Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes

  • R. Taylor RabornEmail author
  • Volker P. Brendel
Part of the Methods in Molecular Biology book series (MIMB, volume 1858)


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., 2016) and TSRchitect (Raborn and Brendel, TSRchitect: promoter identification from large-scale TSS profiling data. R Bioconductor package version 1.8.0 [Online]. Available:, 2017), providing detailed instructions with the aim of taking the user from raw reads to processed results.

Key words

cis-regulatory regions Promoter architecture Transcription initiation Transcription start sites (TSSs) 



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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of BiologyIndiana UniversityBloomingtonUSA
  2. 2.School of Informatics and ComputingIndiana UniversityBloomingtonUSA

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