RBP Footprint Challenge @ RNA Society 2021 Meeting

Call for participation: Community analysis to identify footprints of RNA-binding proteins from SHAPE data.  

Click here to register.

The organizers of the RNA Society meeting 2021 would like to solicit participation in a communal effort to identify and/or develop methods for identifying footprints of RNA-binding proteins from structure probing data. We encourage participation from experimentalists with interest in a specific protein and computational biologists interested in method development.  


Dr. Michelle Meyer, Boston College

Dr. Sharon Aviran, UC Davis



RNA binding proteins (RBP) play critical roles in post-transcriptional regulation. There are hundreds of RBPs in the human genome, and while a detailed molecular understanding of the interaction is available for some, in most cases our knowledge of the combination of sequence and secondary structure required for specific binding is insufficient for large-scale prediction of all binding sites. Yet, the availability of high-throughput data describing the RNA structurome (e.g., SHAPE data) and the region of RBP binding (e.g., CLIP data) continues to grow. One of the grand challenges currently faced by our community is the significant lag between such studies and the detailed analysis of these datasets required to derive hypotheses for experimental validation that in turn drive biological insight.


Select a protein of your choice and use publicly accessible structure probing data to identify signatures associated with protein binding. Use these patterns to detect and rank putative new protein binding sites. Compare your findings with CLIP-detected sites for your protein and rank the sites that are detected based on structure but not CLIP-detected. Submit your top five hits. 


Publicly accessible large-scale structure probing data. Several studies generating such data are listed below, but this list is not exhaustive.   

Corley et al., Mol Cell, 2020 (Pubmed: 32243832); Lu et al., Cell, 2016 (Pubmed: 27180905); Spitale et al. Nature 2015 (Pubmed:25799993); Sun et al. Nature Struct. Biol. (Pubmed: 30886404); Sun et al., Cell Res., 2021 (Pubmed: 33623109). 

One resource for identifying other datasets is Li et al. Nucl. Acids Res. 2020 (Pubmed: 33068412)


1.     You may use any publicly accessible CLIP data to map binding sites independently of your structure-based analysis.  

2.   You may study any large abundant RNA (e.g., viruses, lncRNAs, transcriptome-wide) and any organism.

3.     You may not use SHAPE-eCLIP datasets since these are already enriched in binding sites for specific proteins. Only non-enriched structural datasets are allowed.       

4.     You may not use other types of experimental data.

5.     You may integrate other types of expert-based knowledge (e.g., comparative genomics).

6.     We strongly encourage introduction of new analysis methods. However, you may use or adapt existing methods for your study.


1.     Top five predicted RBP binding sites not previously identified from CLIP studies.

2.     Description of analysis methodology including the structural probing and CLIP datasets utilized to make the predictions.


Methods and findings will be presented at the RNA Society meeting 2021. Predicted binding sites for individual proteins will be tested for protein binding using experimental assays by the Yeo lab and other labs.

Participants will be ranked based on method effectiveness (e.g., the number of validated hits), method creativity, and presentation of findings at the RNA Society meeting.

Expected outcome:

1.     Presentation of methods and predictions at the RNA Society meeting 2021. 

2.     Up to five most successful teams will be awarded a travel fellowship for the RNA Society meeting 2022. 

Timeline and participation:

March 19th, 2021 – Registration. 

You can choose to participate as a team leader or team member. Team leaders are expected to propose a protein of interest and can recruit up to 4 team members. Participants that do not indicate a preferred team leader will be assigned to existing teams and can request to be assigned together with one other participant.

March 26, 2021 – Teams and projects finalized

May 15, 2021 – Submit your method and findings (i.e., top hits)

May 29, 2021 – Present at the RNA Society meeting

June 2021 – April 2022 – Experimental validation

May 15, 2022 – Final decision

RNA Society meeting 2022 – Awards