Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

Ameres, 2010, Target RNA-directed trimming and tailing of small silencing RNAs, Science, 328, 1534, 10.1126/science.1187058 Anders, 2010, Differential expression analysis for sequence count data, Genome Biol., 11, R106, 10.1186/gb-2010-11-10-r106 Apostolou, 2013, Chromatin dynamics during cellular reprogramming, Nature, 502, 462, 10.1038/nature12749 Bailey, 2009, Activation of Rap1 promotes prostate cancer metastasis, Cancer Res., 69, 4962, 10.1158/0008-5472.CAN-08-4269 Boyle, 2004, GO:TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes, Bioinformatics, 20, 3710, 10.1093/bioinformatics/bth456 Buganim, 2012, Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase, Cell, 150, 1209, 10.1016/j.cell.2012.08.023 Carey, 2010, Single-gene transgenic mouse strains for reprogramming adult somatic cells, Nat. Methods, 7, 56, 10.1038/nmeth.1410 Carey, 2011, Reprogramming factor stoichiometry influences the epigenetic state and biological properties of induced pluripotent stem cells, Cell Stem Cell, 9, 588, 10.1016/j.stem.2011.11.003 Chang, 2014, High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells, Cell Res., 24, 293, 10.1038/cr.2013.173 Cooke, 2014, Processed pseudogenes acquired somatically during cancer development, Nat. Commun., 5, 3644, 10.1038/ncomms4644 de Hoon, 2004, Open source clustering software, Bioinformatics, 20, 1453, 10.1093/bioinformatics/bth078 Flicek, 2014, Ensembl 2014, Nucleic Acids Res., 42, D749, 10.1093/nar/gkt1196 Flynn, 2014, Long noncoding RNAs in cell-fate programming and reprogramming, Cell Stem Cell, 14, 752, 10.1016/j.stem.2014.05.014 Goding, 2014, Cancer: pathological nuclear reprogramming?, Nat. Rev. Cancer, 14, 568, 10.1038/nrc3781 Gupta, 2010, Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis, Nature, 464, 1071, 10.1038/nature08975 Gurdon, 2008, Nuclear reprogramming in cells, Science, 322, 1811, 10.1126/science.1160810 Guttman, 2011, lincRNAs act in the circuitry controlling pluripotency and differentiation, Nature, 477, 295, 10.1038/nature10398 Han, 2014, The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes, Nat. Commun., 5, 3963, 10.1038/ncomms4963 Hemberger, 2009, Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington’s canal, Nat. Rev. Mol. Cell Biol., 10, 526, 10.1038/nrm2727 Huang, 2014, miRNA-491-5p and GIT1 serve as modulators and biomarkers for oral squamous cell carcinoma invasion and metastasis, Cancer Res., 74, 751, 10.1158/0008-5472.CAN-13-1297 Johnson, 2007, Genome-wide mapping of in vivo protein-DNA interactions, Science, 316, 1497, 10.1126/science.1141319 Karnoub, 2008, Ras oncogenes: split personalities, Nat. Rev. Mol. Cell Biol., 9, 517, 10.1038/nrm2438 Kim, 2010, Epigenetic memory in induced pluripotent stem cells, Nature, 467, 285, 10.1038/nature09342 Krizhanovsky, 2009, Stem cells: the promises and perils of p53, Nature, 460, 1085, 10.1038/4601085a Kuhn, 2013, The UCSC genome browser and associated tools, Brief. Bioinform., 14, 144, 10.1093/bib/bbs038 Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25 Laugesen, 2014, Chromatin repressive complexes in stem cells, development, and cancer, Cell Stem Cell, 14, 735, 10.1016/j.stem.2014.05.006 Law, 2010, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat. Rev. Genet., 11, 204, 10.1038/nrg2719 Lee, 2012, Epigenetic regulation by long noncoding RNAs, Science, 338, 1435, 10.1126/science.1231776 Lee, 2014, Neuregulin autocrine signaling promotes self-renewal of breast tumor-initiating cells by triggering HER2/HER3 activation, Cancer Res., 74, 341, 10.1158/0008-5472.CAN-13-1055 Loewer, 2010, Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells, Nat. Genet., 42, 1113, 10.1038/ng.710 Marchetto, 2013, Differential L1 regulation in pluripotent stem cells of humans and apes, Nature, 503, 525, 10.1038/nature12686 Moazed, 2009, Small RNAs in transcriptional gene silencing and genome defence, Nature, 457, 413, 10.1038/nature07756 Onder, 2012, Chromatin-modifying enzymes as modulators of reprogramming, Nature, 483, 598, 10.1038/nature10953 Orkin, 2011, Chromatin connections to pluripotency and cellular reprogramming, Cell, 145, 835, 10.1016/j.cell.2011.05.019 Papp, 2013, Epigenetics of reprogramming to induced pluripotency, Cell, 152, 1324, 10.1016/j.cell.2013.02.043 Polo, 2010, Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells, Nat. Biotechnol., 28, 848, 10.1038/nbt.1667 Polo, 2012, A molecular roadmap of reprogramming somatic cells into iPS cells, Cell, 151, 1617, 10.1016/j.cell.2012.11.039 Raj, 2008, Imaging individual mRNA molecules using multiple singly labeled probes, Nat. Methods, 5, 877, 10.1038/nmeth.1253 Ramsköld, 2012, Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells, Nat. Biotechnol., 30, 777, 10.1038/nbt.2282 Rinn, 2012, Genome regulation by long noncoding RNAs, Annu. Rev. Biochem., 81, 145, 10.1146/annurev-biochem-051410-092902 Roberts, 2013, Streaming fragment assignment for real-time analysis of sequencing experiments, Nat. Methods, 10, 71, 10.1038/nmeth.2251 Saldanha, 2004, Java Treeview—extensible visualization of microarray data, Bioinformatics, 20, 3246, 10.1093/bioinformatics/bth349 Schieke, 2008, Mitochondrial metabolism modulates differentiation and teratoma formation capacity in mouse embryonic stem cells, J. Biol. Chem., 283, 28506, 10.1074/jbc.M802763200 Smith, 2010, Dynamic single-cell imaging of direct reprogramming reveals an early specifying event, Nat. Biotechnol., 28, 521, 10.1038/nbt.1632 Stadtfeld, 2010, Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells, Nature, 465, 175, 10.1038/nature09017 Stadtfeld, 2012, Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells, Nat. Genet., 44, 398, 10.1038/ng.1110 Stuwe, 2014, Small but sturdy: small RNAs in cellular memory and epigenetics, Genes Dev., 28, 423, 10.1101/gad.236414.113 Suvà, 2013, Epigenetic reprogramming in cancer, Science, 339, 1567, 10.1126/science.1230184 Takahashi, 2006, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 126, 663, 10.1016/j.cell.2006.07.024 Tam, 2008, Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes, Nature, 453, 534, 10.1038/nature06904 Theunissen, 2014, Molecular control of induced pluripotency, Cell Stem Cell, 14, 720, 10.1016/j.stem.2014.05.002 Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120 Trapnell, 2010, Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nat. Biotechnol., 28, 511, 10.1038/nbt.1621 Trimarchi, 2014, Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia, Cell, 158, 593, 10.1016/j.cell.2014.05.049 Varambally, 2002, The polycomb group protein EZH2 is involved in progression of prostate cancer, Nature, 419, 624, 10.1038/nature01075 Watanabe, 2011, Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus, Science, 332, 848, 10.1126/science.1203919 Yang, 2010, RasGRP3 contributes to formation and maintenance of the prostate cancer phenotype, Cancer Res., 70, 7905, 10.1158/0008-5472.CAN-09-4729 Yildirim, 2013, Xist RNA is a potent suppressor of hematologic cancer in mice, Cell, 152, 727, 10.1016/j.cell.2013.01.034 Ying, 2008, The ground state of embryonic stem cell self-renewal, Nature, 453, 519, 10.1038/nature06968 Zhang, 2013, The human long non-coding RNA-RoR is a p53 repressor in response to DNA damage, Cell Res., 23, 340, 10.1038/cr.2012.164 Zhao, 2010, Genome-wide identification of polycomb-associated RNAs by RIP-seq, Mol. Cell, 40, 939, 10.1016/j.molcel.2010.12.011