Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells

DNA Research

Volumn 16, Issue 1, 2009, Pages 45-58

  Sharova, Lioudmila V ^a   Sharov, Alexei A ^a   Nedorezov, Timur ^a   Piao, Yulan ^a   Shaik, Nabeebi ^a   Ko, Minoru S H ^a  

^a NATIONAL INSTITUTE ON AGING   (United States)

Author keywords

AU rich elements (ARE); Cell differentiation; Embryonic stem cells; Exon junction; Leukemia inhibitory factor (LIF); Microarray; Mouse strain; MRNA decay; MRNA degradation; Retinoic acid (RA); Transcript

Indexed keywords

CPG OLIGODEOXYNUCLEOTIDE; MESSENGER RNA; TRANSCRIPTION FACTOR;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; CELL DIFFERENTIATION; CONTROLLED STUDY; CYTOSKELETON; DATA BASE; DNA MICROARRAY; EMBRYO; EMBRYONIC STEM CELL; EXON; EXTRACELLULAR MATRIX; FOXA2 GENE; GADD45 G GENE; GENE; GENE EXPRESSION; GENE STRUCTURE; HALF LIFE TIME; HES5 GENE; MAMMAL; METABOLISM; MOUSE; NONHUMAN; ONCOGENE MYC; OPEN READING FRAME; PLURIPOTENT STEM CELL; PRDM1 GENE; PROTEIN MOTIF; RNA ANALYSIS; RNA DEGRADATION; RNA STABILITY; STEADY STATE; TRIB1 GENE; ANIMAL; C57BL MOUSE; CELL CULTURE; COMPARATIVE STUDY; CYTOLOGY; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; HUMAN; METHODOLOGY; MOUSE STRAIN;

MAMMALIA;

3' UNTRANSLATED REGIONS; ANIMALS; CELL DIFFERENTIATION; CELLS, CULTURED; DATABASES, GENETIC; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; HALF-LIFE; HUMANS; MICE; MICE, INBRED C57BL; MICE, INBRED STRAINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLURIPOTENT STEM CELLS; RNA STABILITY; RNA, MESSENGER;

EID: 65249141709     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsn030     Document Type: Article

References (54)

1. Raghavan, A. and Bohjanen, P. R. 2004, Microarray-based analyses of mRNA decay in the regulation of mammalian gene expression, Brief Funct. Genomic Proteomic., 3, 112-124.
2. Bolognani, F. and Perrone-Bizzozero, N. I. 2008, RNA - protein interactions and control of mRNA stability in neurons, J. Neurosci. Res., 86, 481-489.
3. Raghavan, A., Ogilvie, R. L., Reilly, C., et al. 2002, Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes, Nucleic Acids Res., 30, 5529-5538.
4. Yang, E., van Nimwegen, E., Zavolan, M., et al. 2003, Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes, Genome Res., 13, 1863-1872.
5. Lam, L. T., Pickeral, O. K., Peng, A. C., et al. 2001, Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol, Genome Biol., 2, research0041.1-research0041. 11.
6. Newbury, S. F. 2006, Control of mRNA stability in eukaryotes, Biochem Soc. Trans., 34, 30-34.
7. Garcia-Martinez, J., Aranda, A. and Perez-Ortin, J. E. 2004, Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms, Mol. Cell, 15, 303-313.
8. Wang, J., Chang, Y. F., Hamilton, J. I. and Wilkinson, M. F. 2002, Nonsense-associated altered splicing: a frame-dependent response distinct from nonsense-mediated decay, Mol. Cell, 160, 951-957.
9. Hollams, E. M., Giles, K. M., Thomson, A. M. and Leedman, P. J. 2002, MRNA stability and the control of gene expression: implications for human disease, Neurochem. Res., 27, 957-980.
10. Sahmi, M., Nicola, E. S. and Price, C. A. 2006, Hormonal regulation of cytochrome P450 aromatase mRNA stability in non-luteinizing bovine granulosa cells in vitro, J. Endocrinol., 190, 107-115.
11. Gowrishankar, G., Winzen, R., Bollig, F., et al. 2005, Inhibition of mRNA deadenylation and degradation by ultraviolet light, Biol. Chem., 386, 1287-1293.
12. Herruer, M. H., Mager, W. H., Raue, H. A., Vreken, P., Wilms, E. and Planta, R. J. 1988, Mild temperature shock affects transcription of yeast ribosomal protein genes as well as the stability of their mRNAs, Nucleic Acids Res., 16, 7917-7929.
13. Greatrix, B. W. and van Vuuren, H. J. 2006, Expression of the HXT13, HXT15 and HXT17 genes in Saccharomyces cerevisiae and stabilization of the HXT1 gene transcript by sugar-induced osmotic stress, Curr. Genet., 49, 205-217.
14. Benard, L. 2004, Inhibition of 5′ to 3′ mRNA degradation under stress conditions in Saccharomyces cerevisiae: from GCN4 to MET16, RNA, 10, 458-468.
15. Jona, G., Choder, M. and Gileadi, O. 2000, Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast, Biochim. Biophys. Acta, 1491, 37-48.
16. Shock, J. L., Fischer, K. F. and DeRisi, J. L. 2007, Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle, Genome Biol., 8, R134.
17. Herpin, A., Rohr, S., Riedel, D., Kluever, N., Raz, E. and Schartl, M. 2007, Specification of primordial germ cells in medaka (Oryzias latipes), BMC Dev. Biol., 7, 3.
18. Deschenes-Furry, J., Perrone-Bizzozero, N. and Jasmin, B. J. 2006, The RNA-binding protein HuD: a regulator of neuronal differentiation, maintenance and plasticity, Bioessays, 28, 822-833.
19. Ratti, A., Fallini, C., Cova, L., et al. 2006, A role for the ELAV RNA-binding proteins in neural stem cells: stabilization of Msi1 mRNA, J. Cell Sci., 119, 1442-1452.
20. Figueroa, C. and Vojtek, A. B. 2003, Akt negatively regulates translation of the ternary complex factor Elk-1, Oncogene, 22, 5554-5561.
21. Champelovier, P., Pautre, V., Elatifi, M., et al. 2006, Resistance to phorbol ester-induced differentiation in human myeloid leukemia cells: a hypothetic role for the mRNA stabilization process, Leuk. Res., 30, 1407-1416.
22. Benjamin, D. and Moroni, C. 2007, mRNA stability and cancer: an emerging link?, Expert Opin. Biol. Ther., 7, 1515-1529.
23. Heier, C. R., Gogliotti, R. G. and DiDonato, C. J. 2007, SMN transcript stability: could modulation of messenger RNA degradation provide a novel therapy for spinal muscular atrophy?, J. Child Neurol., 22, 1013-1018.
24. Stoecklin, G., Mayo, T. and Anderson, P. 2006, ARE-mRNA degradation requires the 5′-3′ decay pathway, EMBO Rep., 7, 72-77.
25. Le Hir, H., Gatfield, D., Izaurralde, E. and Moore, M. J. 2001, The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay, EMBO J., 20, 4987-4997.
26. Le Hir, H., Izaurralde, E., Maquat, L. E. and Moore, M. J. 2000, The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon - exon junctions, EMBO J., 19, 6860-6869.
27. Yamasaki, S., Stoecklin, G., Kedersha, N., Simarro, M. and Anderson, P. 2007, T-cell intracellular antigen-1 (TIA-1)-induced translational silencing promotes the decay of selected mRNAs, J. Biol. Chem., 282, 30070-30077.
28. Goldstrohm, A. C., Hook, B. A., Seay, D. J. and Wickens, M. 2006, PUF proteins bind Pop2p to regulate messenger RNAs, Nat. Struct. Mol. Biol., 13, 533-539.
29. White, E. K., Moore-Jarrett, T. and Ruley, H. E. 2001, PUM2, a novel murine puf protein, and its consensus RNA-binding site, RNA, 7, 1855-1866.
30. Kennell, D. 2002, Processing endoribonucleases and mRNA degradation in bacteria, J. Bacteriol., 184, 4645-4657. Discussion 4665.
31. Sobell, H. M. 1985, Actinomycin and DNA transcription, Proc. Natl Acad. Sci. USA, 82, 5328-5331.
32. Narsai, R., Howell, K. A., Millar, A. H., O'Toole, N., Small, I. and Whelan, J. 2007, Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana, Plant Cell, 19, 3418-3436.
33. Wegmuller, D., Raineri, I., Gross, B., Oakeley, E. J. and Moroni, C. 2007, A cassette system to study embryonic stem cell differentiation by inducible RNA interference, Stem Cells, 25, 1178-1185.
34. Carter, M. G., Sharov, A. A., VanBuren, V., et al. 2005, Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray, Genome Biol., 6, R61.
35. Benjamini, Y. and Hochberg, Y. 1995, Controlling the false discovery rate - a practical and powerful approach to multiple testing, J. R. Stat. Soc. Ser. B, 57, 289-300.
36. Sharov, A. A., Dudekula, D. B. and Ko, M. S. 2005, Genome-wide assembly and analysis of alternative transcripts in mouse, Genome Res., 15, 748-754.
37. Carter, M. G., Hamatani, T., Sharov, A. A., et al. 2003, In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling, Genome Res., 13, 1011-1021.
38. Sharova, L. V., Sharov, A. A., Piao, Y., et al. 2007, Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells of different origins and strains, Dev. Biol., 307, 446-459.
39. Wang, J., Rao, S., Chu, J., et al. 2006, A protein interaction network for pluripotency of embryonic stem cells, Nature, 444, 364-368.
40. Wang, J., Levasseur, D. N. and Orkin, S. H. 2008, Requirement of Nanog dimerization for stem cell self-renewal and pluripotency, Proc. Natl Acad. Sci. USA, 105, 6326-6331.
41. Cairrao, F., Arraiano, C. and Newbury, S. 2005, Drosophila gene tazman, an orthologue of the yeast exosome component Rrp44p/Dis3, is differentially expressed during development, Dev. Dyn., 232, 733-737.
42. Seago, J. E., Chernukhin, I. V. and Newbury, S. F. 2001, The Drosophila gene twister, an orthologue of the yeast helicase SKI2, is differentially expressed during development, Mech. Dev., 106, 137-141.
43. Till, D. D., Linz, B., Seago, J. E., et al. 1998, Identification and developmental expression of a 5′-3′ exoribonuclease from Drosophila melanogaster, Mech. Dev., 79, 51-55.
44. Zhao, C. and Hamilton, T. 2007, Introns regulate the rate of unstable mRNA decay, J. Biol. Chem., 282, 20230-20237.
45. Chen, C. Y. and Shyu, A. B. 1995, AU-rich elements: characterization and importance in mRNA degradation, Trends Biochem. Sci., 20, 465-470.
46. Shaw, G. and Kamen, R. 1986, A conserved AU sequence from the 3′ untranslated region of GM-CSF mRNA mediates selective mRNA degradation, Cell, 46, 659-667.
47. Bakheet, T., Frevel, M., Williams, B. R., Greer, W. and Khabar, K. S. 2001, ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins, Nucleic Acids Res., 29, 246-254.
48. Xie, X., Lu, J., Kulbokas, E. J., et al. 2005, Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals, Nature, 434, 338-345.
49. Cora, D., Di Cunto, F., Caselle, M. and Provero, P. 2007, Identification of candidate regulatory sequences in mammalian 3′ UTRs by statistical analysis of oligonu-cleotide distributions, BMC Bioinformatics, 8, 174.
50. Chang, Y. F., Imam, J. S. and Wilkinson, M. F. 2007, The nonsense-mediated decay RNA surveillance pathway, Annu. Rev. Biochem., 76, 51-74.
51. Garneau, N. L., Wilusz, J. and Wilusz, C. J. 2007, The highways and byways of mRNA decay, Nat. Rev. Mol. Cell Biol., 8, 113-126.
52. Tebo, J., Der, S., Frevel, M., Khabar, K. S., Williams, B. R. and Hamilton, T. A. 2003, Heterogeneity in control of mRNA stability by AU-rich elements, J. Biol. Chem., 278, 12085-12093.
53. Young, J. I., Hong, E. P., Castle, J. C., et al. 2005, Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2, Proc. Natl Acad. Sci. USA, 102, 17551-17558.
54. Wheeler, D. L., Barrett, T., Benson, D. A., et al. 2008, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res, 36, D13-21.