Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo

Cell Stem Cell

Volumn 12, Issue 5, 2013, Pages 616-628

  Ramos, Alexander D ^a,b   Diaz, Aaron ^b   Nellore, Abhinav ^b   Delgado, Ryan N ^a,b   Park, Ki Youb ^a,b   Gonzales Roybal, Gabriel ^a,b   Oldham, Michael C ^b   Song, Jun S ^a,b   Lim, Daniel A ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SAN FRANCISCO VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DLX1AS PROTEIN; EPIDERMAL GROWTH FACTOR RECEPTOR; LONG UNTRANSLATED RNA; MEMBRANE PROTEIN; SIX3OS PROTEIN; UNCLASSIFIED DRUG;

ADULT STEM CELL; ALZHEIMER DISEASE; ANIMAL CELL; ARTICLE; BRAIN REGION; CELL DIFFERENTIATION; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; CORPUS STRIATUM; CORRELATION ANALYSIS; FLUORESCENCE ACTIVATED CELL SORTING; GENE MAPPING; GENETIC ASSOCIATION; HISTONE MODIFICATION; HUNTINGTON CHOREA; MICROARRAY ANALYSIS; MOUSE; NERVOUS SYSTEM DEVELOPMENT; NEURAL STEM CELL; NEUROLOGIC DISEASE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROGENY; PROTEIN EXPRESSION; PROTEIN FUNCTION; RNA SEQUENCE; SEIZURE; SEQUENCE ANALYSIS; SUBVENTRICULAR ZONE;

ADULT STEM CELLS; ALTERNATIVE SPLICING; ANIMALS; CELL DIFFERENTIATION; CELL LINEAGE; CEREBRAL VENTRICLES; EMBRYONIC STEM CELLS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME; HISTONES; HUMANS; LYSINE; MALE; METHYLATION; MICE; MICE, INBRED C57BL; NEURAL STEM CELLS; NEUROGENESIS; NEURONS; PROTEIN ISOFORMS; PROTEIN PROCESSING, POST-TRANSLATIONAL; REPRODUCIBILITY OF RESULTS; RNA, LONG NONCODING; RNA, MESSENGER; TIME FACTORS;

EID: 84877575447     PISSN: 19345909     EISSN: 18759777     Source Type: Journal    
DOI: 10.1016/j.stem.2013.03.003     Document Type: Article

References (55)

1. K. Agger, P.A.C. Cloos, J. Christensen, D. Pasini, S. Rose, J. Rappsilber, I. Issaeva, E. Canaani, A.E. Salcini, and K. Helin UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development Nature 449 2007 731 734
2. A.E. Ayoub, S. Oh, Y. Xie, J. Leng, J. Cotney, M.H. Dominguez, J.P. Noonan, and P. Rakic Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing Proc. Natl. Acad. Sci. USA 108 2011 14950 14955
3. T.G. Belgard, A.C. Marques, P.L. Oliver, H.O. Abaan, T.M. Sirey, A. Hoerder-Suabedissen, F. García-Moreno, Z. Molnár, E.H. Margulies, and C.P. Ponting A transcriptomic atlas of mouse neocortical layers Neuron 71 2011 605 616
4. B.E. Bernstein, T.S. Mikkelsen, X. Xie, M. Kamal, D.J. Huebert, J. Cuff, B. Fry, A. Meissner, M. Wernig, and K. Plath A bivalent chromatin structure marks key developmental genes in embryonic stem cells Cell 125 2006 315 326
5. S. Bertani, S. Sauer, E. Bolotin, and F. Sauer The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin Mol. Cell 43 2011 1040 1046
6. A.M. Bond, M.J.W. Vangompel, E.A. Sametsky, M.F. Clark, J.C. Savage, J.F. Disterhoft, and J.D. Kohtz Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry Nat. Neurosci. 12 2009 1020 1027
7. C.J. Bult, J.T. Eppig, J.A. Kadin, J.E. Richardson, J.A. Blake Mouse Genome Database Group The Mouse Genome Database (MGD): mouse biology and model systems Nucleic Acids Res. 36 Database issue 2008 D724 D728
8. M.N. Cabili, C. Trapnell, L. Goff, M. Koziol, B. Tazon-Vega, A. Regev, and J.L. Rinn Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses Genes Dev. 25 2011 1915 1927
9. J.D. Cahoy, B. Emery, A. Kaushal, L.C. Foo, J.L. Zamanian, K.S. Christopherson, Y. Xing, J.L. Lubischer, P.A. Krieg, and S.A. Krupenko A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function J. Neurosci. 28 2008 264 278
10. K. Cui, C. Zang, T.Y. Roh, D.E. Schones, R.W. Childs, W. Peng, and K. Zhao Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation Cell Stem Cell 4 2009 80 93
11. M.E. Dinger, P.P. Amaral, T.R. Mercer, K.C. Pang, S.J. Bruce, B.B. Gardiner, M.E. Askarian-Amiri, K. Ru, G. Soldà, and C. Simons Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation Genome Res. 18 2008 1433 1445
12. F. Doetsch, L. Petreanu, I. Caille, J.M. Garcia-Verdugo, and A. Alvarez-Buylla EGF converts transit-amplifying neurogenic precursors in the adult brain into multipotent stem cells Neuron 36 2002 1021 1034
13. J. Feng, C. Bi, B.S. Clark, R. Mady, P. Shah, and J.D. Kohtz The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator Genes Dev. 20 2006 1470 1484
14. J. Goecks, A. Nekrutenko, J. Taylor Galaxy Team Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol. 11 2010 R86
15. C. Gregg, J. Zhang, B. Weissbourd, S. Luo, G.P. Schroth, D. Haig, and C. Dulac High-resolution analysis of parent-of-origin allelic expression in the mouse brain Science 329 2010 643 648
16. M. Guttman, I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, B.W. Carey, and J.P. Cassady Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals Nature 458 2009 223 227
17. M. Guttman, M. Garber, J.Z. Levin, J. Donaghey, J. Robinson, X. Adiconis, L. Fan, M.J. Koziol, A. Gnirke, and C. Nusbaum Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs Nat. Biotechnol. 28 2010 503 510
18. M. Guttman, J. Donaghey, B.W. Carey, M. Garber, J.K. Grenier, G. Munson, G. Young, A.B. Lucas, R. Ach, and L. Bruhn lincRNAs act in the circuitry controlling pluripotency and differentiation Nature 477 2011 295 300
19. S. Horvath, and J. Dong Geometric interpretation of gene coexpression network analysis PLoS Comput. Biol. 4 2008 e1000117
20. J. Hsieh Orchestrating transcriptional control of adult neurogenesis Genes Dev. 26 2012 1010 1021
21. M. Huarte, M. Guttman, D. Feldser, M. Garber, M.J. Koziol, D. Kenzelmann-Broz, A.M. Khalil, O. Zuk, I. Amit, and M. Rabani A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response Cell 142 2010 409 419
22. T. Hung, Y. Wang, M.F. Lin, A.K. Koegel, Y. Kotake, G.D. Grant, H.M. Horlings, N. Shah, C. Umbricht, and P. Wang Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters Nat. Genet. 43 2011 621 629
23. R.A. Ihrie, and A. Alvarez-Buylla Lake-front property: a unique germinal niche by the lateral ventricles of the adult brain Neuron 70 2011 674 686
24. T. Jenuwein, and C.D. Allis Translating the histone code Science 293 2001 1074 1080
25. W.J. Kent BLAT - the BLAST-like alignment tool Genome Res. 12 2002 656 664
26. A.M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, B.E. Bernstein, and A. van Oudenaarden Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression Proc. Natl. Acad. Sci. USA 106 2009 11667 11672
27. E.J. Kim, C.T. Leung, R.R. Reed, and J.E. Johnson In vivo analysis of Ascl1 defined progenitors reveals distinct developmental dynamics during adult neurogenesis and gliogenesis J. Neurosci. 27 2007 12764 12774
28. L. Kong, Y. Zhang, Z.-Q. Ye, X.-Q. Liu, S.-Q. Zhao, L. Wei, and G. Gao CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine Nucleic Acids Res. 35 Web Server issue 2007 W345 W349
29. A. Kriegstein, and A. Alvarez-Buylla The glial nature of embryonic and adult neural stem cells Annu. Rev. Neurosci. 32 2009 149 184
30. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
31. E.S. Lein, M.J. Hawrylycz, N. Ao, M. Ayres, A. Bensinger, A. Bernard, A.F. Boe, M.S. Boguski, K.S. Brockway, and E.J. Byrnes Genome-wide atlas of gene expression in the adult mouse brain Nature 445 2007 168 176
32. W.-H. Lien, X. Guo, L. Polak, L.N. Lawton, R.A. Young, D. Zheng, and E. Fuchs Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage Cell Stem Cell 9 2011 219 232
33. D.A. Lim, M. Suárez-Fariñas, F. Naef, C.R. Hacker, B. Menn, H. Takebayashi, M. Magnasco, N. Patil, and A. Alvarez-Buylla In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis Mol. Cell. Neurosci. 31 2006 131 148
34. D.A. Lim, Y.-C. Huang, T. Swigut, A.L. Mirick, J.M. Garcia-Verdugo, J. Wysocka, P. Ernst, and A. Alvarez-Buylla Chromatin remodelling factor Mll1 is essential for neurogenesis from postnatal neural stem cells Nature 458 2009 529 533
35. J.K. Liu, I. Ghattas, S. Liu, S. Chen, and J.L. Rubenstein Dlx genes encode DNA-binding proteins that are expressed in an overlapping and sequential pattern during basal ganglia differentiation Dev. Dyn. 210 1997 498 512
36. C.Y. McLean, D. Bristor, M. Hiller, S.L. Clarke, B.T. Schaar, C.B. Lowe, A.M. Wenger, and G. Bejerano GREAT improves functional interpretation of cis-regulatory regions Nat. Biotechnol. 28 2010 495 501
37. T.R. Mercer, M.E. Dinger, S.M. Sunkin, M.F. Mehler, and J.S. Mattick Specific expression of long noncoding RNAs in the mouse brain Proc. Natl. Acad. Sci. USA 105 2008 716 721
38. T.R. Mercer, I.A. Qureshi, S. Gokhan, M.E. Dinger, G. Li, J.S. Mattick, and M.F. Mehler Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation BMC Neurosci. 11 2010 14
39. T.R. Mercer, D.J. Gerhardt, M.E. Dinger, J. Crawford, C. Trapnell, J.A. Jeddeloh, J.S. Mattick, and J.L. Rinn Targeted RNA sequencing reveals the deep complexity of the human transcriptome Nat. Biotechnol. 30 2012 99 104
40. T.S. Mikkelsen, M. Ku, D.B. Jaffe, B. Issac, E. Lieberman, G. Giannoukos, P. Alvarez, W. Brockman, T.-K. Kim, and R.P. Koche Genome-wide maps of chromatin state in pluripotent and lineage-committed cells Nature 448 2007 553 560
41. M.C. Oldham, G. Konopka, K. Iwamoto, P. Langfelder, T. Kato, S. Horvath, and D.H. Geschwind Functional organization of the transcriptome in human brain Nat. Neurosci. 11 2008 1271 1282
42. E. Pastrana, L.-C. Cheng, and F. Doetsch Simultaneous prospective purification of adult subventricular zone neural stem cells and their progeny Proc. Natl. Acad. Sci. USA 106 2009 6387 6392
43. N.A. Rapicavoli, and S. Blackshaw New meaning in the message: noncoding RNAs and their role in retinal development Dev. Dyn. 238 2009 2103 2114
44. N.A. Rapicavoli, E.M. Poth, H. Zhu, and S. Blackshaw The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity Neural Dev. 6 2011 32
45. B. Scheffler, N.M. Walton, D.D. Lin, A.K. Goetz, G. Enikolopov, S.N. Roper, and D.A. Steindler Phenotypic and functional characterization of adult brain neuropoiesis Proc. Natl. Acad. Sci. USA 102 2005 9353 9358
46. A. Subramanian, P. Tamayo, V.K. Mootha, S. Mukherjee, B.L. Ebert, M.A. Gillette, A. Paulovich, S.L. Pomeroy, T.R. Golub, E.S. Lander, and J.P. Mesirov Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles Proc. Natl. Acad. Sci. USA 102 2005 15545 15550
47. E.A. Thomas, G. Coppola, B. Tang, A. Kuhn, S. Kim, D.H. Geschwind, T.B. Brown, R. Luthi-Carter, and M.E. Ehrlich In vivo cell-autonomous transcriptional abnormalities revealed in mice expressing mutant huntingtin in striatal but not cortical neurons Hum. Mol. Genet. 20 2011 1049 1060
48. C. Trapnell, L. Pachter, and S.L. Salzberg TopHat: discovering splice junctions with RNA-Seq Bioinformatics 25 2009 1105 1111
49. C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, and L. Pachter Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat. Biotechnol. 28 2010 511 515
50. M.-C. Tsai, O. Manor, Y. Wan, N. Mosammaparast, J.K. Wang, F. Lan, Y. Shi, E. Segal, and H.Y. Chang Long noncoding RNA as modular scaffold of histone modification complexes Science 329 2010 689 693
51. I. Ulitsky, A. Shkumatava, C.H. Jan, H. Sive, and D.P. Bartel Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution Cell 147 2011 1537 1550
52. K.C. Wang, Y.W. Yang, B. Liu, A. Sanyal, R. Corces-Zimmerman, Y. Chen, B.R. Lajoie, A. Protacio, R.A. Flynn, and R.A. Gupta A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression Nature 472 2011 120 124
53. Y. Zhang, T. Liu, C.A. Meyer, J. Eeckhoute, D.S. Johnson, B.E. Bernstein, C. Nusbaum, R.M. Myers, M. Brown, W. Li, and X.S. Liu Model-based analysis of ChIP-Seq (MACS) Genome Biol. 9 2008 R137
54. Y. Zhang, S. De, J.R. Garner, K. Smith, S.A. Wang, and K.G. Becker Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information BMC Med. Genomics 3 2010 1
55. Q. Zhou, and D.J. Anderson The bHLH transcription factors OLIG2 and OLIG1 couple neuronal and glial subtype specification Cell 109 2002 61 73