title: 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.
abstract: Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows the regulatory inputs driving gene expression to be studied, which in turn enables the construction of transcriptional networks. Here we provide an optimized protocol for the construction of CAGE libraries on the basis of the preparation of 27-nt-long tags corresponding to initial bases at the 5' ends of capped RNAs. We have optimized the methods using simple steps based on filtration, which altogether takes 4 d to complete. The CAGE tags can be readily sequenced with Illumina sequencers, and upon modification they are also amenable to sequencing using other platforms.
authors.affiliation: RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan.
authors.forename: Hazuki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Timo
authors.initials: T
authors.lastname: Lassmann
authors.forename: Mitsuyoshi
authors.initials: M
authors.lastname: Murata
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D023281:Genomics / Q000379:methods*; D012315:RNA Caps / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012315:RNA Caps