Defining the 5'and 3'landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq

Shaked Afik, Osnat Bartok, Maxim N. Artyomov, Alexander A. Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, Sebastian Kadener*

*Corresponding author for this work

Research output: Contribution to journalArticle

4 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)e95
JournalNucleic acids research
Volume45
Issue number11
DOIs
StatePublished - Jun 1 2017

ASJC Scopus subject areas

  • Genetics

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    Afik, S., Bartok, O., Artyomov, M. N., Shishkin, A. A., Kadri, S., Hanan, M., Zhu, X., Garber, M., & Kadener, S. (2017). Defining the 5'and 3'landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq. Nucleic acids research, 45(11), e95. https://doi.org/10.1093/nar/gkx133