Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
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.
Plessy
Charles
C
RIKEN Yokohama Institute, Omics Science Center, Yokohama, Japan. plessy@riken.jp
Bertin
Nicolas
N
Takahashi
Hazuki
H
Simone
Roberto
R
Salimullah
Md
M
Lassmann
Timo
T
Vitezic
Morana
M
Severin
Jessica
J
Olivarius
Signe
S
Lazarevic
Dejan
D
Hornig
Nadine
N
Orlando
Valerio
V
Bell
Ian
I
Gao
Hui
H
Dumais
Jacqueline
J
Kapranov
Philipp
P
Wang
Huaien
H
Davis
Carrie A
CA
Gingeras
Thomas R
TR
Kawai
Jun
J
Daub
Carsten O
CO
Hayashizaki
Yoshihide
Y
Gustincich
Stefano
S
Carninci
Piero
P
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*
D012313:RNA