RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).
BACKGROUND
Next generation sequencing based technologies are being extensively used to study transcriptomes. Among these, cap analysis of gene expression (CAGE) is specialized in detecting the most 5' ends of RNA molecules. After mapping the sequenced reads back to a reference genome CAGE data highlights the transcriptional start sites (TSSs) and their usage at a single nucleotide resolution.


RESULTS
We propose a pipeline to group the single nucleotide TSS into larger reproducible peaks and compare their usage across biological states. Importantly, our pipeline discovers broad peaks as well as the fine structure of individual transcriptional start sites embedded within them. We assess the performance of our approach on a large CAGE datasets including 156 primary cell types and two cell lines with biological replicas. We demonstrate that genes have complicated structures of transcription initiation events. In particular, we discover that narrow peaks embedded in broader regions of transcriptional activity can be differentially used even if the larger region is not.


CONCLUSIONS
By examining the reproducible fine scaled organization of TSS we can detect many differentially regulated peaks undetected by previous approaches.
Hiroko
H
Ohmiya
Morana
M
Vitezic
Martin C
MC
Frith
Masayoshi
M
Itoh
Piero
P
Carninci
Alistair R R
AR
Forrest
Yoshihide
Y
Hayashizaki
RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, 230-0045 Yokohama, Japan. lassmann@gsc.riken.jp.
Timo
T
Lassmann
D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006367:HeLa Cells; D006801:Humans; D020407:Internet; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D012315:RNA Caps; D015203:Reproducibility of Results; D012984:Software; D024363:Transcription Initiation Site
D012315:RNA Caps