3,989
Views
10
CrossRef citations to date
0
Altmetric
Extra View

Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming

, , , &
Pages 1148-1155 | Received 06 Nov 2014, Accepted 07 Jan 2015, Published online: 18 Apr 2015

References

  • Inoue H, Nagata N, Kurokawa H, Yamanaka S. iPS cells: a game changer for future medicine. EMBO J 2014; 33:409-17; PMID:24500035; http://dx.doi.org/10.1002/embj.201387098.
  • Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, et al. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 2011; 144:439-52; PMID:21295703; http://dx.doi.org/10.1016/j.cell.2010.12.032.
  • Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J, et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009; 5:111-23; PMID:19570518; http://dx.doi.org/10.1016/j.stem.2009.06.008.
  • Ghosh Z, Wilson KD, Wu Y, Hu S, Quertermous T, Wu JC. Persistent donor cell gene expression among human induced pluripotent stem cells contributes to differences with human embryonic stem cells. PloS One 2010; 5:e8975; PMID:20126639; http://dx.doi.org/10.1371/journal.pone.0008975.
  • Marchetto MC, Yeo GW, Kainohana O, Marsala M, Gage FH, Muotri AR. Transcriptional signature and memory retention of human-induced pluripotent stem cells. PloS One 2009; 4:e7076; PMID:19763270; http://dx.doi.org/10.1371/journal.pone.0007076.
  • Guenther MG, Frampton GM, Soldner F, Hockemeyer D, Mitalipova M, Jaenisch R, Young RA. Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 2010; 7:249-57; PMID:20682450; http://dx.doi.org/10.1016/j.stem.2010.06.015.
  • Consortium EP, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489:57-74; PMID:22955616; http://dx.doi.org/10.1038/nature11247.
  • Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat Genet 2014; 46:558-66; PMID:24777452; http://dx.doi.org/10.1038/ng.2965.
  • Takahashi H, Lassmann T, Murata M, Carninci P. 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 2012; 7:542-61; PMID:22362160; http://dx.doi.org/10.1038/nprot.2012.005.
  • Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M, et al. CAGE: cap analysis of gene expression. Nat Methods 2006; 3:211-22; PMID:16489339; http://dx.doi.org/10.1038/nmeth0306-211.
  • Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A. A code for transcription initiation in mammalian genomes. Genome Res 2008; 18:1-12; PMID:18032727; http://dx.doi.org/10.1101/gr.6831208.
  • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26:139-40; PMID:19910308; http://dx.doi.org/10.1093/bioinformatics/btp616.
  • Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, Guenther MG, Johnston WK, Wernig M, Newman J, et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008; 134:521-33; PMID:18692474; http://dx.doi.org/10.1016/j.cell.2008.07.020.
  • Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010; 467:430-5; PMID:20720539; http://dx.doi.org/10.1038/nature09380.
  • Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 2013; 153:307-19; PMID:23582322; http://dx.doi.org/10.1016/j.cell.2013.03.035.
  • Loven J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, Bradner JE, Lee TI, Young RA. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 2013; 153:320-34; PMID:23582323; http://dx.doi.org/10.1016/j.cell.2013.03.036.
  • Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005; 15:1034-50; PMID:16024819; http://dx.doi.org/10.1101/gr.3715005.
  • Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, Chan YS, Ng HH, Bourque G. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 2010; 42:631-4; PMID:20526341; http://dx.doi.org/10.1038/ng.600.
  • Lu X, Sachs F, Ramsay L, Jacques PE, Goke J, Bourque G, Ng HH. The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol 2014; 21:423-5; PMID:24681886; http://dx.doi.org/10.1038/nsmb.2799.
  • Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 2013; 504:306-10; PMID:24213634; http://dx.doi.org/10.1038/nature12716.
  • Silva J, Nichols J, Theunissen TW, Guo G, van Oosten AL, Barrandon O, Wray J, Yamanaka S, Chambers I, Smith A. Nanog is the gateway to the pluripotent ground state. Cell 2009; 138:722-37; PMID:19703398; http://dx.doi.org/10.1016/j.cell.2009.07.039.
  • Hall J, Guo G, Wray J, Eyres I, Nichols J, Grotewold L, Morfopoulou S, Humphreys P, Mansfield W, Walker R, et al. Oct4 and LIF/Stat3 additively induce Kruppel factors to sustain embryonic stem cell self-renewal. Cell Stem Cell 2009; 5:597-609; PMID:19951688; http://dx.doi.org/10.1016/j.stem.2009.11.003.
  • Takashima Y, Guo G, Loos R, Nichols J, Ficz G, Krueger F, Oxley D, Santos F, Clarke J, Mansfield W, et al. Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human. Cell 2014; 158:1254-69; PMID:25215486; http://dx.doi.org/10.1016/j.cell.2014.08.029.
  • Li Q, Ramirez-Bergeron DL, Dunwoodie SL, Yang YC. Cited2 gene controls pluripotency and cardiomyocyte differentiation of murine embryonic stem cells through Oct4 gene. J Biol Chem 2012; 287:29088-100; PMID:22761414; http://dx.doi.org/10.1074/jbc.M112.378034.
  • Li Q, Hakimi P, Liu X, Yu WM, Ye F, Fujioka H, Raza S, Shankar E, Tang F, Dunwoodie SL, et al. Cited2, a transcriptional modulator protein, regulates metabolism in murine embryonic stem cells. J Biol Chem 2014; 289:251-63; PMID:24265312; http://dx.doi.org/10.1074/jbc.M113.497594.
  • Okita K, Ichisaka T, Yamanaka S. Generation of germline-competent induced pluripotent stem cells. Nature 2007; 448:313-7; PMID:17554338; http://dx.doi.org/10.1038/nature05934.
  • Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, Bernstein BE, Jaenisch R. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 2007; 448:318-24; PMID:17554336; http://dx.doi.org/10.1038/nature05944.
  • Boland MJ, Hazen JL, Nazor KL, Rodriguez AR, Gifford W, Martin G, Kupriyanov S, Baldwin KK. Adult mice generated from induced pluripotent stem cells. Nature 2009; 461:91-4; PMID:19672243; http://dx.doi.org/10.1038/nature08310.
  • Newman AM, Cooper JB. Lab-specific gene expression signatures in pluripotent stem cells. Cell Stem Cell 2010; 7:258-62; PMID:20682451; http://dx.doi.org/10.1016/j.stem.2010.06.016.
  • Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al. Landscape of transcription in human cells. Nature 2012; 489:101-8; PMID:22955620; http://dx.doi.org/10.1038/nature11233.
  • Ohnuki M, Tanabe K, Sutou K, Teramoto I, Sawamura Y, Narita M, Nakamura M, Tokunaga Y, Nakamura M, Watanabe A, et al. Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential. Proc Natl Acad Sci U S A 2014; 111:12426-31; PMID:25097266; http://dx.doi.org/10.1073/pnas.1413299111.
  • Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006; 126:663-76; PMID:16904174; http://dx.doi.org/10.1016/j.cell.2006.07.024.
  • Ying QL, Wray J, Nichols J, Batlle-Morera L, Doble B, Woodgett J, Cohen P, Smith A. The ground state of embryonic stem cell self-renewal. Nature 2008; 453:519-23; PMID:18497825; http://dx.doi.org/10.1038/nature06968.
  • Lassmann T, Hayashizaki Y, Daub CO. TagDust–a program to eliminate artifacts from next generation sequencing data. Bioinformatics 2009; 25:2839-40; PMID:19737799; http://dx.doi.org/10.1093/bioinformatics/btp527.
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25:1754-60; PMID:19451168; http://dx.doi.org/10.1093/bioinformatics/btp324.
  • Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, et al. Ensembl 2013. Nucleic Acids Res 2013; 41:D48-55; PMID:23203987; http://dx.doi.org/10.1093/nar/gks1236.
  • Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005; 110:462-7; PMID:16093699; http://dx.doi.org/10.1159/000084979.
  • Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 2011; 470:279-83; PMID:21160473; http://dx.doi.org/10.1038/nature09692.
  • Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009; 459:108-12; PMID:19295514; http://dx.doi.org/10.1038/nature07829.