publication . Article . 2017

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

Shaked Afik; Xiaopeng Zhu; Sabah Kadri;
Open Access English
  • Published: 01 Feb 2017 Journal: Nucleic Acids Research, volume 45, issue 11, pages e95-e95 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press
  • Country: United States
Abstract
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...
Subjects
free text keywords: Methods Online, Genetics
Funded by
NIH| University of Massachusetts Center for Clinical and Translational Science
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1UL1TR001453-01
  • Funding stream: NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES
,
NIH| Electrophysiology & Animal Behavior (EAB) Core
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U54HD082013-02
  • Funding stream: EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT
,
EC| Brain circRNAs
Project
Brain circRNAs
Rounding the circle: Unravelling the biogenesis, function and mechanism of action of circRNAs in the Drosophila brain.
  • Funder: European Commission (EC)
  • Project Code: 647989
  • Funding stream: H2020 | ERC | ERC-COG
,
NIH| Rules of gene expression modeled on human dendritic cell response to pathogens
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HG007910-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
77 references, page 1 of 6

1.Yosef N., Regev A.Impulse control: temporal dynamics in gene transcription. Cell. 2011; 144:886–896.21414481 [OpenAIRE] [PubMed]

2.Moore M.J.From birth to death: the complex lives of eukaryotic mRNAs. Science. 2005; 309:1514–1518.16141059 [PubMed]

3.Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C.The transcriptional landscape of the mammalian genome. Science. 2005; 309:1559–1563.16141072 [OpenAIRE] [PubMed]

4.Davuluri R. V, Suzuki Y., Sugano S., Plass C., Huang T.H.-M.The functional consequences of alternative promoter use in mammalian genomes. Trends Genet.2008; 24:167–177.18329129 [OpenAIRE] [PubMed]

5.Elkon R., Ugalde A.P., Agami R.Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet.2013; 14:496–506.23774734 [OpenAIRE] [PubMed]

6.de Klerk E., ’t Hoen P.A.C.Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. Trends Genet.2015; 31:128–139.25648499 [OpenAIRE] [PubMed]

7.Zhang Z., Dietrich F.S.Mapping of transcription start sites in Saccharomyces cerevisiae using 5΄ SAGE. Nucleic Acids Res.2005; 33:2838–2851.15905473 [OpenAIRE] [PubMed]

8.Ni T., Corcoran D.L., Rach E.A., Song S., Spana E.P., Gao Y., Ohler U., Zhu J.A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat. Methods. 2010; 7:521–527.20495556 [OpenAIRE] [PubMed]

9.Ozsolak F., Kapranov P., Foissac S., Kim S.W., Fishilevich E., Monaghan A.P., John B., Milos P.M.Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell. 2010; 143:1018–1029.21145465 [OpenAIRE] [PubMed]

10.Plessy C., Bertin N., Takahashi H., Simone R., Salimullah M., Lassmann T., Vitezic M., Severin J., Olivarius S., Lazarevic D.Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat. Methods. 2010; 7:528–534.20543846 [OpenAIRE] [PubMed]

11.Fu Y., Sun Y., Li Y., Li J., Rao X., Chen C., Xu A.Differential genome-wide profiling of tandem 3΄ UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res.2011; 21:741–747.21474764 [OpenAIRE] [PubMed]

12.Kanamori-Katayama M., Itoh M., Kawaji H., Lassmann T., Katayama S., Kojima M., Bertin N., Kaiho A., Ninomiya N., Daub C.O.Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res.2011; 21:1150–1159.21596820 [OpenAIRE] [PubMed]

13.Shepard P.J., Choi E.A., Lu J., Flanagan L.A., Hertel K.J., Shi Y.Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA. 2011; 17:761–772.21343387 [OpenAIRE] [PubMed]

14.Haenni S., Ji Z., Hoque M., Rust N., Sharpe H., Eberhard R., Browne C., Hengartner M.O., Mellor J., Tian B.Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3΄-end-seq. Nucleic Acids Res.2012; 40:6304–6318.22467213 [OpenAIRE] [PubMed]

15.Smibert P., Miura P., Westholm J.O., Shenker S., May G., Duff M.O., Zhang D., Eads B.D., Carlson J., Brown J.B.Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep.2012; 1:277–289.22685694 [OpenAIRE] [PubMed]

77 references, page 1 of 6
Abstract
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...
Subjects
free text keywords: Methods Online, Genetics
Funded by
NIH| University of Massachusetts Center for Clinical and Translational Science
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1UL1TR001453-01
  • Funding stream: NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES
,
NIH| Electrophysiology & Animal Behavior (EAB) Core
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U54HD082013-02
  • Funding stream: EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT
,
EC| Brain circRNAs
Project
Brain circRNAs
Rounding the circle: Unravelling the biogenesis, function and mechanism of action of circRNAs in the Drosophila brain.
  • Funder: European Commission (EC)
  • Project Code: 647989
  • Funding stream: H2020 | ERC | ERC-COG
,
NIH| Rules of gene expression modeled on human dendritic cell response to pathogens
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HG007910-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
77 references, page 1 of 6

1.Yosef N., Regev A.Impulse control: temporal dynamics in gene transcription. Cell. 2011; 144:886–896.21414481 [OpenAIRE] [PubMed]

2.Moore M.J.From birth to death: the complex lives of eukaryotic mRNAs. Science. 2005; 309:1514–1518.16141059 [PubMed]

3.Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C.The transcriptional landscape of the mammalian genome. Science. 2005; 309:1559–1563.16141072 [OpenAIRE] [PubMed]

4.Davuluri R. V, Suzuki Y., Sugano S., Plass C., Huang T.H.-M.The functional consequences of alternative promoter use in mammalian genomes. Trends Genet.2008; 24:167–177.18329129 [OpenAIRE] [PubMed]

5.Elkon R., Ugalde A.P., Agami R.Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet.2013; 14:496–506.23774734 [OpenAIRE] [PubMed]

6.de Klerk E., ’t Hoen P.A.C.Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. Trends Genet.2015; 31:128–139.25648499 [OpenAIRE] [PubMed]

7.Zhang Z., Dietrich F.S.Mapping of transcription start sites in Saccharomyces cerevisiae using 5΄ SAGE. Nucleic Acids Res.2005; 33:2838–2851.15905473 [OpenAIRE] [PubMed]

8.Ni T., Corcoran D.L., Rach E.A., Song S., Spana E.P., Gao Y., Ohler U., Zhu J.A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat. Methods. 2010; 7:521–527.20495556 [OpenAIRE] [PubMed]

9.Ozsolak F., Kapranov P., Foissac S., Kim S.W., Fishilevich E., Monaghan A.P., John B., Milos P.M.Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell. 2010; 143:1018–1029.21145465 [OpenAIRE] [PubMed]

10.Plessy C., Bertin N., Takahashi H., Simone R., Salimullah M., Lassmann T., Vitezic M., Severin J., Olivarius S., Lazarevic D.Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat. Methods. 2010; 7:528–534.20543846 [OpenAIRE] [PubMed]

11.Fu Y., Sun Y., Li Y., Li J., Rao X., Chen C., Xu A.Differential genome-wide profiling of tandem 3΄ UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res.2011; 21:741–747.21474764 [OpenAIRE] [PubMed]

12.Kanamori-Katayama M., Itoh M., Kawaji H., Lassmann T., Katayama S., Kojima M., Bertin N., Kaiho A., Ninomiya N., Daub C.O.Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res.2011; 21:1150–1159.21596820 [OpenAIRE] [PubMed]

13.Shepard P.J., Choi E.A., Lu J., Flanagan L.A., Hertel K.J., Shi Y.Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA. 2011; 17:761–772.21343387 [OpenAIRE] [PubMed]

14.Haenni S., Ji Z., Hoque M., Rust N., Sharpe H., Eberhard R., Browne C., Hengartner M.O., Mellor J., Tian B.Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3΄-end-seq. Nucleic Acids Res.2012; 40:6304–6318.22467213 [OpenAIRE] [PubMed]

15.Smibert P., Miura P., Westholm J.O., Shenker S., May G., Duff M.O., Zhang D., Eads B.D., Carlson J., Brown J.B.Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep.2012; 1:277–289.22685694 [OpenAIRE] [PubMed]

77 references, page 1 of 6
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