publication . Article . Other literature type . 2010

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

Piero Carninci; Charles Plessy; Jun Kawai; Roberto Simone; Stefano Gustincich; Salimullah; Carrie A. Davis; Yoshihide Hayashizaki; Timo Lassmann; Valerio Orlando; ...
Open Access English
  • Published: 13 Jun 2010 Journal: Nature methods, volume 7, issue 7, pages 528-534 (issn: 1548-7091, eissn: 1548-7105, Copyright policy)
Large-scale sequencing projects have revealed an unexpected complexity in the origins, structures and functions of mammalian transcripts. Many loci are known to produce overlapping coding and non-coding RNAs with capped 5′ ends that vary in size. Methods that identify the 5′ ends of transcripts will facilitate the discovery of novel promoters and 5′ ends derived from secondary capping events. Such methods often require high input amounts of RNA not obtainable from highly refined samples such as tissue microdissections and subcellular fractions. Therefore, we have developed nanoCAGE (Cap Analysis of Gene Expression), a method that captures the 5′ ends of transcri...
free text keywords: Article, Biotechnology, Cell Biology, Biochemistry, Molecular Biology, Regulation of gene expression, Genetics, Biology, Computational biology, Non-coding RNA, RNA, Gene expression, Promoter, Transcriptome, Transcription (biology), Gene expression profiling
Funded by
NIH| Comprehensive Characterization and Classification of the Human Transcriptome
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U54HG004557-02
26 references, page 1 of 2

Shiraki, T. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci USA. 2003; 100: 15776-15781 [OpenAIRE] [PubMed]

Kodzius, R. CAGE: cap analysis of gene expression. Nat Methods. 2006; 3: 211-222 [OpenAIRE] [PubMed]

Carninci, P. Cap-Analysis Gene Expression (CAGE): Genome-Scale Promoter Identification and Association with Expression Profile and Regulatory Networks. 2009

Carninci, P. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet. 2006; 38: 626-635 [PubMed]

Suzuki, H. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet. 2009; 41: 553-562 [OpenAIRE] [PubMed]

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature. 2009; 457: 1028-1032 [OpenAIRE] [PubMed]

Kapranov, P. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007; 316: 1484-1488 [OpenAIRE] [PubMed]

Fullwood, MJ, Wei, C, Liu, ET, Ruan, Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009; 19: 521-532 [OpenAIRE] [PubMed]

Valen, E. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res. 2009; 19: 255-265 [OpenAIRE] [PubMed]

Zhu, YY, Machleder, EM, Chenchik, A, Li, R, Siebert, PD. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. BioTechniques. 2001; 30: 892-897 [OpenAIRE] [PubMed]

Hirzmann, J, Luo, D, Hahnen, J, Hobom, G. Determination of messenger RNA 5′-ends by reverse transcription of the cap structure. Nucleic Acids Res. 1993; 21: 3597-3598 [OpenAIRE] [PubMed]

Ohtake, H, Ohtoko, K, Ishimaru, Y, Kato, S. Determination of the capped site sequence of mRNA based on the detection of cap-dependent nucleotide addition using an anchor ligation method. DNA Res. 2004; 11: 305-309 [OpenAIRE] [PubMed]

Cheng, J. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 2005; 308: 1149-1154 [PubMed]

Meisel, A, Bickle, TA, Kruger, DH, Schroeder, C. Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage. Nature. 1992; 355: 467-469 [OpenAIRE] [PubMed]

Maeda, N. Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. BioTechniques. 2008; 45: 95-97 [PubMed]

26 references, page 1 of 2
Any information missing or wrong?Report an Issue