MINRbase v1.0 : a database for the interactive exploration of mitochondrial and nuclear rRNA fragments

07/01/2023 stats: 130,238 expressed rRFs | 11,632 datasets | 130,420 genomic instances

MINRbase¹ is a database of rRNA fragments (rRFs). You can use MINRbase to browse, filter, and visualize one or multiple rRFs from different rRNAs or potential parental genomic loci. To make the exploration of MINRbase easier several filters let you sub-select and personalize the information you are viewing. Similarly, we have designed several different ways to view its contents called vistas. In each vista, you are presented with more options to sort, peruse, and edit the results of your search.

In this page we will briefly introduce MINRbase. For more information please see publications.

What are rRNA fragments (rRFs)

The rRFs are fragments of rRNAs, the RNA of ribosomes.

The ribosomes are responsible for protein synthesis, a very important function for all organisms. They consist of rRNA and proteins. There are six different rRNAs in the human genome, 5S, 5.8S, 12S, 16S, 18S, and 28S². They are located on both the nuclear (5S, 5.8S, 18S, and 28S) and the mitochondrial (12S and 16S) genomes ^2,3. The ribosome is important in both health and disease due to it's regulatory role. A class of diseases called ribosomopathies that can lead to mutations that affect the encoding or assembly of ribosomal components inlcude a type of anemia (Diamond-Blackfan) and increased cancer susceptibility². Finally, 80% of the RNA in the cell is rRNAs. The rRNA versions included in MINRbase are listed in the following table.

Molecule	NCBI Reference
5S	NR_023374.1
12S	NR_137294.1
16S	NR_137295.1
45S pre-ribosomal N1 (RNA45SN1) *	NR_145819.1

* 45S contains 18S, 5.8S and 28S rRNA, see link for more details.

rRNA-derived fragments (rRFs) are short non-coding RNAs (ncRNAs) derived from both the nuclear and mitochondrial genome ⁴. In this publication we showed that rRF production, its identity and abundance depends on the sex and population each person belongs to. Please visit our website to learn more about rRNAs and rRFs.

The MINRbase filters

MINRbase currently contains eight filters. Hover over the search form below to read about the filters, and continue reading below for more details.

Genome: Currently only hg38 is available
Minimum RPM value: The minimum RPM value that an rRF ought to have in a sample so that the sample and rRF will be included in the results.
Reset: Click to bring the form to its default state.
Submit: Click to get the results of your selections.
Molecule: Select whether you are interested in only rRNAs or also the spacers of the 45s precursor.
rRNAs: Select one or multiple rRNAs and spacers.
Types: Select one or multiple rRF types.
Search by rRF: Type the nucleic sequence or the license-plate of the rRF of your preference.
Search by metadata: Type a keyword to view results coming only from that term. See the full list of metadata available.
Orientation / Internal Start-End: Select the orientation and the position of the rRF compared to the potential parental rRNA.

The MINRbase Vistas

MINRbase consists of five vistas. Each is designed to highlight a different aspect of rRFs. Switching from one to another can be seamlessly done using the internal links of each vista. They are the following:

Genomic loci Vista: This vista lists the potential genomic locations of the potential parental rRNAs of the rRFs.
RNA molecule Vista: This vista lists all rRFs that satisfy the filters selected together with their basic characteristics.
rRNA alignment Vista: This vista visualizes the rRFs that satisfy the filters on the potential parental rRNA, and the expression of the rRNA.
Expression Vista: This vista lists all samples that satisfy the filters for a given rRF.
Summary Vista: This vista provides detailed information of a given rRF and visualizes its expression patterns.

Downloads

In addition to MINRbase, we have made available the following tools/content that are relevant for those studying rRFs:

Download matrix containing rRF expression (RPM) across samples (130,238 rRFs x 11,632 datasets).
License Plates, an automated short RNA nomenclature.

References

Pliatsika, V, Cherlin, T, Loher, P, Vlantis, P, Nagarkar, P, Nersisyan, S, Rigoutsos, I. MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs). Nucleic Acids Res. 2023; :. doi: 10.1093/nar/gkad833. PubMed PMID:37843123.
Tafforeau, L, Zorbas, C, Langhendries, JL, Mullineux, ST, Stamatopoulou, V, Mullier, R, et al. The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of pre-rRNA processing factors. Molecular Cell. 2013;51:539-51. doi: 10.1016/j.molcel.2013.08.011.
De Silva, D, Tu, Y-T, Amunts, A, Fontanesi, F, Barrientos, A. Mitochondrial ribosome assembly in health and disease. Cell Cycle. 2015;14:2226-50. doi: 10.1080/15384101.2015.1053672.
Cherlin, T, Magee, R, Jing, Y, Pliatsika, V, Loher, P, Rigoutsos, I. Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner. BMC Biol 18, 38 (2020). doi: 10.1186/s12915-020-0763-0. PubMed PMID:32279660.