Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

We performed a genome-wide analysis of transcriptional start sites (TSSs) in human genes by multifaceted use of a massively parallel sequencer. By analyzing 800 million sequences that were obtained from various types of transcriptome analyses, we characterized 140 million TSS tags in 12 human cell t...

Full description

Saved in:
Bibliographic Details
Published in:Genome research 2011-05, Vol.21 (5), p.775-789
Main Authors: Yamashita, Riu, Sathira, Nuankanya P, Kanai, Akinori, Tanimoto, Kousuke, Arauchi, Takako, Tanaka, Yoshiaki, Hashimoto, Shin-Ichi, Sugano, Sumio, Nakai, Kenta, Suzuki, Yutaka
Format: Article
Language:English
Subjects:
Binding Sites
Cell Line
Chromatin
DNA, Complementary - genetics
DNA, Complementary - metabolism
Gene Expression Profiling - methods
Genome, Human
HEK293 Cells
Humans
Nucleosomes - genetics
Nucleosomes - metabolism
Organ Specificity
Proteins - genetics
Proteins - metabolism
Resource
RNA Polymerase II - genetics
RNA Polymerase II - metabolism
Sequence Analysis, DNA
Sequence Analysis, RNA
Transcription Initiation Site - physiology
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:We performed a genome-wide analysis of transcriptional start sites (TSSs) in human genes by multifaceted use of a massively parallel sequencer. By analyzing 800 million sequences that were obtained from various types of transcriptome analyses, we characterized 140 million TSS tags in 12 human cell types. Despite the large number of TSS clusters (TSCs), the number of TSCs was observed to decrease sharply with increasing expression levels. Highly expressed TSCs exhibited several characteristic features: Nucleosome-seq analysis revealed highly ordered nucleosome structures, ChIP-seq analysis detected clear RNA polymerase II binding signals in their surrounding regions, evaluations of previously sequenced and newly shotgun-sequenced complete cDNA sequences showed that they encode preferable transcripts for protein translation, and RNA-seq analysis of polysome-incorporated RNAs yielded direct evidence that those transcripts are actually translated into proteins. We also demonstrate that integrative interpretation of transcriptome data is essential for the selection of putative alternative promoter TSCs, two of which also have protein consequences. Furthermore, discriminative chromatin features that separate TSCs at different expression levels were found for both genic TSCs and intergenic TSCs. The collected integrative information should provide a useful basis for future biological characterization of TSCs.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.110254.110