7 results on '"Mattick JS"'
Search Results
2. The eukaryotic genome as an RNA machine.
- Author
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Amaral PP, Dinger ME, Mercer TR, and Mattick JS
- Subjects
- Animals, Evolution, Molecular, Genome, Genome, Human, Humans, Protein Biosynthesis, RNA Processing, Post-Transcriptional, RNA, Untranslated metabolism, Transcription, Genetic, Eukaryotic Cells metabolism, Gene Expression Regulation, RNA, Untranslated genetics
- Abstract
The past few years have revealed that the genomes of all studied eukaryotes are almost entirely transcribed, generating an enormous number of non-protein-coding RNAs (ncRNAs). In parallel, it is increasingly evident that many of these RNAs have regulatory functions. Here, we highlight recent advances that illustrate the diversity of ncRNA control of genome dynamics, cell biology, and developmental programming.
- Published
- 2008
- Full Text
- View/download PDF
3. The transcriptional landscape of the mammalian genome.
- Author
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Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, and Hayashizaki Y
- Subjects
- 3' Untranslated Regions, Animals, Base Sequence, Conserved Sequence, DNA, Complementary chemistry, Genome, Human, Genomics, Humans, Promoter Regions, Genetic, Proteins genetics, RNA chemistry, RNA classification, RNA Splicing, RNA, Untranslated chemistry, Regulatory Sequences, Ribonucleic Acid, Genome, Mice genetics, Terminator Regions, Genetic, Transcription Initiation Site, Transcription, Genetic
- Abstract
This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
- Published
- 2005
- Full Text
- View/download PDF
4. The functional genomics of noncoding RNA.
- Author
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Mattick JS
- Subjects
- Animals, Base Sequence, Conserved Sequence, DNA-Binding Proteins antagonists & inhibitors, Humans, Mice, NFATC Transcription Factors, Nuclear Proteins antagonists & inhibitors, RNA, Untranslated antagonists & inhibitors, RNA, Untranslated genetics, Transcription Factors antagonists & inhibitors, beta Karyopherins metabolism, Genomics, RNA Interference, RNA, Untranslated physiology
- Abstract
Large numbers of noncoding RNA transcripts (ncRNAs) are being revealed by complementary DNA cloning and genome tiling array studies in animals. The big and as yet largely unanswered question is whether these transcripts are relevant. A paper by Willingham et al. shows the way forward by developing a strategy for large-scale functional screening of ncRNAs, involving small interfering RNA knockdowns in cell-based screens, which identified a previously unidentified ncRNA repressor of the transcription factor NFAT. It appears likely that ncRNAs constitute a critical hidden layer of gene regulation in complex organisms, the understanding of which requires new approaches in functional genomics.
- Published
- 2005
- Full Text
- View/download PDF
5. Mathematics/computation. Accelerating networks.
- Author
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Mattick JS and Gagen MJ
- Subjects
- Computers, Engineering, Gene Expression Regulation, Industry, Software, Mathematics, Systems Biology
- Published
- 2005
- Full Text
- View/download PDF
6. Ultraconserved elements in the human genome.
- Author
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Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, and Haussler D
- Subjects
- Alternative Splicing, Animals, Base Sequence, Chickens genetics, Computational Biology, DNA, Intergenic, Dogs genetics, Evolution, Molecular, Exons, Gene Expression Regulation, Genes, Genome, Humans, Introns, Mice genetics, Molecular Sequence Data, Mutation, Nucleic Acid Conformation, RNA chemistry, RNA genetics, RNA metabolism, Rats genetics, Takifugu genetics, Conserved Sequence, Genome, Human
- Abstract
There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes. Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively. Many are also significantly conserved in fish. These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development. Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to be essential for the ontogeny of mammals and other vertebrates.
- Published
- 2004
- Full Text
- View/download PDF
7. Extracellular DNA required for bacterial biofilm formation.
- Author
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Whitchurch CB, Tolker-Nielsen T, Ragas PC, and Mattick JS
- Subjects
- Culture Media, Cystic Fibrosis complications, Cystic Fibrosis drug therapy, Cystic Fibrosis microbiology, Deoxyribonuclease I pharmacology, Deoxyribonuclease I therapeutic use, Humans, Microscopy, Confocal, Pseudomonas Infections prevention & control, Biofilms growth & development, DNA, Bacterial physiology, Deoxyribonuclease I metabolism, Pseudomonas aeruginosa physiology
- Published
- 2002
- Full Text
- View/download PDF
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