2009
|
Taft, R. J.; Glazov, E. A.; Cloonan, N.; Simons, C.; Stephen, S.; Faulkner, G. J.; Lassmann, T.; Forrest, A. R. R.; Grimmond, S. M.; Schroder, K.; Irvine, K.; Arakawa, T.; Nakamura, M.; Kubosaki, A.; Hayashida, K.; Kawazu, C.; Murata, M.; Nishiyori, H.; Fukuda, S.; Kawai, J.; Daub, C. O.; Hume, D. A.; Suzuki, H.; Orlando, V.; Carninci, P.; Hayashizaki, Y.; Mattick, J. S. Tiny RNAs associated with transcription start sites in animals (Journal Article) In: Nature Genetics, vol. 41, no. 5, pp. 572–578, 2009, ISSN: 10614036. @article{taft_tiny_2009,
title = {Tiny RNAs associated with transcription start sites in animals},
author = {R. J. Taft and E. A. Glazov and N. Cloonan and C. Simons and S. Stephen and G. J. Faulkner and T. Lassmann and A. R. R. Forrest and S. M. Grimmond and K. Schroder and K. Irvine and T. Arakawa and M. Nakamura and A. Kubosaki and K. Hayashida and C. Kawazu and M. Murata and H. Nishiyori and S. Fukuda and J. Kawai and C. O. Daub and D. A. Hume and H. Suzuki and V. Orlando and P. Carninci and Y. Hayashizaki and J. S. Mattick},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-67349157682&doi=10.1038%2fng.312&partnerID=40&md5=c2b1a4560d94c55fb48fac8d83784276},
doi = {10.1038/ng.312},
issn = {10614036},
year = {2009},
date = {2009-01-01},
journal = {Nature Genetics},
volume = {41},
number = {5},
pages = {572--578},
abstract = {It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. In conjunction with the FANTOM4 project, we have identified tiny RNAs with a modal length of 18 nt that map within 60 to +120 nt of transcription start sites (TSSs) in human, chicken and Drosophila. These transcription initiation RNAs (tiRNAs) are derived from sequences on the same strand as the TSS and are preferentially associated with G+C-rich promoters. The 5′ ends of tiRNAs show peak density 10-30 nt downstream of TSSs, indicating that they are processed. tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes. © 2009 Nature America, Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. In conjunction with the FANTOM4 project, we have identified tiny RNAs with a modal length of 18 nt that map within 60 to +120 nt of transcription start sites (TSSs) in human, chicken and Drosophila. These transcription initiation RNAs (tiRNAs) are derived from sequences on the same strand as the TSS and are preferentially associated with G+C-rich promoters. The 5′ ends of tiRNAs show peak density 10-30 nt downstream of TSSs, indicating that they are processed. tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes. © 2009 Nature America, Inc. All rights reserved. |
Taft, R. J.; Glazov, E. A.; Cloonan, N.; Simons, C.; Stephen, S.; Faulkner, G. J.; Lassmann, T.; Forrest, A. R. R.; Grimmond, S. M.; Schroder, K.; Irvine, K.; Arakawa, T.; Nakamura, M.; Kubosaki, A.; Hayashida, K.; Kawazu, C.; Murata, M.; Nishiyori, H.; Fukuda, S.; Kawai, J.; Daub, C. O.; Hume, D. A.; Suzuki, H.; Orlando, V.; Carninci, P.; Hayashizaki, Y.; Mattick, J. S. Erratum: Tiny RNAs associated with transcription start sites in animals (Nature Genetics (2009) 41 (572-578)). (Journal Article) In: Nature Genetics, vol. 41, no. 7, pp. 859, 2009, ISSN: 10614036. @article{taft_erratum_2009,
title = {Erratum: Tiny RNAs associated with transcription start sites in animals (Nature Genetics (2009) 41 (572-578)).},
author = {R. J. Taft and E. A. Glazov and N. Cloonan and C. Simons and S. Stephen and G. J. Faulkner and T. Lassmann and A. R. R. Forrest and S. M. Grimmond and K. Schroder and K. Irvine and T. Arakawa and M. Nakamura and A. Kubosaki and K. Hayashida and C. Kawazu and M. Murata and H. Nishiyori and S. Fukuda and J. Kawai and C. O. Daub and D. A. Hume and H. Suzuki and V. Orlando and P. Carninci and Y. Hayashizaki and J. S. Mattick},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-67649858457&doi=10.1038%2fng0709-859a&partnerID=40&md5=fd38027ed5a49e2edb9e566c4e929b3c},
doi = {10.1038/ng0709-859a},
issn = {10614036},
year = {2009},
date = {2009-01-01},
journal = {Nature Genetics},
volume = {41},
number = {7},
pages = {859},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
2008
|
Maeda, N.; Nishiyori, H.; Nakamura, M.; Kawazu, C.; Murata, M.; Sano, H.; Hayashida, K.; Fukuda, S.; Tagami, M.; Hasegawa, A.; Murakami, K.; Schroder, K.; Irvine, K.; Hume, D. A.; Hayashizaki, Y.; Carninci, P.; Suzuki, H. Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer (Journal Article) In: BioTechniques, vol. 45, no. 1, pp. 95–97, 2008, ISSN: 07366205. @article{maeda_development_2008,
title = {Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer},
author = {N. Maeda and H. Nishiyori and M. Nakamura and C. Kawazu and M. Murata and H. Sano and K. Hayashida and S. Fukuda and M. Tagami and A. Hasegawa and K. Murakami and K. Schroder and K. Irvine and D. A. Hume and Y. Hayashizaki and P. Carninci and H. Suzuki},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-47949091256&doi=10.2144%2f000112814&partnerID=40&md5=261dacfb8af2de67f09124fdf83dfde8},
doi = {10.2144/000112814},
issn = {07366205},
year = {2008},
date = {2008-01-01},
journal = {BioTechniques},
volume = {45},
number = {1},
pages = {95--97},
abstract = {CAGE (cap analysis of gene expression) is a method for identifying transcription start sites by sequencing the first 20 or 21 nucleotides from the 5′ end of capped transcripts, allowing genome-wide promoter analyses to be performed. The potential of the CAGE as a form of expression profiling was limited previously by sequencing technology and the labor-intensive protocol. Here we describe an improved CAGE method for use with a next generation sequencer. This modified method allows the identification of the RNA source of each CAGE tag within a pooled library by introducing DNA tags (barcodes). The method not only drastically improves the sequencing capacity, but also contributes to savings in both time and budget. Additionally, this pooled CAGE tag method enables the dynamic changes in promoter usage and gene expression to be monitored.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
CAGE (cap analysis of gene expression) is a method for identifying transcription start sites by sequencing the first 20 or 21 nucleotides from the 5′ end of capped transcripts, allowing genome-wide promoter analyses to be performed. The potential of the CAGE as a form of expression profiling was limited previously by sequencing technology and the labor-intensive protocol. Here we describe an improved CAGE method for use with a next generation sequencer. This modified method allows the identification of the RNA source of each CAGE tag within a pooled library by introducing DNA tags (barcodes). The method not only drastically improves the sequencing capacity, but also contributes to savings in both time and budget. Additionally, this pooled CAGE tag method enables the dynamic changes in promoter usage and gene expression to be monitored. |
2004
|
Irvine, K.; Stirling, R.; Hume, D.; Kennedy, D. Rasputin, more promiscuous than ever: A review of G3BP (Journal Article) In: International Journal of Developmental Biology, vol. 48, no. 10, pp. 1065–1077, 2004, ISSN: 02146282. @article{irvine_rasputin_2004,
title = {Rasputin, more promiscuous than ever: A review of G3BP},
author = {K. Irvine and R. Stirling and D. Hume and D. Kennedy},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-13144276292&doi=10.1387%2fijdb.041893ki&partnerID=40&md5=02ac347bb651d9b7e8c902f03a964efb},
doi = {10.1387/ijdb.041893ki},
issn = {02146282},
year = {2004},
date = {2004-01-01},
journal = {International Journal of Developmental Biology},
volume = {48},
number = {10},
pages = {1065--1077},
abstract = {The foregoing discussion highlights what G3BP's domain structure initially suggested; that G3BPs are "scaffolding" proteins linking signal transduction to RNA metabolism. Whilst it is most attractive to hypothesise about G3BP's role in signalling to mRNA metabolism, it is not known whether all G3BP functions impinge on their RNA-binding activities, so any theories are naturally subject to this qualification. It is hypothesised that, in coordination with an array of other proteins, G3BP, in a phosphorylation- dependent manner, is involved in the post-transcriptional regulation of a subset of mRNAs, at least some of which are in common with those regulated by Hu proteins. These transcripts, partially controlled at the post-transcriptional level by G3BPs, code for proteins important in transcription (e.g. c-Myc) and cytoskeletal arrangement (e.g. Tau), amongst other as yet undetermined pathways. The subtle differences between G3BP family members could dictate binding to a variety of signalling proteins, so each of the G3BPs may participate in different, though possibly related mRNPs, which are assembled in response to different stimuli. The combinatorial nature of the mRNP complex offers a powerful means of regulating gene expression, beyond that provided by a simple mRNA sequence. The ways in which mRNP flexibility and specificity may be harnessed to coordinate gene expression of functionally or structurally related mRNAs are not yet fully appreciated. Characterising mRNP composition and the function/s of mRNP components, such as the G3BPs, will aid in the understanding of how post-transcriptional mechanisms contribute to the global regulation of gene expression.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The foregoing discussion highlights what G3BP's domain structure initially suggested; that G3BPs are "scaffolding" proteins linking signal transduction to RNA metabolism. Whilst it is most attractive to hypothesise about G3BP's role in signalling to mRNA metabolism, it is not known whether all G3BP functions impinge on their RNA-binding activities, so any theories are naturally subject to this qualification. It is hypothesised that, in coordination with an array of other proteins, G3BP, in a phosphorylation- dependent manner, is involved in the post-transcriptional regulation of a subset of mRNAs, at least some of which are in common with those regulated by Hu proteins. These transcripts, partially controlled at the post-transcriptional level by G3BPs, code for proteins important in transcription (e.g. c-Myc) and cytoskeletal arrangement (e.g. Tau), amongst other as yet undetermined pathways. The subtle differences between G3BP family members could dictate binding to a variety of signalling proteins, so each of the G3BPs may participate in different, though possibly related mRNPs, which are assembled in response to different stimuli. The combinatorial nature of the mRNP complex offers a powerful means of regulating gene expression, beyond that provided by a simple mRNA sequence. The ways in which mRNP flexibility and specificity may be harnessed to coordinate gene expression of functionally or structurally related mRNAs are not yet fully appreciated. Characterising mRNP composition and the function/s of mRNP components, such as the G3BPs, will aid in the understanding of how post-transcriptional mechanisms contribute to the global regulation of gene expression. |