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

Publication ,  Journal Article
Ni, T; Corcoran, DL; Rach, EA; Song, S; Spana, EP; Gao, Y; Ohler, U; Zhu, J
Published in: Nat Methods
July 2010

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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Published In

Nat Methods

DOI

EISSN

1548-7105

Publication Date

July 2010

Volume

7

Issue

7

Start / End Page

521 / 527

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • RNA
  • Promoter Regions, Genetic
  • Nucleic Acid Amplification Techniques
  • Gene Expression Regulation, Developmental
  • Embryo, Nonmammalian
  • Drosophila melanogaster
  • Drosophila Proteins
  • Developmental Biology
  • Animals
 

Citation

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Ni, T., Corcoran, D. L., Rach, E. A., Song, S., Spana, E. P., Gao, Y., … Zhu, J. (2010). A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods, 7(7), 521–527. https://doi.org/10.1038/nmeth.1464
Ni, Ting, David L. Corcoran, Elizabeth A. Rach, Shen Song, Eric P. Spana, Yuan Gao, Uwe Ohler, and Jun Zhu. “A paired-end sequencing strategy to map the complex landscape of transcription initiation.Nat Methods 7, no. 7 (July 2010): 521–27. https://doi.org/10.1038/nmeth.1464.
Ni T, Corcoran DL, Rach EA, Song S, Spana EP, Gao Y, et al. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods. 2010 Jul;7(7):521–7.
Ni, Ting, et al. “A paired-end sequencing strategy to map the complex landscape of transcription initiation.Nat Methods, vol. 7, no. 7, July 2010, pp. 521–27. Pubmed, doi:10.1038/nmeth.1464.
Ni T, Corcoran DL, Rach EA, Song S, Spana EP, Gao Y, Ohler U, Zhu J. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods. 2010 Jul;7(7):521–527.

Published In

Nat Methods

DOI

EISSN

1548-7105

Publication Date

July 2010

Volume

7

Issue

7

Start / End Page

521 / 527

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • RNA
  • Promoter Regions, Genetic
  • Nucleic Acid Amplification Techniques
  • Gene Expression Regulation, Developmental
  • Embryo, Nonmammalian
  • Drosophila melanogaster
  • Drosophila Proteins
  • Developmental Biology
  • Animals