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

Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, Md, Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarevic, D., Hornig, N., Orlando, V., Bell, I., Gao, H., Dumais, J., Kapranov, P., Wang, H., Davis, C. A., Gingeras, T. R., Kawai, J., Daub, C. O., Hayashizaki, Y., Gustincich, S., Carninci, P. (June 2010) Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods, 7 (7). pp. 528-34. ISSN 15487091 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/20543846
DOI: 10.1038/nmeth.1470

Abstract

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 noncoding RNAs with capped 5′ ends that vary in size. Methods to identify the 5′ ends of transcripts will facilitate the discovery of new 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 developed nano–cap analysis of gene expression (nanoCAGE), a method that captures the 5′ ends of transcripts from as little as 10 ng of total RNA, and CAGEscan, a mate-pair adaptation of nanoCAGE that captures the transcript 5′ ends linked to a downstream region. Both of these methods allow further annotation-agnostic studies of the complex human transcriptome.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > ncRNA
CSHL Authors:
Communities: CSHL labs > Gingeras lab
CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User: CSHL Librarian
Date: 13 June 2010
Date Deposited: 04 Oct 2011 15:28
Last Modified: 26 Dec 2014 20:48
PMCID: PMC2906222
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15507

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