Rfam 14.5 is live

March 18, 2021

We are happy to announce a new Rfam release, version 14.5, featuring 112 updated microRNA families and 10 families improved using the 3D structure information. Read on for details or explore 3,940 RNA families at rfam.org.

Updated microRNA families

As described in our most recent paper, we are in the process of synchronising microRNA families between Rfam and miRBase. In this release 112 of the existing microRNA families have been updated with new manually curated seed alignments from miRBase, new gathering thresholds, and new family members found in the Rfamseq sequence database. 

In total, 852 new microRNA families have been created (356 in release 14.3 and 496 in release 14.4) and 152 existing families have been updated (40 in release 14.3 and 112 in release 14.5). As the miRBase-Rfam synchronisation is about 50% complete, additional microRNA families will be made available in the upcoming releases. You can view a list of the 112 updated families or browse all 1,385 microRNA families on the Rfam website. 

Updating families using information from 3D structures

We are also in the process of reviewing the families with the experimentally determined 3D structures in order to compare the Rfam annotations with the 3D models. Our goal is to incorporate the 3D information into Rfam seed alignments as many families have been created before the corresponding 3D structures became available. We manually review each PDB structure, verify basepair annotations from matching PDBs, and obtain a more consistent consensus secondary structure model. 

In multiple cases we were able to add missing base pairs and pseudoknots. For example, in the SAM riboswitch (RF00162), we added two base pairs in the base of helix P2, corrected a basepair in P3 and added four basepairs in P4 (one in the base of the helix and three near the terminal loop). The updated consensus secondary structure presents a more accurate central core annotation with more structure in the four-way junction.

SAM riboswitch secondary structure before and after the updates

In another example, one base pair was added in P1 and another one in P3 of the SAM-I/IV variant riboswitch (RF01725). We also corrected a base pair in P3 and included a P4 stem loop that was not integrated before.

SAM-I/IV riboswitch secondary structure before and after the updates

The SAM-I/IV riboswitch is characterised by a similar SAM binding core conformation to that of the SAM riboswitch but it differs in the k-turn motif in P2 which is found in SAM riboswitches but not in SAM-I/IV. These two families also have different pseudoknots interactions, where SAM riboswitch forms a pseudoknot between a P2 loop and the stem of P3, while the SAM-I/IV riboswitch contains a pseudoknot between a P3 loop and the 5′ region.

The first 10 families updated with 3D information include:

  1. RF00162 – SAM riboswitch
  2. RF01725 – SAM-I/IV variant riboswitch
  3. RF00164 – Coronavirus 3’ stem-loop II-like motif (s2m)
  4. RF00013 – 6S / SsrS RNAP
  5. RF00003 – U1 spliceosomal RNA
  6. RF00015 – U4 spliceosomal RNA
  7. RF00442 – Guanidine-I riboswitch
  8. RF00027 – let-7 microRNA precursor
  9. RF01054 – preQ1-II (pre queuosine) riboswitch and
  10. RF02680 – preQ1-III riboswitch

We will continue reviewing the families with known 3D structure in future releases.

Other family updates

Initially reported by Aspegren et al. 2004, Class I (RF01414) and Class II (RF01571) RNAs were found in social amoeba Dictyostelium discoideum and later on investigated in more detail by Avesson et al. 2011. Now a new report from Kjellin et al. 2021 presents a comprehensive analysis of the Class I RNA genes in dictyostelid social amoebas. Based on this study, we updated the Dicty Class I RNA family RF01414 with a new seed alignment and removed the family RF01571, thus merging both families into one. We thank Dr Jonas Kjellin (Uppsala University) for suggesting this update.

Goodbye Ioanna!

Rfam 14.5 is the last release prepared by Dr Ioanna Kalvari who will be leaving the team at the end of March 2021. We would like to take the opportunity to thank Ioanna for her contributions over the last 5.5 years and wish her best of luck in the future!

Get in touch

As always, we would be very happy to hear from you if you have any feedback or suggestions for Rfam. Please feel free to email us or get in touch on Twitter

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