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CRM Discovery Beyond Model Insects

  • Majid KazemianEmail author
  • Marc S. HalfonEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1858)

Abstract

Although the number of sequenced insect genomes numbers in the hundreds, little is known about gene regulatory sequences in any species other than the well-studied Drosophila melanogaster. We provide here a detailed protocol for using SCRMshaw, a computational method for predicting cis-regulatory modules (CRMs, also “enhancers”) in sequenced insect genomes. SCRMshaw is effective for CRM discovery throughout the range of holometabolous insects and potentially in even more diverged species, with true-positive prediction rates of 75% or better. Minimal requirements for using SCRMshaw are a genome sequence and training data in the form of known Drosophila CRMs; a comprehensive set of the latter can be obtained from the SCRMshaw download site. For basic applications, a user with only modest computational know-how can run SCRMshaw on a desktop computer. SCRMshaw can be run with a single, narrow set of training data to predict CRMs regulating a specific pattern of gene expression, or with multiple sets of training data covering a broad range of CRM activities to provide an initial rough regulatory annotation of a complete, newly-sequenced genome.

Key words

Non-model insects Regulatory genomics Transcriptional gene regulation Genome annotation Enhancer prediction 

Notes

Acknowledgments

We thank Kushal Suryamohan for comments on the manuscript. This work was supported by USDA grant 2012-67013-19361 (MSH) and NIH grant 5K22HL125593-02 (MK).

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Copyright information

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

Authors and Affiliations

  1. 1.Departments of Biochemistry and Computer SciencePurdue UniversityWest LafayetteUSA
  2. 2.Departments of Biochemistry, Biomedical Informatics, and Biological SciencesUniversity at Buffalo-State University of New YorkBuffaloUSA
  3. 3.NY State Center of Excellence in Bioinformatics and Life SciencesBuffaloUSA
  4. 4.Department of Molecular and Cellular Biology and Program in Cancer GeneticsRoswell Park Comprehensive Cancer CenterBuffaloUSA

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