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
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
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
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
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
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
Lenhard B, Sandelin A, Carninci P (2012) Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet 13(4):233–245
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
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
Raborn RT, Spitze K, Brendel VP, Lynch M (2016) Promoter architecture and sex-specific gene expression in Daphnia pulex. Genetics 204(2):593–612
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
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
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
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
Cvetesic N, Lenhard B (2017) Core promoters across the genome. Nat Biotechnol 35(2):123–124
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
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
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
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
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)
ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74
Consortium E (2017) Rampage and cage data standards and processing pipeline [Online]. Available: https://www.encodeproject.org/rampage/
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
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
Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration (2011) The sequence read archive. Nucleic Acids Res 39(Database issue):D19–D21
Brendel VP, Raborn RT (2016) GoRAMPAGE- a workflow for promoter detection by 5’-Read mapping. https://github.com/BrendelGroup/GoRAMPAGE
Aronesty E (2013) Comparison of sequencing utility programs. Open Bioinform J 7(1):1–8
Lab H, FASTX Toolkit [Online]. Available: http://hannonlab.cshl.edu/fastx_toolkit/
Lassmann T (2015) TagDust2: a generic method to extract reads from sequencing data. BMC Bioinform 16(1):1
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
Dobin A, Gingeras TR (2016) Optimizing RNA-Seq mapping with STAR. In: Transcription factor regulatory networks. Springer, New York, pp 245–262
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
Lawrence M, Morgan M (2014) Scalable genomics with R and Bioconductor. Stat Sci 29(2):214–226
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
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
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
Pagès H (2016) BSgenome: infrastructure for biostrings-based genome data packages and support for efficient SNP representation. R package version 1.42.0
Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14(2):178–192
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
Tange O (2018) GNU parallel 2018, p 112. ISBN 978-1-387-50988-1
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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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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