LSD1 regulates the balance between self-renewal and differentiation in human embryonic stem cells (original) (raw)

• Azuara, V. et al. Chromatin signatures of pluripotent cell lines. Nat. Cell Biol. 8, 532–538 (2006).
  Article CAS PubMed Google Scholar
• Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).
  Article CAS PubMed Google Scholar
• Pan, G. et al. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1, 299–312 (2007).
  Article CAS PubMed Google Scholar
• Zhao, X. et al. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1, 286–298 (2007).
  Article CAS PubMed Google Scholar
• Boyer, L. A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349–353 (2006).
  Article CAS PubMed Google Scholar
• Lee, T. I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Stock, J. K. et al. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat. Cell Biol. 9, 1428–1435 (2007).
  Article CAS PubMed Google Scholar
• Agger, K. et al. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449, 731–734 (2007).
  Article CAS PubMed Google Scholar
• Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Pardo, M. et al. An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell 6, 382–395 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, J. et al. A protein interaction network for pluripotency of embryonic stem cells. Nature 444, 364–368 (2006).
  Article CAS PubMed Google Scholar
• Shi, Y. et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941–953 (2004).
  Article CAS PubMed Google Scholar
• Ballas, N. et al. Regulation of neuronal traits by a novel transcriptional complex. Neuron 31, 353–365 (2001).
  Article CAS PubMed Google Scholar
• Wang, Y. et al. LSD1 is a subunit of the NuRD complex and targets the metastasis programs in breast cancer. Cell 138, 660–672 (2009).
  Article CAS PubMed Google Scholar
• Metzger, E. et al. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 437, 436–439 (2005).
  Article CAS PubMed Google Scholar
• Wissmann, M. et al. Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat. Cell Biol. 9, 347–353 (2007).
  Article CAS PubMed Google Scholar
• Huang, J. et al. p53 is regulated by the lysine demethylase LSD1. Nature 449, 105–108 (2007).
  Article CAS PubMed Google Scholar
• Wang, J. et al. The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nat. Genet. 41, 125–129 (2009).
  Article CAS PubMed Google Scholar
• Kontaki, H. & Talianidis, I. Lysine methylation regulates E2F1-induced cell death. Mol. Cell. 39, 152–160 (2010).
  Article CAS PubMed Google Scholar
• Raya, A. et al. Generation of cardiomyocytes from new human embryonic stem cell lines derived from poor-quality blastocysts. Cold Spring Harb. Symp. Quant. Biol. 73, 127–135 (2008).
  Article CAS PubMed Google Scholar
• Lee, M. G., Wynder, C., Cooch, N. & Shiekhattar, R. An essential role forCoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 437, 432–435 (2005).
  Article CAS PubMed Google Scholar
• Ku, M. et al. Genome-wide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008).
  Article PubMed PubMed Central Google Scholar
• Bruce, A. W. et al. Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes. Proc. Natl Acad. Sci. USA 101, 10458–10463 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Niakan, K. K. et al. Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes Dev. 24, 312–326 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Seguin, C. A., Draper, J. S., Nagy, A. & Rossant, J. Establishment of endoderm progenitors by SOX transcription factor expression in human embryonic stem cells. Cell Stem Cell 3, 182–195 (2008).
  Article CAS PubMed Google Scholar
• Buckley, N. J., Johnson, R., Sun, Y. M. & Stanton, L. W. Is REST a regulator of pluripotency? Nature 457, E5-6; discussion E7 (2009).
• Jorgensen, H. F., Chen, Z. F., Merkenschlager, M. & Fisher, A. G. Is REST required for ESC pluripotency? Nature 457 E4-5; discussion E7 (2009).
• Yamada, Y., Aoki, H., Kunisada, T. & Hara, A. Rest promotes the early differentiation of mouse ESCs but is not required for their maintenance. Cell Stem Cell 6, 10–15 (2010).
  Article CAS PubMed Google Scholar
• Liang, J. et al. Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat. Cell Biol 10, 731–739 (2008).
  Article CAS PubMed Google Scholar
• van den Berg, D. L. et al. An Oct4-centred protein interaction network in embryonic stem cells. Cell Stem Cell 6, 369–381 (2010).
  CAS PubMed PubMed Central Google Scholar
• Tsai, M. C. et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, 689–693 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Foster, C. T. et al. Lysine-specific demethylase 1 regulates the embryonic transcriptome and CoREST stability. Mol. Cell. Biol. 30, 4851–4863 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Macfarlan, T. S. et al. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev. (2011).
• de la Cruz, C. C. et al. Developmental regulation of Suz 12 localization. Chromosoma 114, 183–192 (2005).
  Article PubMed Google Scholar
• Greco, S. J., Smirnov, S. V., Murthy, R. G. & Rameshwar, P. Synergy between the RE-1 silencer of transcription and NF_κ_B in the repression of the neurotransmitter gene TAC1 in human mesenchymal stem cells. J. Biol. Chem. 282, 30039–30050 (2007).
  Article CAS PubMed Google Scholar
• Wiznerowicz, M. & Trono, D. Conditional suppression of cellular genes: lentivirus vector-mediated drug-inducible RNA interference. J. Virol. 77, 8957–8961 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Pratt, T., Sharp, L., Nichols, J., Price, D. J. & Mason, J. O. Embryonic stem cells and transgenic mice ubiquitously expressing a tau-tagged green fluorescent protein. Dev. Biol. 228, 19–28 (2000).
  Article CAS PubMed Google Scholar
• Ritchie, M. E. et al. A comparison of background correction methods for two-colour microarrays. Bioinformatics 23, 2700–2707 (2007).
  Article CAS PubMed Google Scholar
• Smyth, G. K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genetics Mol. Biol. 3,1–26 Article3 (2004).
  Article Google Scholar
• Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 1, 289–300 (1995).
  Google Scholar
• Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
  Article PubMed PubMed Central Google Scholar
• Rosenbloom, K. R. et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 38, D620–D625 (2010).
  Article CAS PubMed Google Scholar
• Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocols 4, 44–57 (2009).
  Article PubMed Google Scholar