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

Afik, Shaked and Bartok, Osnat and Artyomov, Maxim N. and Shishkin, Alexander A. and Kadri, Sabah and Hanan, Mor and Zhu, Xiaopeng and Garber, Manuel and Kadener, Sebastian (2017) Defining the 5' and 3' landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq. Nucleic Acids Research, 45 (11). Art. No. e95. ISSN 0305-1048. PMCID PMC5499799. https://resolver.caltech.edu/CaltechAUTHORS:20170403-153613905

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/nar/gkx133DOIArticle
https://academic.oup.com/nar/article/3044355/DefiningPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499799/PubMed CentralArticle
Additional Information:© 2017 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 25 May 2016; Revision Received: 10 February 2017; Accepted: 15 February 2017; Published: 22 February 2017. We thank Reut Ashwal-Fluss for help with some of the computational analysis and Patrick McDonel for help with protocol optimization. Funding: International Human Frontiers Science Program Organization [PG #31/2011 to S.K.]; European Research Council Consolidator Grant [ERC #647989 to S.K.]; Defense Advanced Research Project Agency [D13AP00074 to M.G., S.K.]; National Institute of Health [U01HG007910-01, UL1TR001453-01, 5U54HD082013-02 to M.G.). Funding for open access charge: European Research Council Consolidator Grant [ERC #647989 to S.K.]. Conflict of interest statement: Alexander A. Shishkin is an inventor on a massively multiplexed RNA-sequencing patent (publication number WO 2014152155 A1). The authors declare that they don't have any other conflict of interest.
Funders:
Funding AgencyGrant Number
Human Frontiers Science Program31/2011
European Research Council (ERC)647989
Defense Advanced Research Projects Agency (DARPA)D13AP00074
NIHU01HG007910-01
NIHUL1TR001453-01
NIH5U54HD082013-02
Issue or Number:11
PubMed Central ID:PMC5499799
Record Number:CaltechAUTHORS:20170403-153613905
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170403-153613905
Official Citation:Shaked Afik, Osnat Bartok, Maxim N. Artyomov, Alexander A. Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, Sebastian Kadener; Defining the 5΄ and 3΄ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq. Nucleic Acids Res 2017; 45 (11): e95. doi: 10.1093/nar/gkx133
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:75654
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:03 Apr 2017 22:55
Last Modified:03 Oct 2019 16:52

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