Documentation for HyperTRIBE

For source code please visit GitHub

About HyperTRIBE

HyperTRIBE is a technique used for the identification of the targets of RNA binding proteins (RBP) in vivo. This is an improved version of a previously developed technique called TRIBE (Targets of RNA-binding proteins Identified By Editing). HyperTRIBE couples an RBP to the catalytic domain of the Drosophila RNA editing enzyme ADAR and expresses the fusion protein in vivo. As the RBP-ADARcd (catalytic domain) fusion protein lacks the RNA recognition features of ADAR, the specificity of the RBP should determine the editing specificity of the fusion protein. RBP targets are marked with novel RNA editing events and identified by sequencing RNA. This repository provides the necessary computational pipeline needed to analyze these RNA sequencing libraries.

For more details please see:

1. Xu, W., Rahman, R., Rosbash, M. Mechanistic Implications of Enhanced Editing by a HyperTRIBE RNA-binding protein. RNA 24, 173-182 (2018). doi:10.1261/rna.064691.117
2. McMahon, A.C., Rahman, R., Jin, H., Shen, J.L., Fieldsend, A., Luo, W., Rosbash, M., TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins. Cell 165, 742-753 (2016). doi: 10.1016/j.cell.2016.03.007.

For previous version of this software (TRIBE), please visit GitHub

Contents:

• Installation
  • Software Dependencies (tested version)
  • Source Code
  • Install MySQL (MariaDB) database and Perl modules
  • Update Perl Scripts
  • Download Annotations and Genome Sequences
  • Update Shell Scripts
• Run
  • Optional: Download Test Datasets
  • 1. Trim and align sequence libraries to Genome
  • 2. Load alignment data to MySQL database
  • Optional: Confirm MySQL Tables contains the data
  • 3.A. Find RNA edit sites using gDNA-RNA approaches
  • 3.B. Find RNA edit sites using wtRNA-RNA approaches
  • 4. Post-processing of editing outputsOutputs
  • 5. Column descriptions for bedgraph output files
  • 6. Create list of Edited Transcripts
• Example Run
• MariaDB Set Up
  • Install MariaDB 10.x

Support

Please use Github issues to bring up any errors that occur with software.