveals sequential waves of co-ordinated transcription and decay. PLoS Comput. Biol. 8: e1002772.
PubMed Link
Caiazzo, M. and 16 others. 2011. Direct generation of functional dopaminergic neurons from mouse and human fibroblasts. Nature 476: 224–227.
PubMed Link
Cao, Y. and 7 others. 2006. Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters. EMBO J. 25: 502–511.
PubMed Link
Capuano, F., M. Mülleder, R. Kok, H. J. Blom and M. Ralser. 2014. Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. Anal. Chem. 86: 3697–3702.
PubMed Link
Cavelti-Weder, C., W. Li, G. C. Weir and Q. Zhou. 2014. Direct lineage conversion of pancreatic exocrine to endocrine beta cells in vivo with defined factors. Methods Mol. Biol. 1150: 247–262.
PubMed Link
Chan, S. S. and M. Kyba. 2013. What is a master regulator? J. Stem Cell Res. Ther. 3: 114.
PubMed Link
Charlet-B, N., P. Logan, G. Singh and T. A. Cooper. 2002. Dynamic antagonism between ETR-3 and PTB regulates cell type-specific alternative splicing. Mol. Cell 9: 649–658.
PubMed Link
Chen, H., Y. Tian, W. Shu, X. Bo, and S. Wang. 2012. Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome. PLoS One 7: e41374.
PubMed Link
Chong, J. A. and 9 others. 1995. REST: A mammalian silencer protein that restricts sodium channel gene expression to neurons. Cell 80: 949–957.
PubMed Link
Chow, R. L., C. R. Altmann, R. A. Lang and A. A. Hemmati-Brivanlou. 1999. Pax6 induces ectopic eyes in a vertebrate. Development 126: 4213–4222.
PubMed Link
Ciccone, D. N. and 8 others. 2009. KDM1B is a histone H3K4 demethylatase required to establish maternal genomic imprints. Nature 461: 415–418.
PubMed Link
Cirillo, C. P., F. R. Lin, I. Cuesta, D. Friedman, M. Jarnik and K. S. Zaret. 2002. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell. 9: 279–289.
PubMed Link
Clop, A. and 16 others. 2006. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nature Genet. 38: 813–818.
PubMed Link
Core, L. J. and J. T. Lis. 2008. Transcriptional regulation through promoter-proximal pausing of RNA polymerase II. Science 319: 1791–1792.
PubMed Link
Cosgrove, M. S., J. D. Boeke and C. Wolberger. 2004. Regulated nucleosome mobility and the histone code. Nature Struct. Mol. Biol. 11: 1037–1043.
PubMed Link
Costa, P. R., M. L. Acencio and N. Lemke. 2013. Cooperative RNA polymerase molecules behavior on a stochastic sequence-dependent model for transcription elongation. PLoS One. 8: e57328
PubMed Link
Cvekl, A. and J. Piatigorsky. 1996. Lens development and crystallin gene expression: Many roles for Pax-6. BioEssays 18: 621–630.
PubMed Link
Daneholt, B. 1975. Transcription in polytene chromosomes. Cell 4: 1–9.
PubMed Link
Davey, C. A., D. F. Sargent, K. Luger, A. W. Maeder and T. J. Richmond. 2002. Solvent-mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319: 1097–1113.
PubMed Link
Davidson, E. H. 2006. The Regulatory Genome. Academic Press, New York.
Davidson, E. H. and M. S. Levine. 2008. Properties of developmental gene regulatory networks. Proc. Natl. Acad. Sci. USA 105: 20063–20066.
PubMed Link
Deaton, A. M. and A. Bird. 2011. CpG islands and the regulation of transcription.Genes Dev. 25: 1010–1022.
PubMed Link
Decker, C. J. and R. Parker. 1995. Mechanisms of mRNA degradation in eukaryotes. Trends Biochem. 19: 336–340.
PubMed Link
Dekens, M. P., F. J. Pelegri, H. M. Maischein and C. Nüsslein-Volhard. 2003. The maternal-effect gene futile cycle is essential for pronuclear congression and mitotic spindle assembly in the zebrafish zygote. Development 130: 3907–3916.
PubMed Link
Deng, W. and 7 others. 2012. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 149:1233–1244.
PubMed Link
Deschênes-Furry, J., K. Mousavi, F. Bolognani, R. L. Neve, R. J. Parks, N. I. Perrone-Bizzozero and B. J. Jasmin. 2007. The RNA-binding protein HuD binds acetylcholinesterase mRNA in neurons and regulates its expression after axotomy. J. Neurosci. 27: 665–675.
PubMed Link
Deschênes-Furry, J., N. Perrone-Bizzozero and B. J. Jasmin. 2006. The RNA-binding protein HuD: A regulator of neuronal differentiation, maintenance and plasticity. Bioessays 28: 822–833.
PubMed Link
Djuranovic, S. and 6 others. 2010. Allosteric regulation of Argonaute proteins by miRNAs. Nature Struct. Mol. Biol. 17:144–150.
PubMed Link
Djuranovic, S., A. Nahvi and R. Green. 2011. A parsimonious model for gene regulation by miRNAs. Science 331: 550–553.
PubMed Link
Down, T. A. and T. J. P. Hubbard. 2002. Computational detection and location of trhanscription start sites in mammalian genomic DNA. Genome Res. 12: 458–461.
PubMed Link
Edgar, B. A., F. Sprenger, R. J. Duronio, P. Leopold and P. H. O’Farrell. 1994. Distinct molecular mechanism regulates cell cycle timing at successive stages ofDrosophila embryogenesis. Genes Dev. 8: 440–452.
PubMed Link
Ferguson-Smith, A. C. 2011. Genomic imprinting: the emergence of the epigenetic paradigm. Nature Rev. Genet. 12: 565–574.
PubMed Link
Ferguson-Smith, A. C., H. Sasaki, B. M. Cattanach and M. A. Surani. 1993. Parental-origin-specific epigenetic modification of the mouse H19 gene. Nature362: 751–755.
PubMed Link
Ferguson-Smith, A., S-P. Lin, C-E. Tsai, N. Youngson and M. Tevendale. 2003. Genomic imprinting: Insights from studies in mice. Seminars Cell Dev. Biol. 14: 43–49.
PubMed Link
Ferré-D’Amaré, A. R., G. C. Predergast, E. B. Ziff and S. K. Burley. 1993. Recognition by Max of its cognate DNA through a dimeric bHLH/Z domain.Nature 363: 38–45.
PubMed Link
Filipowicz, W., S. N. Bhattacharyya and N. Sonenberg. 2008. Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight? Nature Rev. Genet. 9: 102–114.
PubMed Link
Fire, A., S. Q. Xu, M. K. Montgomery, S. A. Kostas, S. E. Driver and C. C. Mello. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 39: 806–811.
PubMed Link
Francis, O. L., J. L. Payne, R. J. Su and K. J. Payne. 2011. Regulator of myeloid differentiation and function: The secret life of Ikaros. World J. Biol. Chem. 2: 119–125.
PubMed Link
Friedman, R. C., K. K. Farh, C. B. Burge and D. P. Bartel. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19: 92–105.
PubMed Link
Fuks, F. 2005. DNA methylation and histone modifications: Teaming up to silence genes. Curr. Opin. Genet. Dev. 15: 490–495.
PubMed Link
Gedamu, L. and G. H. Dixon. 1978. Effect of enzymatic decapping on protamine messenger RNA translation in wheat-germ S-30. Biochem. Biophys. Res. Comm.85: 114–125.
PubMed Link
Giraldez, A. J. and 7 others. 2006. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312: 75–79.
PubMed Link
Goldman, D. and K. Domschke. 2014. Making sense of deep sequencing. Int. J. Neuropsychopharmacol. 17: 1717–1725.
PubMed Link
Grossniklaus, U. and R. Paro. 2007. Transcriptional silencing by Polycomb Group proteins. In C. D. Allis, T. Jenuwein, D. Reinberg and M.-L. Caparros (eds.), Epigenetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 211–230.
Groudine, M. and H. Weintraub. 1981. Activation of globin genes during chick development. Cell 24: 393–401.
PubMed Link
Gu, T. P. and 14 others. 2011. Role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477: 606–610.
PubMed Link
Guo, H., N. T. Ingolia, J. S. Weissman and D. P. Bartel. 2010. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835–840.
PubMed Link
Guo, S., and K. J. Kemphues. 1995. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell 81: 611– 620.
PubMed Link
Gurdon, J. B. 1962. The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpoles. J. Embryol. Exp. Morphol. 10: 622–640.
PubMed Link
Gurdon, J. B. 2016. Cell fate determination by transcription factors. Curr. Top. Dev. Biol. 116: 445–454.
PubMed Link
Guyette, W. A., R. J. Matusik and J. M. Rosen. 1979. Prolactin-mediated transcriptional and post-transcriptional control of casein gene expression. Cell17: 1013–1023.
PubMed Link
Halder, G., P. Callaerts and W. J. Gehring. 1995. Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. Science 267: 1788–1792.
PubMed Link
Hammes, A. and 7 others. 2001. Two splice variants of the Wilms’ tumor 1 gene have distinct functions during sex determination and nephron formation. Cell106: 319–329.
PubMed Link
Hastie, N. D. 2001. Life, sex, and WT1 isoforms: Three amino acids can make all the difference. Cell 106: 391–394.
PubMed Link
Hayashi, S., M. Yano, M. Igarashi, H. J. Okano and H. Okano. 2015. Alternative role of HuD splicing variants in neuronal differentiation. J. Neurosci. Res. 93: 399–409.
PubMed Link
He, L. and G. J. Hannon. 2004. MicroRNAs: Small RNAs with a big role in gene regulation. Nature Rev. Genet. 5: 522–531.
PubMed Link
Hinman, V. F. and A. M. Cheatle Jarvela. 2014. Developmental gene regulatory network evolution: Insights from comparative studies in echinoderms. Genesis 52: 193–207. doi: 10.1002/dvg.22757.
PubMed Link
Heller, H. and E. Bengal. 1998. TFIID (TBP) stabilizes the binding of MyoD to its DNA site at the promoter and MyoD facilitates the association of TFIIB with the preinitiation complex. Nucl. Acids Res. 26: 2112–2119.
PubMed Link
Giraldez, A. J. 2010. microRNAs, the cell’s Nepenthe: clearing the past during the maternal-to-zygotic transition and cellular reprogramming. Curr. Opin. Genet. Dev. 20: 369–375.
PubMed Link
Hodgman, R., J. Tay, R. Mendez and J. D. Richter. 2001. CPEB phosphorylation and cytoplasmic polyadenylation are catalyzed by the kinase IAK1/Eg2 in maturing mouse oocytes. Development 128: 2815–2822.
PubMed Link
Hotchkiss, R. D. 1948. The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J. Biol. Chem. 175: 315–332.
PubMed Link
Hu, C. W., J. L. Chen, Y. W. Hsu, C. C. Yen and M. R. Chao. 2015. Trace analysis of methylated and hydroxymethylated cytosines in DNA by isotope-dilution LC-MS/MS: First evidence of DNA methylation in Caenorhabditis elegans. Biochem. J. 465: 39–47.
PubMed Link
Humpherys, D. and 7 others. 2001. Epigenetic instability in ES cells and cloned mice. Science 293: 95–97.
PubMed Link
Hussain, M. A. and J.-F. Habener. 1999. Glucagon gene transcription activation mediated by synergistic interactions of Pax6 and Cdx2 with the p300 co-activator. J. Biol. Chem. 274: 28950–28957.
PubMed Link
Jaenisch, R. and I. Wilmut. 2001. Don’t clone humans! Science 291: 2552.
PubMed Link
Jansen, R., J. D. Embden, W. Gaastra and L. M. Schouls. 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43: 1565–1575.
PubMed Link
Jinek, M., K. Chylinski, I. Fonfara, M. Hauer, J. A. Doudnaand E. Charpentier. 2012. A pogrammable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816–821.
PubMed Link
Johnson, D. S., A. Mortazavi, R. M. Myers and B. Wold. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497–1502.
PubMed Link
Jothi, R., S. Cuddapah, A. Barski, K. Cui and K. Zhao. 2008. Genome-wide identification of the in vivo protein-DNA binding sites from ChIP-Seq data. Nucl. Acids. Res. 36: 5221–5231.
PubMed Link
Junion, G. and 6 others. 2012. A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell 148: 473–486.
PubMed Link
Kallunki, P., G. M. Edelman and F. S. Jones. 1997. Tissue-specific expression of the L1 cell adhesion molecule is modulated by the neural restrictive silencer element. J. Cell Biol. 138: 1343–1355.
PubMed Link
Kallunki, P., S. Jenkinson, G. M. Edelman and F. S. Jones. 1995. Silencer elements modulate the expression of the gene for neuron-glia cell adhesion molecule, Ng-CAM. J. Biol. Chem. 270: 21291–21298.
PubMed Link
Kamachi, Y., M. Uchikawa, J. Collignon, R. Lovell-Badge and H. Kondoh. 1998. Involvement of Sox1, 2, and 3 in the early and subsequent molecular events of lens induction. Development 125: 2521–2532.
PubMed Link
Kammandel, B., K. Chowdhury, A. Stoykova, S. Aparicio, S. Brenner and P. Gruss. 1998. Distinct cis-essential modules direct the time-space pattern ofPax6 gene activity. Dev. Biol. 205: 79–97.
PubMed Link
Kastern, W. H., M. Swindlehurst, C. Aaron, J. Hooper and S. J. Berry. 1982. Control of mRNA translation in oocytes and developing embryos of giant moths. I. Functions of the 5′ terminal “cap” in the tobacco hornworm Manduca sexta.Dev. Biol. 89: 437–449.
PubMed Link
Ke, S. and L. A. Chasin. 2011. Context-dependent splicing regulation: Exon definition, co-occuring motif pairs, and tissue specificity. RNA Biol. 8: 384–388.
PubMed Link
Kim, S., N. K. Yu and B. K. Kaang. 2015. CTCF as a multifunctional protein in genome regulation and gene expression. Exp. Mol. Med. 47: e166.
PubMed Link
Kolata, G. 2001. Researchers find big risk of defect in cloning animals. New York Times, 25 March.
Kondrashov, N. and 8 others. 2011. Ribosome-mediated specificity in Hox mRNA translation and vertebrate tissue patterning. Cell 145(3): 383–397.
PubMed Link
Kornberg, R. D. and J. D. Thomas. 1974. Chromatin structure: Oligomers of histones. Science 184: 865–868.
PubMed Link
Kostrewa, D., M. E. Zeller, K. J. Armache, M. Seizl, K. Leike, M. Thomm and P. Cramer. 2009. RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462: 323–330.
PubMed Link
Kouzarides, T. and S. L. Berger. 2007. Chromatin modifications and their mechanisms of action. In C. D. Allis, T. Jenuwein and D. Reinberg (eds.),Epigenetics. Cold Spring Harbor Press, New York, pp. 191–209.
Kwan, K.-M. 2002. Conditional alleles in mice: practical considerations for tissue-specific knockouts. Genesis 32: 48–62.
PubMed Link
Lécuyer, E. and 8 others. 2007. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131: 174–187.
PubMed Link
Lagos-Quintana, M., R. Rauhut, J. Meyer, A. Borkhardt and T. Tuschl. 2003. New microRNAs from mouse and human. RNA 9: 175–179.
PubMed Link
Lan, F. and 12 others. 2007. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449: 689–694.
PubMed Link
Ledford, H. 2008. Human genes are multitaskers. Nature 456: 9
PubMed Link
Lee, R. C., R. L. Feinbaum and V. Ambros. 1993. The C. elegansheterochromatic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–855.
PubMed Link
Lettice, L. A., A. E. Hill, P. S. Devenney and R. E. Hill. 2008. Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly. Human Mol. Genet. 2008 17: 97–985.
PubMed Link
Li, B., M. Carey and J. L. Workman. 2007. The role of chromatin during transcription. Cell 128: 707–719.
PubMed Link
Licatalosi, D. D. and 6 others. 2012. Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. Genes Dev. 26: 1626–1642.
PubMed Link
Liu, E. T., S. Pott and M. Huss. 2010. Q&A: ChIP-seq technologies and the study of gene regulation. BMC Biol. 8: 56.
PubMed Link
Luger, K., A. W. Mäder, R. K. Richmond, D. F. Sargent and T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution.Nature 389: 251–260.
PubMed Link
Luo, M. L., Z. Zhou, K. Magni, C. Christoforides, J. Rappsilber, M. Mann and R. Reed. 2001. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly. Nature 413: 644–647.
PubMed Link
Lupien, M. and 8 others. 2008. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132: 958–970.
PubMed Link
Malik, S. and Roeder, R. G. 2010. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nature Rev. Genet. 11: 761–772.
PubMed Link
Malone, J. H. and B. Oliver. 2011. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol. 9: 34.
PubMed Link
Maniatis, T., S. Goodbourn and J. A. Fischer. 1987. Regulation of inducible and tissue-specific gene expression. Science 236: 1237–1245.
PubMed Link
Margueron, R. and 12 others. 2009. Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461: 762–767.
PubMed Link
Mavilio, F. and 9 others. 1983. Molecular mechanisms for human hemoglobin switching: Selective undermethylation and expression of globin genes in embryonic, fetal, and adult erythroblasts. Proc. Natl. Acad. Sci. USA 80: 6907–6911.
PubMed Link
McAlinden A., N. Havlioglu and L. J. Sandell. 2004. Regulation of protein diversity by alternative pre-mRNA splicing with specific focus on chondrogenesis. Birth Def. Res. C 72: 51–68.
PubMed Link
McKinnell, I. W. and 7 others. 2008. Pax7 activates myogenic genes by recruitment of a histone methyltransferase complex. Nature Cell Biol. 10: 77–84.
PubMed Link
McPherron, A. C., A. M. Lawler and S. J. Lee. 1997. Regulation of skeletal muscle mass in mice by a new TGF-beta superfamily member. Nature 387: 83–90.
PubMed Link
Melton, D. A. 2016. Applied developmental biology: Making human pancreatic beta cells for diabetics. Curr. Top. Dev. Biol. 117: 65–73.
PubMed Link
Mendez, R. and J. D. Richter. 2001. Translational control by CPEB: A means to the end. Nature Rev. Mol. Cell Biol. 2: 521–529.
PubMed Link
Mendez, R., K. G. Murthy, K. Ryan, J. L. Manley and J. D. Richter. 2000. Phosphorylation of CPEB by Eg2 mediates the recruitment of CPSF into an active cytoplasmic polyadenylation complex. Mol. Cell 6: 1253–1259.
PubMed Link
Merkin, J., C. Russell, P. Chen and C. B. Burge. 2012. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 338: 1593–1599.
PubMed Link
Millard, S. S. and S. L. Zipursky. 2008. Dscam-mediated repulsion controls tiling and self-avoidance. Curr. Opin. Neurobiol. 18: 84–89.
PubMed Link
Miura, S. K., A. Martins, K. X. Zhang, B. R. Graveley and S. L. Zipursky. 2013. Probabilistic splicing of Dscam1 establishes identity at the level of single neurons. Cell 155: 1166–1177.
PubMed Link
Murugan, R. and Kreiman G. 2012. Theory on the coupled stochastic dynamics of transcription and splice-site recognition. PLoS Comput. Biol. 8: e1002747.
PubMed Link
Muse, G. W. and 7 others. 2007. RNA polymerase is poised for activation across the genome. Nature Genet. 39: 1507–1511.
PubMed Link
Muta, M., Y. Kamachi, A. Yoshimoto, Y. Higashi and H. Kondoh. 2002. Distinct roles of Sox2, Pax6, and Maf transcription factors in the regulation of lens-specific d1 crystallin enhancer. Genes Cells 7: 791–805.
PubMed Link
Nelson, C. E. and 14 others. 2016. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science 351: 403–407.
PubMed Link
Neuert, G., B. Munsky, R. Z. Tan, L. Teytelman, M. Khammash, A. van Oudenaarden. 2013. Systematic identification of signal-activated stochastic gene regulation. Science 339: 584–587.
PubMed Link
Nilsen, T. W. and B. R. Graveley. 2010. Expansion of the eukaryotic proteome by alternative splicing. Nature 463: 457–463.
PubMed Link
Noordermeer, D. and 9 others. 2011. Variegated gene expression caused by cell-specific long-range DNA interactions. Nature Cell Biol. 13: 944–951.
PubMed Link
Noordermeer, D. and D. Duboule. 2013. Chromatin looping and organization at developmentally regulated gene loci. WIRES Dev. Biol. doi: 10.1002/wdev.103
Link
Norma, K, C. D. Allis and S. I. Grewal. 2001. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293: 1150–1155.
PubMed Link
Nüsslein-Volhard, C. and E. Wieschaus. 1980. Mutations affecting segment number and polarity in Drosophila. Nature 287: 795–801.
PubMed Link
Ogryzko, V. V., R. L. Schlitz, V. Russanova, B. H. Howard and Y. Nakatani. 1996. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87: 953–959.
PubMed Link
Ohlsson, R. 2010. The coherent Mediator. Nature 467: 406–407.
PubMed Link
Okano, H. J. and R. B. Darnell. 1997. A hierarchy of Hu RNA binding proteins in developing and adult neurons. J. Neurosci. 17: 3024–3037.
PubMed Link
Oliveri, P., Q. Tu and E. H. Davidson. 2008. Global regulatory logic for specification of an embryonic cell lineage. Proc. Nat. Acad. Sci. USA 105(16): 5955–5962.
PubMed Link
Ong, T.-C. and V. G. Corces. 2011. Enhancer function: New insights into the regulation of tissue-specific gene expression. Nature Rev. Genet. 12: 283–293.
PubMed Link
Palacios, I. M. 2007. How does an mRNA find its way? Intracellular localisation of transcripts. Semin. Cell Dev. Biol. 163–170.
PubMed Link
Parviz, F., J. Li, K. H. Kaestner and S. A. Duncan. 2002. Generation of a conditionally null allele of hnf4alpha. Genesis 32: 130–133.
PubMed Link
Perrone-Bizzozero, N. and C. W. Bird. 2013. Role of HuD in nervous system function and pathology. Front. Biosci. (Schol. Ed.) 5: 554–563.
PubMed Link
Peter, I. S. and E. H. Davidson. 2011. A gene regulatory network controlling the embryonic specification of endoderm. Nature 474: 635–639.
PubMed Link
Pfisterer, U. and 9 others. 2011. Direct conversion of human fibroblasts to dopaminergic neurons. Proc. Natl. Acad. Sci. USA 108: 10343–10348.
PubMed Link
Plaza, S., C. Dozier and S. Saule. 1993. Quail PAX6 (PAX-QNR) encodes a transcription factor able to bind and transactivate its own promoter. Cell Growth Diff. 4: 1041–1050.
PubMed Link
Pogenberg, V. and 8 others. 2012. Restricted leucine zipper dimerization and specificity of DNA recognition of the melanocyte master regulator MITF. Genes Dev. 26: 2647–2658.
PubMed Link
Pohodich, A. E. and H. Y. Zoghbi. 2015. Rett syndrome: Disruption of epigenetic control of postnatal neurological functions. Hum. Mol. Genet. 24: R10–16.
PubMed Link
Price, E. R. and 7 others. 1998. Lineage-specific signaling in melanocytes: c-Kit stimulation recruits p300/CBP to microphthalmia. J. Biol. Chem. 273: 33042–33047.
PubMed Link
Qiang, L. and 11 others. 2011. Directed conversion of Alzheimer’s disease patient skin fibroblasts into functional neurons. Cell 146: 359–371.
PubMed Link
Rabani, M. and 11 others. 2014. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell 159: 1698–1710.
PubMed Link
Raff, R. A., H. V. Colot, S. E. Selvig and P. R. Gross. 1972. Oogenetic origin of messenger RNA for embryonic synthesis of microtubule proteins. Nature 235: 211–214.
PubMed Link
Rosenthal, E., T. Hunt and J. V. Ruderman. 1980. Selective translation of mRNA controls the pattern of protein synthesis during early development of the surf clam, Spisula solidissima. Cell 20: 487–495.
PubMed Link
Rupp, R. A. and P. B. Becker. 2005. Gene regulation by histone H1: New links to DNA methylation. Cell 123: 1178–1179.
PubMed Link
Ryan, K. J. and T. A. Cooper. 1996. Muscle-specific splicing enhancers regulate inclusion of the cardiac troponin T alternative exon in embryonic skeletal muscle. Mol. Cell Biol. 16: 4014–4023.
PubMed Link
Saito, Y. and 8 others. 2000. The developmental and aging changes of Down’s syndrome cell adhesion molecule expression in normal and Down’s syndrome brains. Acta Neuropathol. 100: 654–664.
PubMed Link
Sander, M., A. Neubüser, H. Ee, G. R. Martin and M. S. German. 1997. Genetic analysis reveals that Pax6 is required for normal transcription of pancreatic hormone genes and islet development. Genes Dev. 11: 1662–1673.
PubMed Link
Sankaran, V. G. and 11 others. 2011. A functional element necessary for fetal hemoglobin silencing. N. Engl. J. Med. 365: 807–814.
PubMed Link
Satija, R., J. A. Farrell, D. Gennert, A. F. Schier and A. Regev. 2015. Spatial reconstruction of single-cell gene expression data. Nature Biotechnol. 33: 495–502.
PubMed Link
Sauer, F., J. D. Fondell, Y. Ohkuma, R. G. Roeder and H. Jäckle. 1995. Control of transcription by Krüppel through interactions with TFIIB and TFIIE. Nature 375: 162–165.
PubMed Link
Schlissel, M. S. and D. D. Brown. 1984. The transcriptional regulation of Xenopus 5S RNA genes in chromatin: The roles of active stable transcription complex and histone H1. Cell 37: 903–913.
PubMed Link
Schmucker, D. 2007. Molecular diversity of Dscam: Recognition of molecular identity in neuronal wiring. Nature Rev. Neurosci. 8: 915–920.
PubMed Link
Schmucker, D. and 7 others. 2000. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101: 671–684.
PubMed Link
Schoenherr, C. J. and D. J. Anderson. 1995. The neuron-restrictive silencer factor (NRSF): A coordinate repressor of multiple neuron-specific genes. Science267: 1360–1363.
PubMed Link
Schones, D. E. and K. Zhao. 2008. Genome-wide approaches to studying chromatin modifications. Nature Rev. Genet. 9: 179–191.
PubMed Link
Schuelke, M. and 8 others. 2004. Myostatin mutation associated with gross muscle hypertrophy in a child. N. Engl. J. Med. 350: 2682–2688.
PubMed Link
Sekiya, S. and A. Suzuki. 2011. Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors. Nature 475: 390–393.
PubMed Link
Sen, G. L. and H. M. Blau. 2006. A brief history of RNAi: The silence of the genes. FASEB J. 20: 1293–1299.
PubMed Link
Shatkin, A. J. 1976. Capping of eucaryotic mRNAs. Cell 9: 645–653.
PubMed Link
Shaw, G. and R. Kamen. 1986. A conserved AU sequence from the 3′ untranslated region of GM-CSF mRNA mediates selective mRNA degradation.Cell 46: 659–667.
PubMed Link
Sheiness, D. and J. E. Darnell. 1973. Polyadenylic segment in mRNA becomes shorter with age. Nature New Biol. 241: 265–268.
PubMed Link
Signer, E. N. and 6 others. 1998. DNA fingerprinting Dolly. Nature 394: 329–330.
PubMed Link
Sironi, M., U. Pozzoli, R. Cagliani, G. P. Comi, A. Bardoni and N. Bresolin. 2001. Analysis of splicing parameters in the dystrophin gene: Relevance for physiological and pathogenetic splicing mechanisms. Hum. Genet. 109: 73–84.
PubMed Link
Smale, S. T. 2010. Pioneer factors in embryonic stem cells and differentiation. Curr. Top. Genet. Dev. 20: 519–526.
PubMed Link
So, P. L. and P. S. Danielian. 1999. Cloning and expression analysis of a mouse gene related to Drosophila odd-skipped. Mech. Dev. 84: 157–160.
PubMed Link
Son, E.Y. and 6 others. 2011. Conversion of mouse and human fibroblasts into functional spinal motor neurons. Cell Stem Cell 9: 205–218.
PubMed Link
Standart, N., T. Hunt and J. V. Ruderman. 1986. Differential accumulation of ribonucleotide reductase subunits in clam oocytes: The large subunit is stored as a polypeptide, the small subunit as untranslated mRNA. J. Cell Biol. 103: 2129–2136.
PubMed Link
Stebbins-Boaz, B., Q. Cao, C. H. de Moor, R. Mendez and J. D. Richter. 1999. Maskin is a CPEB-associated factor that transiently interacts with elF-4E. Mol. Cell 4: 1017–1027.
PubMed Link
Steingrímsson, E. and 10 others. 1994. Molecular basis of mouse microphthalmia (mi) mutations helps explain their developmental and phenotypic consequences. Nature Genet. 8: 256–263.
PubMed Link
Strahl, B. D. and C. D. Allis. 2000. The language of covalent histone modifications. Nature 403: 41–45.
PubMed Link
Strasser, K. and E. Hurt. 2001. Splicing factor Sub2p is required for nuclear mRNA export through its interaction withYra1p. Nature 413: 648–652.
PubMed Link
Szalkowski, A. M. and C. D. Schmid. 2011. Rapid innovation in ChiP-Seq peak-calling algorithms is outdistancing benchmarking efforts. Brief Bioinform. 12: 626–633.
PubMed Link
Takahashi K. and S. Yamanaka. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663–676.
PubMed Link
Takechi, M., T. Hamaoka and S. Kawamura. 2003. Fluorescence visualization of ultraviolet-sensitive cone photoreceptor development in living zebrafish. FEBS Letters 553: 90–94.
PubMed Link
Tan, C. C. and 10 others. 2008. Transcription factor Ap2d associates with Ash2l and ALR, a trithorax family histone methyltransferase, to activate Hoxc8 transcription. Proc. Natl. Acad. Sci. USA 105: 7472–7477.
PubMed Link
Terzian, T. and N. Box. 2013. Genetics of ribosomal proteins: "Curiouser and curiouser." PLoS Genet. 9: e1003300.
PubMed Link
Thoma, F., T. Koller and A. Klug. 1979. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J. Cell Biol. 83: 403–427.
PubMed Link
Tsujimura, K. and 13 others. 2015. miR-199a links MeCP2 with mTOR signaling and its dysregulation leads to Rett Syndrome phenotypes. Cell Rep. 12: 1887–1901.
PubMed Link
van der Ploeg, L. H. T. and R. D. Flavell. 1980. DNA methylation in the human g-d-b-globin locus in erythroid and non-erythroid cells. Cell 19: 947–958.
Visel, A., E. M. Rubin and L. A. Pennacchio. 2009. Genomic views of distant-acting enhancers. Nature 461: 199–205.
PubMed Link
Wagenaar, E. B. and D. Mazia. 1978. The effect of emetine on the first cleavage division of the sea urchin, Strongylocentrotus purpuratus. In E. R. Dirksen, D. M. Prescott and L. F. Fox (eds.), Cell Reproduction: In Honor of Daniel Mazia. Academic Press, New York, pp. 539–545.
Walter, J. and M. Paulsen. 2003. Imprinting and disease. Seminars Cell Dev. Biol. 14: 101–110.
PubMed Link
Wang, E. T. and 8 others. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470–476.
PubMed Link
Watkins-Chow, D. E. and 21 others. 2013. Mutation of the diamond-blackfan anemia gene rps7 in mouse results in morphological and neuroanatomical phenotypes. PLoS Genet. 9: e1003094
PubMed Link
Watt, F. and P. L. Molloy. 1988. Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter. Genes Dev. 2: 1136–1143.
PubMed Link
Weaver, I. C., and 6 others. 2005. Reversal of maternal programming of stress responses in adult offspring through methyl supplementation: Altering epigenetic marking later in life. J. Neurosci. 25: 11045–11054.
PubMed Link
Weintraub, H. 1984. Histone-H1-dependent chromatin superstructures and the suppression of gene activity. Cell 38: 17–27.
PubMed Link
Weintraub, H. 1985. Assembly and propagation of repressed and depressed chromosomal states. Cell 42: 705–711.
PubMed Link
Weiszmann, R., A. S. Hammonds and S. E. Celniker. 2009. Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos. Nature Protoc. 4: 605–618.
PubMed Link
Wendt, K. and 17 others. 2008. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451: 796–801.
PubMed Link
Wickens, M. and K. Takayama. 1995. Deviants—or emissaries? Nature 367: 17–18.
PubMed Link
Wightman, B., I. Ha and G. Ruvkun. 1993. Posttranslational regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855–862.
PubMed Link
Williams, S. C., C. R. Altmann, R. L. Chow, A. Hemmati-Brivanlou and R. A. Lang. 1998. A highly conserved lens transcriptional control element from thePax-6 gene. Mech. Dev. 73: 225–229.
PubMed Link
Wilmut, I., A. E. Schnieke, J. McWhir, A. J. Kind and K. H. S. Campbell. 1997. Viable offspring from fetal and adult mammalian cells. Nature 385: 810–814.
PubMed Link
Wilmut, I., K. Campbell and C. Tudge. 2000. The Second Creation: Dolly and the Age of Biological Control. Harvard University Press, Cambridge, MA.
Wilson, E. B. 1896. The Cell in Development and Inheritance. Macmillan.
Wilson, R. C. and J. A. Doudna. 2013. Molecular mechanisms of RNA interference. Annu. Rev. Biophys. 42: 217–239.
PubMed Link
Wilson, T. and R. Treisman. 1988. Removal of poly(A) and consequent degradation of c-fos mRNA facilitated by 3′ AU-rich sequences. Nature 336: 396–399.
PubMed Link
Wolf, L. V. and 7 others. 2009. Identification of Pax6-dependent gene regulatory networks in the mouse lens. PLoS One: e4159
PubMed Link
Wood, A. J., Severson, A, F., and Meyer, B. J. 2010. Condensin and cohesin complexity: The expanding repertoire of functions. Nature Rev. Genet. 11: 291–404.
PubMed Link
Woods, G. L. and 7 others. 2003. A mule cloned from fetal cells by nuclear transfer. Science 301: 1063.
PubMed Link
Wu, W., G. Ahlsen, D. Baker, L. Shapiro, and L. Zipursky. 2012. Complementary chimeric isoforms reveal Dscam1 binding specificity in vivo.Neuron 74: 261–268.
PubMed Link
Yamakawa, K., Y. K. Huot , M. A. Haendelt, R. Hubert, X.-N. Chen, G. E. Lyons and J. R. Korenberg. 1998. DSCAM: A novel member of the immunoglobulin superfamily maps in a Down syndrome region and is involved in the development of the nervous system. Hum. Mol. Genet. 7: 227–237.
PubMed Link
Yang, Y. and 13 others. 2006. Regulation of aA-crystallin via Pax6, c-Maf, CREB and a broad domain of lens-specific chromatin. EMBO J. 25: 2107–2118.
PubMed Link
Yasumoto, K.-I., K. Yokoyama, K. Takahashi, Y. Tomita and S. Shibihara. 1997. Functional analysis of microphthalmia-associated transcription factor in pigment cell-specific transcription of human tyrosinase family genes. J. Biol. Chem. 272: 503–509.
PubMed Link
Yusufzai, T. M., H. Tagami, Y. Nakatani and G. Felsenfeld. 2004. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol. Cell 13: 291–298.
PubMed Link
Zaret, K. S., A. Watts, J. Xu, E. Wandzioch, S. T. Smale and T. Sekiya. 2008. Pioneer factors, genetic competence, and inductive signaling: Programming liver and pancreas progenitors from the endoderm. Cold Spring Harb. Symp. Quant. Biol. 73: 119–126
PubMed Link
Zeitlinger, J. and A. Stark. 2010. Developmental gene regulation in the era of genomics. Dev. Biol. 339: 230–239.
PubMed Link
Zhang, X. and 7 others. 2006. Pax6 is regulated by Meis and Pbx homeoproteins during pancreatic development. Dev. Biol. 300: 748–757.
PubMed Link
Zhang, X., S. Heaney and R. L. Maas. 2002. Cre-LoxP fate-mapping of Pax6enhancer active retinal and pancreatic progenitors. genesis 35: 22–30.
PubMed Link
Zhou, Q., J. Brown, A. Kanarek, J. Rajagopal and D. A. Melton. 2008. In vivo reprogramming of adult pancreatic exocrine cells to b cells. Nature 455: 627–632.
PubMed Link
Zhou, V. W., A. Goren and B. E. Bernstein. 2011. Charting histone modifications and the functional organization of mammalian genomes. Nature Rev. Genet. 12: 7–18.
PubMed Link
Zinzen, R. P., C. Girardot, J. Gagneur, M. Braun and E. E. Furlong. 2009. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature462: 65–70.
PubMed Link