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Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes

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Insect Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1858))

Abstract

Application of Transcription Start Site (TSS) profiling technologies, coupled with large-scale next-generation sequencing (NGS) has yielded valuable insights into the location, structure, and activity of promoters across diverse metazoan model systems. In insects, TSS profiling has been used to characterize the promoter architecture of Drosophila melanogaster (Hoskins et al., Genome Res 21(2):182–192, 2011) and subsequently was employed to reveal widespread transposon-driven alternative promoter usage in the fruit fly (Batut et al., Genome Res 23:169–180, 2012).

In this chapter we discuss the computational analysis of the experimental data derived from one of TSS profiling methods, RAMPAGE (RNA Annotation and Mapping of Promoters for Analysis of Gene Expression) that can be used for the precise, quantitative identification of promoters in insect genomes. We demonstrate this using the software tools GoRAMPAGE (Brendel and Raborn, GoRAMPAGE—A workflow for promoter detection by 5′-read mapping. https://github.com/BrendelGroup/GoRAMPAGE, 2016) and TSRchitect (Raborn and Brendel, TSRchitect: promoter identification from large-scale TSS profiling data. R Bioconductor package version 1.8.0 [Online]. Available: http://bioconductor.org/packages/release/bioc/html/TSRchitect.html, 2017), providing detailed instructions with the aim of taking the user from raw reads to processed results.

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References

  1. Kadonaga JT (2012) Perspectives on the RNA polymerase II core promoter. Wiley interdisciplinary reviews: developmental biology, vol 1(1). Wiley, New York, pp 40–51

    Article  Google Scholar 

  2. Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M et al (2006) CAGE: cap analysis of gene expression. Nat Methods 3(3):211–222

    Article  CAS  Google Scholar 

  3. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N et al (2005) The transcriptional landscape of the mammalian genome. Science (New York, NY) 309(5740):1559–1563

    Google Scholar 

  4. Hoskins RA, Hoskins RA, Landolin JM, Landolin JM, Brown JB, Brown JB et al (2011) Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res 21(2):182–192

    Article  Google Scholar 

  5. Rach EA, Yuan H-Y, Majoros WH, Tomancak P, Ohler U (2009) Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol 10(7):R73

    Article  Google Scholar 

  6. Lenhard B, Sandelin A, Carninci P (2012) Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet 13(4):233–245

    Article  CAS  Google Scholar 

  7. Ni T, Corcoran DL, Rach EA, Song S, Spana EP, Gao Y et al (2010) A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods 7(7):521–527

    Article  CAS  Google Scholar 

  8. Ohler U, Liao G-c, Niemann H, Rubin GM (2002) Computational analysis of core promoters in the Drosophila genome. Genome Biol 3(12):research0087.1–0087.12

    Article  Google Scholar 

  9. Raborn RT, Spitze K, Brendel VP, Lynch M (2016) Promoter architecture and sex-specific gene expression in Daphnia pulex. Genetics 204(2):593–612

    Article  CAS  Google Scholar 

  10. Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H et al (2013) Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res 23(11):1938–1950

    Article  CAS  Google Scholar 

  11. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J et al (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Gen 38(6):626–635

    Google Scholar 

  12. Mwangi S, Attardo G, Suzuki Y, Aksoy S, Christoffels A (2015) TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis. BMC Genomics 16(1):722

    Google Scholar 

  13. Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, Hashimoto S-i et al (2009) Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res 37(7):2249–2263

    Article  CAS  Google Scholar 

  14. Cvetesic N, Lenhard B (2017) Core promoters across the genome. Nat Biotechnol 35(2):123–124

    Article  CAS  Google Scholar 

  15. Batut PJ, Dobin A, Plessy C, Carninci P, Gingeras TR (2012) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res 23:169–180

    Article  Google Scholar 

  16. Batut PJ, Gingeras TR (2013) RAMPAGE: promoter activity profiling by paired-end sequencing of 5’-complete cDNAs. In: Ausubel FM et al (eds) Current protocols in molecular biology. Wiley, Hoboken, pp 25B.11.1–25B.11.16

    Google Scholar 

  17. Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T et al (2010) Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods 7(7):528–534

    Article  CAS  Google Scholar 

  18. Cumbie JS, Ivanchenko MG, Megraw M (2015) NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites. BMC Genomics 16(1):528

    Google Scholar 

  19. Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A et al (2014) Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. Plant cell 26(7):2746–2760 (2014)

    Article  CAS  Google Scholar 

  20. ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74

    Google Scholar 

  21. Consortium E (2017) Rampage and cage data standards and processing pipeline [Online]. Available: https://www.encodeproject.org/rampage/

  22. Merchant N, Lyons E, Goff S, Vaughn M, Ware D, Micklos D et al (2016) The iPlant collaborative: cyberinfrastructure for enabling data to discovery for the life sciences. PLoS Biol 14(1):e1002342

    Article  Google Scholar 

  23. Stewart CA, Cockerill TM, Foster I, Hancock D, Merchant N, Skidmore E et al (2015) Jetstream: a self-provisioned, scalable science and engineering cloud environment. In: Proceedings of the 2015 XSEDE conference: scientific advancements enabled by enhanced cyberinfrastructure. XSEDE ’15. ACM, New York, pp 29:1–29:8 [Online]. Available: https://doi.org/10.1145/2792745.2792774

  24. Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration (2011) The sequence read archive. Nucleic Acids Res 39(Database issue):D19–D21

    Google Scholar 

  25. Brendel VP, Raborn RT (2016) GoRAMPAGE- a workflow for promoter detection by 5’-Read mapping. https://github.com/BrendelGroup/GoRAMPAGE

  26. Aronesty E (2013) Comparison of sequencing utility programs. Open Bioinform J 7(1):1–8

    Article  Google Scholar 

  27. Lab H, FASTX Toolkit [Online]. Available: http://hannonlab.cshl.edu/fastx_toolkit/

  28. Lassmann T (2015) TagDust2: a generic method to extract reads from sequencing data. BMC Bioinform 16(1):1

    Google Scholar 

  29. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics (Oxford, England) 25(16):2078–2079

    Article  Google Scholar 

  30. Dobin A, Gingeras TR (2016) Optimizing RNA-Seq mapping with STAR. In: Transcription factor regulatory networks. Springer, New York, pp 245–262

    Google Scholar 

  31. R Core Team (2017) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna [Online]. Available: https://www.R-project.org

  32. Lawrence M, Morgan M (2014) Scalable genomics with R and Bioconductor. Stat Sci 29(2):214–226

    Article  Google Scholar 

  33. Raborn RT, Brendel V (2017) TSRchitect: promoter identification from large-scale TSS profiling data. r Bioconductor package version 1.0.0 [Online]. Available: http://bioconductor.org/packages/release/bioc/html/TSRchitect.html

  34. Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D et al (2016) Ensembl (2016). Nucleic Acids Res 44:D1, D710–D716 [Online]. Available: https://doi.org/10.1093/nar/gkv1157

    Article  Google Scholar 

  35. Haberle V, Forrest ARR, Hayashizaki Y, Carninci P, Lenhard B (2015) CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res 43(8):gkv054–e51

    Google Scholar 

  36. Pagès H (2016) BSgenome: infrastructure for biostrings-based genome data packages and support for efficient SNP representation. R package version 1.42.0

    Google Scholar 

  37. Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14(2):178–192

    Article  CAS  Google Scholar 

  38. Sayers EWE, Barrett TT, Benson DAD, Bolton EE, Bryant SHS, Canese KK et al (2012) Database resources of the national center for biotechnology information. Nucleic Acids Res 40(Database issue):D13–D25

    Article  CAS  Google Scholar 

  39. Tange O (2018) GNU parallel 2018, p 112. ISBN 978-1-387-50988-1

    Google Scholar 

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Acknowledgements

The authors would like to thank Philippe Batut for generous technical assistance with the RAMPAGE protocol, and to Nathan Keith for his help establishing the protocol in our laboratory. The authors are grateful to Thomas W. McCarthy for his help testing the code and providing editorial feedback.

Disclosure Declaration The authors declare that they have no competing interests.

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Authors and Affiliations

  1. Department of Biology, Indiana University, Bloomington, IN, USA

    R. Taylor Raborn & Volker P. Brendel

  2. School of Informatics and Computing, Indiana University, Bloomington, IN, USA

    Volker P. Brendel

Authors
  1. R. Taylor Raborn
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  2. Volker P. Brendel
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Corresponding author

Correspondence to R. Taylor Raborn .

Editor information

Editors and Affiliations

  1. Division of Biology, Kansas State University, Manhattan, NY, USA

    Susan J. Brown

  2. Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA

    Michael E. Pfrender

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Raborn, R.T., Brendel, V.P. (2019). Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes. In: Brown, S., Pfrender, M. (eds) Insect Genomics. Methods in Molecular Biology, vol 1858. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8775-7_9

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  • DOI: https://doi.org/10.1007/978-1-4939-8775-7_9

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8774-0

  • Online ISBN: 978-1-4939-8775-7

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