Rfam 14.6 is out

July 27, 2021

We are happy to announce a new release of Rfam (14.6) that includes 121 new microRNA families, a new ribozyme family, 8 new small RNA families found in Bacteroides, as well as 10 additional families with updated secondary structures using 3D structural information. Read on for more information or explore the data in Rfam.

New microRNA families

The new release includes 121 new microRNA families bringing the total number of microRNA families in Rfam to 1,506. This work is part of the ongoing collaboration with miRBase that aims to synchronise microRNAs across miRBase, Rfam, and RNAcentral. Browse Rfam microRNAs or find out more about the microRNA project.

We also resolved an issue with 6 microRNA families that were missing a covariance model on the website and in the FTP archive. Many thanks to Dr Christian Anthon (University of Copenhagen) for pointing out this problem!

Updating families using information from 3D structures

Following on from Rfam 14.5, we updated the secondary structure of 10 additional families with 3D information, including 6 riboswitches, 1 ribozyme, 1 telomerase, 1 localization element and 1 microRNA precursor.

In some families, the updated structure is substantially changed. For example, the central part of the flavin mononucleotide (FMN) riboswitch is now organised by several additional base pairs and two pseudoknots (pK). As a result, the updated structure is more compact and more accurately reflects the experimentally determined 3D structures.

Seven of the updated families include newly annotated pseudoknots, which is an important improvement that helps better model long-distance non-nested interactions. We will continue reviewing and updating the families with 3D structure in future releases. The full list of the updated families can be found in the table below.

FamilyPDB structuresNew  pK
RF00008 – Hammerhead ribozyme (type III)2QUS_A, 2QUS_B, 2QUW_A, 2QUW_B, 2QUW_C, 2QUW_D, 5DI2_A, 5DI4_A, 5DQK_A, 5EAO_A, 5EAQ_A1
RF00025 – Ciliate telomerase RNA6D6V2
RF00050 – FMN riboswitch (RFN element)3F2Q, 3F2T, 3F2W, 3F2X, 3F2Y, 3F3O 2
RF00059 – TPP riboswitch (THI element)2CKY_A, 2CKY_B, 2GDI_X, 2GDI_Y, 2HOJ_A, 2HOK_A, 2HOL_A, 2HOM_A, 2HOO_A, 2HOP_A, 3D2G_A, 3D2G_B, 3D2V_A, 3D2V_B, 3D2X_A, 3D2X_B, 3K0J_E, 3K0J_F, 4NYA_A, 4NYA_B, 4NYB_A, 4NYC_A, 4NYD_A, 4NYG_A
RF00207 – K10 transport/localisation element (TLS)2KE6, 2KUR, 2KUU, 2KU, 2KUW
RF00174 – Cobalamin riboswitch4GMA, 4GXY1
RF00380 – ykoK leader / M-box riboswitch2QBZ_X, 3PDR_X, 3PDR_A1
RF01689 – AdoCbl variant RNA4FRN_A, 4FRN_B, 4FRG_X, 4FRG_B1
RF01831 – THF riboswitch3SD3, 3SUH, 3SUX, 3SUY, 4LVV, 4LVW, 4LVX, 4LVY, 4LVZ, 4LW01
RF02095 – mir-2985-2 microRNA precursor2L3J

Hovlinc ribozyme

A recent paper by Chen Y et al. 2021 describes Hovlinc, a new type of self-cleaving ribozymes found in human and other hominids. Hovlinc was detected in a very long intergenic noncoding RNA in hominids (hominin vlincRNA-located) using a genome-wide approach designed to discover self-cleaving ribozymes. The functions of vlincRNA and the hovlinc ribozyme remain unclear. Hovlinc joins 3 known classes of small, self cleaving ribozymes found in human: (1) Mammalian CPEB3 ribozyme, (2) Hammerhead ribozyme and (3) B2 and ALU retrotransposons. We would like to thank Dr Fei Qi (Huaqiao University) for providing the Hovlinc alignment. View hovlinc family in Rfam.

New Bacteroides families

In a recent article by Ryan et al. 2020, the authors report a high-resolution transcriptome map of the model organism Bacteroides thetaiotaomicron, a common bacteria of the human gut. They recognize 269 non-coding RNAs (ncRNAs) candidates from which nine were validated. Eight of these ncRNAs were integrated as new families:

  1. RF04177 – Bacteroides sRNA BTnc201
  2. RF04178 – Bacteroides sRNA BTnc005
  3. RF04179 – Bacteroides sRNA BTnc049
  4. RF04180 – Bacteroides sRNA BTnc231
  5. RF04181 – rteR sRNA
  6. RF04182 – GibS sRNA
  7. RF04183 – Bacteroidales small SRP
  8. RF04184 – Bacteroides sRNA BTnc060

In addition, the RF01693 – Bacteroidales-1 family was renamed to 6S-Bacteroidales RNA. Bacteroidales-1 was first reported in a comparative genomics-based approach of genome and metagenome sequences from Weinberg et al. 2010. It was identified downstream of L20 ribosomal subunit genes in the order Bacteroidales. Ryan et al. 2020 report that this sRNA is a 6S RNA homolog in Bacteroides thetaiotaomicron. Rfam also has other two families of 6S RNA RF00013-6S/SsrS RNA and RF01685-6S-Flavo. We would like to thank Dr Lars Barquist (University of Würzburg) for providing the data.

Welcome to Emma!

A few weeks ago Emma Cooke joined the Rfam team as Software Developer and is already busy working on new features. Emma has studied Genetics and Software Engineering, and her previous roles have focused on release verification pipelines, software testing, and developing for cloud environments. Please join us in welcoming Emma to the Rfam community and stay tuned for new announcements based on her work.

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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