Title |
Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance
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Published in |
BMC Genomics, March 2015
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DOI | 10.1186/s12864-015-1358-y |
Pubmed ID | |
Authors |
Sho Maekawa, Naoto Imamachi, Takuma Irie, Hidenori Tani, Kyoko Matsumoto, Rena Mizutani, Katsutoshi Imamura, Miho Kakeda, Tetsushi Yada, Sumio Sugano, Yutaka Suzuki, Nobuyoshi Akimitsu |
Abstract |
Histone epigenome data determined by chromatin immunoprecipitation sequencing (ChIP-seq) is used in identifying transcript regions and estimating expression levels. However, this estimation does not always correlate with eventual RNA expression levels measured by RNA sequencing (RNA-seq). Part of the inconsistency may arise from the variance in RNA stability, where the transcripts that are more or less abundant than predicted RNA expression from histone epigenome data are inferred to be more or less stable. However, there is little systematic analysis to validate this assumption. Here, we used stability data of whole transcriptome measured by 5'-bromouridine immunoprecipitation chase sequencing (BRIC-seq), which enabled us to determine the half-lives of whole transcripts including lincRNAs, and we integrated BRIC-seq with ChIP-seq to achieve better estimation of the eventual transcript levels and to understand the importance of post-transcriptional regulation that determine the eventual transcript levels. |
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United States | 2 | 29% |
France | 1 | 14% |
Sao Tome and Principe | 1 | 14% |
Unknown | 3 | 43% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 5 | 71% |
Scientists | 2 | 29% |
Mendeley readers
Geographical breakdown
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Germany | 1 | 1% |
Switzerland | 1 | 1% |
France | 1 | 1% |
Austria | 1 | 1% |
Argentina | 1 | 1% |
United States | 1 | 1% |
Unknown | 89 | 94% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Ph. D. Student | 32 | 34% |
Researcher | 18 | 19% |
Student > Bachelor | 7 | 7% |
Professor > Associate Professor | 5 | 5% |
Student > Master | 5 | 5% |
Other | 10 | 11% |
Unknown | 18 | 19% |
Readers by discipline | Count | As % |
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Agricultural and Biological Sciences | 37 | 39% |
Biochemistry, Genetics and Molecular Biology | 28 | 29% |
Medicine and Dentistry | 9 | 9% |
Computer Science | 1 | 1% |
Environmental Science | 1 | 1% |
Other | 2 | 2% |
Unknown | 17 | 18% |