Genome-wide analysis of mammalian promoter architecture and evolution
- Piero Carninci, A. Sandelin, Y. Hayashizaki
- BiologyNature Genetics
- 28 April 2006
These tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini.
The Transcriptional Landscape of the Mammalian Genome
- Piero Carninci, T. Kasukawa, Y. Hayashizaki
- BiologyScience
- 2 September 2005
Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
Antisense Transcription in the Mammalian Transcriptome
- S. Katayama, Y. Tomaru, C. Wahlestedt
- BiologyScience
- 2 September 2005
Experimental evidence that perturbation of an antisense RNA can alter the expression of sense messenger RNAs is presented, suggesting that antisense transcription contributes to control of transcriptional outputs in mammals.
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
- T. Shiraki, S. Kondo, Y. Hayashizaki
- BiologyProceedings of the National Academy of Sciences…
- 8 December 2003
By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), this work redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit.
A promoter-level mammalian expression atlas
- The Fantom Consortium, Riken Pmii, Y. Hayashizaki
- BiologyNature
- 27 March 2014
It is found that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles.
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
- T. Ravasi, Harukazu Suzuki, Y. Hayashizaki
- BiologyCell
- 5 March 2010
Androgen‐responsive long noncoding RNA CTBP1‐AS promotes prostate cancer
- K. Takayama, K. Horie-Inoue, S. Inoue
- BiologyEMBO Journal
- 12 June 2013
An androgen‐responsive long ncRNA, CTBP1‐AS, located in the AS region of C‐terminal binding protein 1 (CTBP1), which is a corepressor for androgen receptor is reported, providing new insights into the functions of ncRNAs that directly contribute to prostate cancer progression.
Hidden layers of human small RNAs
- H. Kawaji, Mari Nakamura, Y. Hayashizaki
- BiologyBMC Genomics
- 10 April 2008
The data shows that well-characterized non-coding RNA, such as tRNA, snoRNA, and snRNA are cleaved at sites specific to the class of ncRNA, indicating that the small RNAs are a product of dsRNA formation and their subsequent cleavage.
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
- T. Ravasi, Harukazu Suzuki, Y. Hayashizaki
- BiologyCell
- 16 April 2010
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome.
- T. Ravasi, Harukazu Suzuki, J. Mattick
- BiologyGenome Research
- 12 December 2005
Analysis of the genomic landscape around these sequences indicates that some cDNA clones were produced not from terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes.
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