A Paired-end Sequencing Strategy to Map the Complex Landscape of Transcription Initiation

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2010 May 25

PMID 20495556

Citations 99

Authors

Ting Ni

David L Corcoran

Elizabeth A Rach

Shen Song

Eric P Spana

Yuan Gao

Uwe Ohler

Jun Zhu

Affiliations

Soon will be listed here.

Abstract

Recent studies using high-throughput sequencing protocols have uncovered the complexity of mammalian transcription by RNA polymerase II, helping to define several initiation patterns in which transcription start sites (TSSs) cluster in both narrow and broad genomic windows. Here we describe a paired-end sequencing strategy, which enables more robust mapping and characterization of capped transcripts. We used this strategy to explore the transcription initiation landscape in the Drosophila melanogaster embryo. Extending the previous findings in mammals, we found that fly promoters exhibited distinct initiation patterns, which were linked to specific promoter sequence motifs. Furthermore, we identified many 5' capped transcripts originating from coding exons; our analyses support that they are unlikely the result of alternative TSSs, but rather the product of post-transcriptional modifications. We demonstrated paired-end TSS analysis to be a powerful method to uncover the transcriptional complexity of eukaryotic genomes.

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