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

dc.contributor.author

Ni, Ting

dc.contributor.author

Corcoran, David L

dc.contributor.author

Rach, Elizabeth A

dc.contributor.author

Song, Shen

dc.contributor.author

Spana, Eric P

dc.contributor.author

Gao, Yuan

dc.contributor.author

Ohler, Uwe

dc.contributor.author

Zhu, Jun

dc.date.accessioned

2023-06-01T13:37:22Z

dc.date.available

2023-06-01T13:37:22Z

dc.date.issued

2010-07

dc.date.updated

2023-06-01T13:37:17Z

dc.description.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.

dc.identifier

nmeth.1464

dc.identifier.issn

1548-7091

dc.identifier.issn

1548-7105

dc.identifier.uri

https://hdl.handle.net/10161/27476

dc.language

eng

dc.publisher

Springer Science and Business Media LLC

dc.relation.ispartof

Nature methods

dc.relation.isversionof

10.1038/nmeth.1464

dc.subject

Embryo, Nonmammalian

dc.subject

Animals

dc.subject

Drosophila melanogaster

dc.subject

Drosophila Proteins

dc.subject

RNA

dc.subject

Nucleic Acid Amplification Techniques

dc.subject

Transcription, Genetic

dc.subject

Gene Expression Regulation, Developmental

dc.subject

Promoter Regions, Genetic

dc.title

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

dc.type

Journal article

duke.contributor.orcid

Spana, Eric P|0000-0002-2057-8278

pubs.begin-page

521

pubs.end-page

527

pubs.issue

7

pubs.organisational-group

Duke

pubs.organisational-group

School of Medicine

pubs.organisational-group

Trinity College of Arts & Sciences

pubs.organisational-group

Basic Science Departments

pubs.organisational-group

Biostatistics & Bioinformatics

pubs.organisational-group

Biology

pubs.publication-status

Published

pubs.volume

7

Files

Original bundle

Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
A paired-end sequencing strategy to map the complex landscape of transcription initiation.pdf
Size:
1.02 MB
Format:
Adobe Portable Document Format