title: Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
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.
authors.affiliation: RIKEN Yokohama Institute, Omics Science Center, Yokohama, Japan. plessy@riken.jp
authors.forename: Charles
authors.initials: C
authors.lastname: Plessy
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bertin
authors.forename: Hazuki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Roberto
authors.initials: R
authors.lastname: Simone
authors.forename: Md
authors.initials: M
authors.lastname: Salimullah
authors.forename: Timo
authors.initials: T
authors.lastname: Lassmann
authors.forename: Morana
authors.initials: M
authors.lastname: Vitezic
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.forename: Signe
authors.initials: S
authors.lastname: Olivarius
authors.forename: Dejan
authors.initials: D
authors.lastname: Lazarevic
authors.forename: Nadine
authors.initials: N
authors.lastname: Hornig
authors.forename: Valerio
authors.initials: V
authors.lastname: Orlando
authors.forename: Ian
authors.initials: I
authors.lastname: Bell
authors.forename: Hui
authors.initials: H
authors.lastname: Gao
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Dumais
authors.forename: Philipp
authors.initials: P
authors.lastname: Kapranov
authors.forename: Huaien
authors.initials: H
authors.lastname: Wang
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Carsten O
authors.initials: CO
authors.lastname: Daub
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Stefano
authors.initials: S
authors.lastname: Gustincich
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
mesh_terms: D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology*; D015894:Genome, Human; D006801:Humans; D036103:Nanotechnology / Q000379:methods*; D011401:Promoter Regions, Genetic / Q000502:physiology*; D012313:RNA / Q000235:genetics / Q000378:metabolism*
chemical_list: D012313:RNA