Rfam release 14.7

December 21, 2021

We are happy to announce the latest Rfam release, version 14.7. The release includes 121 updated microRNA families, 4 new families, and a redesigned Rfam-PDB mapping pipeline that provides weekly updates as new RNA 3D structures become available. Read on to find out more or explore the data in Rfam.

Updated microRNA families

As part of the Rfam-miRBase synchronisation project discussed in the Rfam 14 paper, we continue revising microRNA families in Rfam using the data provided by miRBase. This release includes 121 updated families, such as mir-6 (RF00143) and mir-22 (RF00653). The following five microRNA families have been deleted from Rfam as the corresponding entries were removed from miRBase due to lack of evidence: mir-1937 (RF01942), mir-1280 (RF02013), mir-353 (RF00800), mir-720 (RF02002), and mir-2973 (RF02096). We would like to thank Lisanne Knol (University of Edinburgh) for bringing the first two of these families to our attention.

We estimate that the Rfam is now approximately 60% in sync with miRBase, with additional families to be released in future versions of Rfam. You can view the full list of updated families here or browse all microRNAs in Rfam

New families

The release includes two new hairpin ribozyme families Hairpin-meta1 (RF04190) and Hairpin-meta2 (RF04191) recently reported by the Weinberg lab. The hairpin ribozymes were discovered in metatranscriptome data and are proposed to occur in circular RNA genomes of as yet uncharacterised organisms. The new family joins the original Hairpin ribozyme family (RF00173).

Based on a recent paper we also created two additional bacterial families, the icd-II ncRNA motif (RF04189) and the carA ncRNA motif (RF04192). We would like to thank Ken Brewer (Yale University) for providing the data.

Weekly updates of PDB structures matching Rfam families

For many years Rfam maintained a mapping between Rfam families and experimentally determined RNA 3D structures available in PDB. However, this mapping lagged behind the weekly PDB updates as it was only updated with Rfam releases. 

The newly implemented pipeline analyses the data every week and makes the data available on the Rfam website and in a new section of the FTP archive that contains a preview of the upcoming release. The new, up-to-date mapping also improves the ability to search PDBe using Rfam and is a key part of an ongoing project to review all Rfam families with known 3D structures. 

Currently there are 127 Rfam families with experimentally determined RNA 3D structures in the PDB. For example, a recent paper describing how a viral RNA hijacks host machinery produced several structural models (7SAM, 7SC6, and 7SCQ) showing the pseudoknot of tRNA-like structure that are now mapped to Rfam family RF01084. Follow Rfam on Twitter to be the first to hear when new RNA families are linked to 3D structures.

Other improvements

  • We continue improving the Gene Ontology (GO) terms associated with Rfam families, and in this release 412 families have been updated to use the latest GO terms. Maintaining the GO terms up-to-date is important as Rfam is used for automatic assignment of GO terms in RNAcentral and other resources. The GO terms are shown in the Curation tab of each family and are also available in the rfam2go file. 
  • The Rfam.seed_tree.tar.gz file hosted on the FTP archive has been fixed. We would like to thank Christian Anthon (University of Copenhagen) for reporting the problem.

Get in touch

As always, we look forward to hearing from you if you have any feedback or suggestions for Rfam. Please feel free to email us or get in touch on Twitter.

Happy holidays from the Rfam team!

This is the first release produced by Emma Cooke and Blake Sweeney who have joined Rfam in the second half of 2021. The Rfam team wishes you a happy holiday season! We look forward to creating lots more families in 2022 and working towards the next major Rfam release, Rfam 15.0!

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