Rfam release 14.8

May 30, 2022

We are happy to announce the release of Rfam version 14.8. This release includes 48 updated and 25 new microRNA families; 10 families updated based on 3D structure annotations; 4 new families and updates to 5 existing families for Hepatitis C virus; a new xRNAs family from the Potato virus; and the integration of LitScan, a literature scanner powered by RNAcentral and Europe PubMed Central. Read on for details on these changes.

Updated microRNA families

Rfam, miRBase and RNAcentral have been working to synchronize miRNA families between all three resources. We are now happy to report that we have completed 77% of the current miRNAs families covering >1300 miRNAs of 1700 alignments provided to us by Profesor Sam Griffiths-Jones at miRBase. The 400 remaining families need an extended review process, and we will be working on their integration in future releases.

Summary of the miRBase and Rfam synchronisation project, we estimate it is 78% completed.

Families updated with 3D structure information

Rfam has been updating families using 3D structure information. This project aims to improve Rfam families through the addition of pseudoknotes, base pairs, and annotations of other structural elements by inspecting 3D structures. In this release we have updated 10 families:

  • Virus families:
    • RF00507-Coronavirus frameshifting stimulation element
    • RF01047-HBV RNA encapsidation signal epsilon
  • Riboswitches families:
    • RF01763-Guanidine-III riboswitch, also know as ykkC-III riboswitch
    • RF01734-Fluoride riboswitch
    • RF01704-Glutamine-II riboswitch, previously known as Downstream peptide
    • RF01750-ZMP/ZTP riboswitch
    • RF01739-Glutamine riboswitch
    • RF02683-NiCo riboswitch
    • RF01826-SAM-V riboswitch
  • Ribozyme family:

We have added pseudoknots to 7 of the 10 updated families and the updated secondary structure diagrams from 5 of these families are shown below.

Examples of families reviewed and updated with 3D information. Pseudoknot structures (pk) were added to each of these five families based on a review of the corresponding 3D structures.

New and updated families of Hepatitis C virus

In release 14.8 we have created 4 new families, updated 5 existing families, and deleted 4 virus families. These changes are the result of our ongoing collaboration between Profesor Manja Marz of the European Virus Bioinformatics Center and Rfam. The Marz group provided Rfam a curated alignment of representative sequences for the entire genome of Hepatitis C virus genome. We used this alignment to update, create or remove existing Rfam families. The new families we have created are summarized in a table below. We have deleted RF00469, which was merged into RF00260 during review. We have also deleted families from RF02585 to RF02588 which have no support in the genomic alignment. 

Rfam IDNameDescription
RF00061IRES_HCVHepatitis C virus internal ribosome entry site
RF00260HepC_CREHepatitis C virus (HCV) cis-acting replication element (CRE)
RF00620HCV_ARF_SLHepatitis C alternative reading frame stem-loop
RF00468HCV_SLVIIHepatitis C virus stem-loop VII
RF00481HCV_X3Hepatitis C virus 3’X element
RF04218HCV_5BSL1Hepatitis C virus stem-loop I
RF04219HCV_J750J750 non-coding RNA (containing SL761 and SL783)
RF04220HCV_SL588SL588 non-coding RNA
RF04221HCV_SL669SL669 non-coding RNA

As part of this project we have reviewed and updated Coronavirus, Flavivirus and HCV viruses families, and we are working on adding RNA families from other viruses, such as Filoviridae (e.g. Ebolavirus) and Rhabdoviridae (e.g. Rabies viruses).

xRNAs in Potato virus

We want to thank Professor Quentin Vicens for sharing the alignment of Potato leafroll virus exoribonuclease-resistant RNA (PLRV-xrRNA). PLRV-xrRNA is a non-coding RNA that blocks the progression of 5′ to 3′ exoribonuclease using only a folded RNA element, and this family is described in RF04222.

LitScan

RNAcentral has recently developed LitScan, a tool to automatically connect non-coding RNA sequences, genes and families to the literature that discusses them. In this release we have integrated the LitScan widget into Rfam. The widget is now shown in the new ‘Publications’ tab on all Rfam families.

Example of LitScan for mir-17 microRNA precursor family, publications can be sorted by citation, journal, year of publication and others.

Please reach out to us with feedback on the widget, or if you would like to use the LitScan widget on your site!

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