A paired-end sequencing strategy to map the complex landscape of transcription initiation.

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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Citation

Published Version (Please cite this version)

10.1038/nmeth.1464

Publication Info

Ni, Ting, David L Corcoran, Elizabeth A Rach, Shen Song, Eric P Spana, Yuan Gao, Uwe Ohler, Jun Zhu, et al. (2010). A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nature methods, 7(7). pp. 521–527. 10.1038/nmeth.1464 Retrieved from https://hdl.handle.net/10161/27476.

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Scholars@Duke

Spana

Eric P. Spana

Associate Professor of the Practice of Biology
Ohler

Uwe Ohler

Adjunct Associate Professor in the Department of Biostatistics & Bioinformatics

Computational Biology of Gene Regulation
Sequence Analysis
Image Expression Analysis
Applied Machine Learning


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