RNA regulation: a new genetics? (original) (raw)

• Wassarman, K. M., Zhang, A. & Storz, G. Small RNAs in Escherichia coli. Trends Microbiol. 7, 37–45 (1999).
  Article CAS PubMed Google Scholar
• Argaman, L. et al. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr. Biol. 11, 941–950 (2001).
  Article CAS PubMed Google Scholar
• Klein, R. J., Misulovin, Z. & Eddy, S. R. Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc. Natl Acad. Sci. USA 99, 7542–7547 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Levine, M. & Tjian, R. Transcription regulation and animal diversity. Nature 424, 147–151 (2003).
  Article CAS PubMed Google Scholar
• Buchler, N. E., Gerland, U. & Hwa, T. On schemes of combinatorial transcription logic. Proc. Natl Acad. Sci. USA 100, 5136–5141 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
• Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).
  Article CAS PubMed Google Scholar
• Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002).
• Aparicio, S. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301–1310 (2002).
  Article CAS PubMed Google Scholar
• Harrison, P. M. et al. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res. 12, 272–280 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Mattick, J. S. Introns: evolution and function. Curr. Opin. Genet. Dev. 4, 823–831 (1994).
  Article CAS PubMed Google Scholar
• Mattick, J. S. & Gagen, M. J. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol. Biol. Evol. 18, 1611–1630 (2001).
  Article CAS PubMed Google Scholar
• Mattick, J. S. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2, 986–991 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Mattick, J. S. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25, 930–939 (2003).
  Article CAS PubMed Google Scholar
• Weng, G., Bhalla, U. S. & Iyengar, R. Complexity in biological signaling systems. Science 284, 92–96 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Dennett, D. Darwin's Dangerous Idea: Evolution and the Meanings of Life (Simon Schuster, New York, 1995).
  Google Scholar
• Li, M. & Vitanyi, P. M. B. An Introduction to Kolmogorov Complexity and its Applications 2nd edn (Springer, New York, 1997).
  Book Google Scholar
• Croft, L. J., Lercher, M. J., Gagen, M. J. & Mattick, J. S. Is prokaryotic complexity limited by accelerated growth in regulatory overhead? Genome Biol. Preprint Depository [online], <http://genomebiology.com/qc/2003/5/1/p2> (2003).
• Gagen, M. J. & Mattick, J. S. Inherent size constraints on prokaryote gene networks due to 'accelerating' growth. arXiv Preprint Archive [online], <http://arXiv.org/abs/q-bio.MN/0312021> (2004).
• Gagen, M. J. & Mattick, J. S. Failed 'nonaccelerating' models of prokaryote gene regulatory networks. arXiv Preprint Archive [online], <http://arXiv.org/abs/q-bio.MN/0312022> (2004).
• Scherer, S. W. et al. Human chromosome 7: DNA sequence and biology. Science 300, 767–772 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Tycowski, K. T., Shu, M. D. & Steitz, J. A. A mammalian gene with introns instead of exons generating stable RNA products. Nature 379, 464–466 (1996).
  Article CAS PubMed Google Scholar
• Kiss, T. Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109, 145–148 (2002).
  Article CAS PubMed Google Scholar
• Bachellerie, J. P., Cavaille, J. & Huttenhofer, A. The expanding snoRNA world. Biochimie 84, 775–790 (2002).
  Article CAS PubMed Google Scholar
• Sutherland, H. F. et al. Identification of a novel transcript disrupted by a balanced translocation associated with DiGeorge syndrome. Am. J. Hum. Genet. 59, 23–31 (1996).
  CAS PubMed PubMed Central Google Scholar
• Bussemakers, M. J. et al. DD3: a new prostate-specific gene, highly overexpressed in prostate cancer. Cancer Res. 59, 5975–5979 (1999).
  CAS PubMed Google Scholar
• Raho, G., Barone, V., Rossi, D., Philipson, L. & Sorrentino, V. The gas 5 gene shows four alternative splicing patterns without coding for a protein. Gene 256, 13–17 (2000).
  Article CAS PubMed Google Scholar
• Charlier, C. et al. Human-ovine comparative sequencing of a 250-kb imprinted domain encompassing the callipyge (clpg) locus and identification of six imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. Genome Res. 11, 850–862 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Wolf, S. et al. B-cell neoplasia associated gene with multiple splicing (BCMS): the candidate B-CLL gene on 13q14 comprises more than 560 kb covering all critical regions. Hum. Mol. Genet. 10, 1275–1285 (2001).
  Article CAS PubMed Google Scholar
• Lee, Y., Jeon, K., Lee, J. T., Kim, S. & Kim, V. N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663–4670 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003).
  Article CAS PubMed Google Scholar
• Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004).
  Article CAS PubMed Google Scholar
• Ashe, H. L., Monks, J., Wijgerde, M., Fraser, P. & Proudfoot, N. J. Intergenic transcription and transinduction of the human β-globin locus. Genes Dev. 11, 2494–2509 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Akhtar, A., Zink, D. & Becker, P. B. Chromodomains are protein–RNA interaction modules. Nature 407, 405–409 (2000).
  Article CAS PubMed Google Scholar
• Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002).
  Article CAS PubMed Google Scholar
• Hutvagner, G. & Zamore, P. D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056–2060 (2002).
  Article CAS PubMed Google Scholar
• Csete, M. E. & Doyle, J. C. Reverse engineering of biological complexity. Science 295, 1664–1669 (2002).
  Article CAS PubMed Google Scholar
• Shabalina, S. A., Ogurtsov, A. Y., Kondrashov, V. A. & Kondrashov, A. S. Selective constraint in intergenic regions of human and mouse genomes. Trends Genet. 17, 373–376 (2001).
  Article CAS PubMed Google Scholar
• Kirkness, E. F. et al. The dog genome: survey sequencing and comparative analysis. Science 301, 1898–1903 (2003).
  Article PubMed Google Scholar
• Thomas, J. W. et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424, 788–793 (2003).
  Article CAS PubMed Google Scholar
• Frazer, K. A. et al. Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional. Genome Res. 14, 367–372 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Ridanpaa, M. et al. Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia. Cell 104, 195–203 (2001).
  Article CAS PubMed Google Scholar
• Vulliamy, T. et al. The RNA component of telomerase is mutated in autosomal dominant dyskeratosis congenita. Nature 413, 432–435 (2001).
  Article CAS PubMed Google Scholar
• Ji, P. et al. MALAT-1, a novel noncoding RNA, and thymosin β4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22, 6087–6097 (2003).
  Article CAS Google Scholar
• Numata, K. et al. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res. 13, 1301–1306 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Storz, G. An expanding universe of noncoding RNAs. Science 296, 1260–1263 (2002).
  Article CAS PubMed Google Scholar
• Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573 (2002).
  Article PubMed Google Scholar
• Kiyosawa, H., Yamanaka, I., Osato, N., Kondo, S. & Hayashizaki, Y. Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res. 13, 1324–1334 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Yelin, R. et al. Widespread occurrence of antisense transcription in the human genome. Nature Biotechnol. 21, 379–386 (2003).
  Article CAS Google Scholar
• Tufarelli, C. et al. Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nature Genet. 34, 157–165 (2003).
  Article CAS PubMed Google Scholar
• Sleutels, F., Zwart, R. & Barlow, D. P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810–813 (2002).
  Article CAS PubMed Google Scholar
• Andersen, A. A. & Panning, B. Epigenetic gene regulation by noncoding RNAs. Curr. Opin. Cell Biol. 15, 281–289 (2003).
  Article CAS PubMed Google Scholar
• Kiyosawa, H. & Abe, K. Speculations on the role of natural antisense transcripts in mammalian X chromosome evolution. Cytogenet. Genome Res. 99, 151–156 (2002).
  Article CAS PubMed Google Scholar
• Hirotsune, S. et al. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423, 91–96 (2003).
  Article CAS PubMed Google Scholar
• Carrington, J. C. & Ambros, V. Role of microRNAs in plant and animal development. Science 301, 336–338 (2003).
  Article CAS PubMed Google Scholar
• Palatnik, J. F. et al. Control of leaf morphogenesis by microRNAs. Nature 425, 257–263 (2003).
  Article CAS PubMed Google Scholar
• Hall, I. M., Noma, K. & Grewal, S. I. RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proc. Natl Acad. Sci. USA 100, 193–198 (2003).
  Article CAS PubMed Google Scholar
• Volpe, T. et al. RNA interference is required for normal centromere function in fission yeast. Chromosome Res. 11, 137–146 (2003).
  Article CAS PubMed Google Scholar
• Mochizuki, K., Fine, N. A., Fujisawa, T. & Gorovsky, M. A. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell 110, 689–699 (2002).
  Article CAS PubMed Google Scholar
• McManus, M. T. MicroRNAs and cancer. Semin. Cancer Biol. 13, 253–258 (2003).
  Article CAS PubMed Google Scholar
• Metzler, M., Wilda, M., Busch, K., Viehmann, S. & Borkhardt, A. High expression of precursor microRNA-155/BIC RNA in children with Burkitt lymphoma. Genes Chromosom. Cancer 39, 167–169 (2004).
  Article CAS PubMed Google Scholar
• Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862 (2001).
  Article CAS PubMed Google Scholar
• Llave, C., Kasschau, K. D., Rector, M. A. & Carrington, J. C. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14, 1605–1619 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Georges, M., Charlier, C. & Cockett, N. The callipyge locus: evidence for the trans interaction of reciprocally imprinted genes. Trends Genet. 19, 248–252 (2003).
  Article CAS PubMed Google Scholar
• Van Laere, A. S. et al. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425, 832–836 (2003).
  Article CAS PubMed Google Scholar
• Drewell, R. A., Bae, E., Burr, J. & Lewis, E. B. Transcription defines the embryonic domains of _cis_-regulatory activity at the Drosophila bithorax complex. Proc. Natl Acad. Sci. USA 99, 16853–16858 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Rank, G., Prestel, M. & Paro, R. Transcription through intergenic chromosomal memory elements of the Drosophila bithorax complex correlates with an epigenetic switch. Mol. Cell Biol. 22, 8026–8034 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Toulme, J. J., Di Primo, C. & Moreau, S. Modulation of RNA function by oligonucleotides recognizing RNA structure. Prog. Nucleic Acid Res. Mol. Biol. 69, 1–46 (2001).
  Article CAS PubMed Google Scholar
• Vasquez, K. M. & Glazer, P. M. Triplex-forming oligonucleotides: principles and applications. Q. Rev. Biophys. 35, 89–107 (2002).
  Article CAS PubMed Google Scholar
• Sczyrba, A., Kruger, J., Mersch, H., Kurtz, S. & Giegerich, R. RNA-related tools on the Bielefeld Bioinformatics Server. Nucleic Acids Res. 31, 3767–3770 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Sadakane, K. & Shibuya, T. Indexing huge genome sequences for solving various problems. Genome Inform. Ser. Workshop Genome Inform. 12, 175–183 (2001).
  CAS Google Scholar
• Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318–356 (1961).
  Article CAS PubMed Google Scholar
• Britten, R. J. & Davidson, E. H. Gene regulation for higher cells: a theory. Science 165, 349–357 (1969).
  Article CAS PubMed Google Scholar
• Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–34 (2001).
  Article CAS PubMed Google Scholar
• Cavalier-Smith, T. Intron phylogeny: a new hypothesis. Trends Genet. 7, 145–148 (1991).
  Article CAS PubMed Google Scholar
• Lynch, M. & Richardson, A. O. The evolution of spliceosomal introns. Curr. Opin. Genet. Dev. 12, 701–710 (2002).
  Article CAS PubMed Google Scholar
• Taft, R. J. & Mattick, J. S. Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences. arXiv Preprint Archive [online], <http://www.arxiv.org/abs/q-bio.GN/0401020> (2003).
• Conway Morris, S. The Cambrian 'explosion': slow-fuse or megatonnage? Proc. Natl Acad. Sci. USA 97, 4426–4429 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499–509 (2004).
  Article CAS PubMed Google Scholar
• Kampa, D. et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331–342 (2004).
  Article CAS PubMed PubMed Central Google Scholar