UMMS Affiliation

Program in Bioinformatics and Integrative Biology

Date

2-22-2017

Document Type

Article

Disciplines

Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology | Genomics | Investigative Techniques | Translational Medical Research

Abstract

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.

Rights and Permissions

© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. Citation: Nucleic Acids Res. 2017 Feb 22. doi: 10.1093/nar/gkx133. Link to article on publisher's site

Related Resources

Link to Article in PubMed

Keywords

UMCCTS funding

PubMed ID

28335028

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

 
 

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