Show simple item record

dc.contributor.authorAfik, Shaked
dc.contributor.authorBartok, Osnat
dc.contributor.authorArtyomov, Maxim N.
dc.contributor.authorShishkin, Alexander A.
dc.contributor.authorKadri, Sabah
dc.contributor.authorHanan, Mor
dc.contributor.authorZhu, Xiaopeng
dc.contributor.authorGarber, Manuel
dc.contributor.authorKadener, Sebastian
dc.date2022-08-11T08:11:02.000
dc.date.accessioned2022-08-23T17:29:16Z
dc.date.available2022-08-23T17:29:16Z
dc.date.issued2017-02-22
dc.date.submitted2017-05-11
dc.identifier.citation<p>Nucleic Acids Res. 2017 Feb 22. doi: 10.1093/nar/gkx133. <a href="https://doi.org/10.1093/nar/gkx133">Link to article on publisher's site</a></p>
dc.identifier.issn0305-1048 (Linking)
dc.identifier.doi10.1093/nar/gkx133
dc.identifier.pmid28335028
dc.identifier.urihttp://hdl.handle.net/20.500.14038/50282
dc.description.abstractCells 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.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=28335028&dopt=Abstract">Link to Article in PubMed</a></p>
dc.rights© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectUMCCTS funding
dc.subjectBiochemistry, Biophysics, and Structural Biology
dc.subjectBioinformatics
dc.subjectComputational Biology
dc.subjectGenomics
dc.subjectInvestigative Techniques
dc.subjectTranslational Medical Research
dc.titleDefining the 5 and 3 landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq
dc.typeJournal Article
dc.source.journaltitleNucleic acids research
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1111&amp;context=umccts_pubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/umccts_pubs/111
dc.identifier.contextkey10152638
refterms.dateFOA2022-08-23T17:29:17Z
html.description.abstract<p>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.</p>
dc.identifier.submissionpathumccts_pubs/111
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology


Files in this item

Thumbnail
Name:
gkx133.pdf
Size:
2.475Mb
Format:
PDF

This item appears in the following Collection(s)

Show simple item record

© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
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.