human-RBP-analysis

Project 2: Interaction of the SARS-CoV-2 genome with human RNA-binding proteins

Workflow:

1. Download a database of human RNA-binding proteins and their PWMs
2. Download the viral reference genome
3. Scan the viral genome for these PWMs.
4. Annotate potential RBP binding sites on the viral genome
5. Check for expression/activity of these RBPs in relevant cell types
6. Check whether any of the RBP binding sites are modified in different isolates of SARS-CoV-2
7. Check whether these RBP binding sites existed in closely related viruses, e.g. the bat coronavirus sequences similar to SARS-CoV-2.

Task tracker:

https://github.com/avantikalal/covid-gene-expression/projects/2

Data sources:

1. RBPDB, a database of RNA-binding proteins and PWMs: http://rbpdb.ccbr.utoronto.ca/index.php
2. SARS-CoV-2 reference genome: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512

Data download:

1. Download the reference genome for SARS-CoV-2 from NCBI: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.
2. Download data on human RNA-binding proteins from RBPDB: http://rbpdb.ccbr.utoronto.ca/downloads/RBPDB_v1.3.1_human_2012-11-21_TDT.zip. Unzip the downloaded directory to get the data tables.
3. Download PWMs (Position Weight Matrices) for these human RNA-binding proteins from RBPDB: http://rbpdb.ccbr.utoronto.ca/downloads/matrices_human.zip. This download contains both PWMs and PFMs. PWM files are in the PWMDir folder.

Identifying binding sites

See find_binding_sites.R for a basic script to find RBP-binding sites on the SARS-CoV-2 genome. To run this script you need to modify the first section with paths to your downloaded data files.

Requirements

The script is in R and uses the following libraries:

1. data.table
2. TFBSTools
3. seqinr
4. Biostrings

Dockerfile

A docker file with all of the R dependencies is available at hpobiolab/rbp-pwm-r

Output

sitesets.RData is the table of potential binding sites produced by find_binding_sites.R. To open this, type in an R terminal:

load("sitesets.RData")