Defining the 5 and 3 landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq
Authors
Afik, ShakedBartok, Osnat
Artyomov, Maxim N.
Shishkin, Alexander A.
Kadri, Sabah
Hanan, Mor
Zhu, Xiaopeng
Garber, Manuel
Kadener, Sebastian
UMass Chan Affiliations
Program in Bioinformatics and Integrative BiologyDocument Type
Journal ArticlePublication Date
2017-02-22Keywords
UMCCTS fundingBiochemistry, Biophysics, and Structural Biology
Bioinformatics
Computational Biology
Genomics
Investigative Techniques
Translational Medical Research
Metadata
Show full item recordAbstract
Cells regulate biological responses in part through changes in transcription start sites (TSS) or cleavage and polyadenylation sites (PAS). To fully understand gene regulatory networks, it is therefore critical to accurately annotate cell type-specific TSS and PAS. Here we present a simple and straightforward approach for genome-wide annotation of 5- and 3-RNA ends. Our approach reliably discerns bona fide PAS from false PAS that arise due to internal poly(A) tracts, a common problem with current PAS annotation methods. We applied our methodology to study the impact of temperature on the Drosophila melanogaster head transcriptome. We found hundreds of previously unidentified TSS and PAS which revealed two interesting phenomena: first, genes with multiple PASs tend to harbor a motif near the most proximal PAS, which likely represents a new cleavage and polyadenylation signal. Second, motif analysis of promoters of genes affected by temperature suggested that boundary element association factor of 32 kDa (BEAF-32) and DREF mediates a transcriptional program at warm temperatures, a result we validated in a fly line where beaf-32 is downregulated. These results demonstrate the utility of a high-throughput platform for complete experimental and computational analysis of mRNA-ends to improve gene annotation.Source
Nucleic Acids Res. 2017 Feb 22. doi: 10.1093/nar/gkx133. Link to article on publisher's site
DOI
10.1093/nar/gkx133Permanent Link to this Item
http://hdl.handle.net/20.500.14038/50282PubMed ID
28335028Related Resources
Rights
© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.Distribution License
http://creativecommons.org/licenses/by/4.0/ae974a485f413a2113503eed53cd6c53
10.1093/nar/gkx133
Scopus Count
Except where otherwise noted, this item's license is described as © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.