MINRbase: a Comprehensive Database of Nuclear- and Mitochondrial-ribosomal-RNA-derived Fragments (rRFs)

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2023 Oct 16

PMID 37843123

Authors

Venetia Pliatsika

Tess Cherlin

Phillipe Loher

Panagiotis Vlantis

Parth Nagarkar

Stepan Nersisyan

Isidore Rigoutsos

Affiliations

Soon will be listed here.

Abstract

We describe the Mitochondrial and Nuclear rRNA fragment database (MINRbase), a knowledge repository aimed at facilitating the study of ribosomal RNA-derived fragments (rRFs). MINRbase provides interactive access to the profiles of 130 238 expressed rRFs arising from the four human nuclear rRNAs (18S, 5.8S, 28S, 5S), two mitochondrial rRNAs (12S, 16S) or four spacers of 45S pre-rRNA. We compiled these profiles by analyzing 11 632 datasets, including the GEUVADIS and The Cancer Genome Atlas (TCGA) repositories. MINRbase offers a user-friendly interface that lets researchers issue complex queries based on one or more criteria, such as parental rRNA identity, nucleotide sequence, rRF minimum abundance and metadata keywords (e.g. tissue type, disease). A 'summary' page for each rRF provides a granular breakdown of its expression by tissue type, disease, sex, ancestry and other variables; it also allows users to create publication-ready plots at the click of a button. MINRbase has already allowed us to generate support for three novel observations: the internal spacers of 45S are prolific producers of abundant rRFs; many abundant rRFs straddle the known boundaries of rRNAs; rRF production is regimented and depends on 'personal attributes' (sex, ancestry) and 'context' (tissue type, tissue state, disease). MINRbase is available at https://cm.jefferson.edu/MINRbase/.

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References

Kumar P, Anaya J, Mudunuri S, Dutta A . Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 2014; 12:78. PMC: 4203973. DOI: 10.1186/s12915-014-0078-0. View

Ciganda M, Williams N . Eukaryotic 5S rRNA biogenesis. Wiley Interdiscip Rev RNA. 2011; 2(4):523-33. PMC: 3278907. DOI: 10.1002/wrna.74. View

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. 2020; 18(1):38. PMC: 7153239. DOI: 10.1186/s12915-020-0763-0. View

Loher P, Karathanasis N, Londin E, Bray P, Pliatsika V, Telonis A . IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets. Bioinformatics. 2021; 37(13):1828-1838. PMC: 8317110. DOI: 10.1093/bioinformatics/btab016. View

Loher P, Londin E, Rigoutsos I . IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies. Oncotarget. 2014; 5(18):8790-802. PMC: 4226722. DOI: 10.18632/oncotarget.2405. View

Guan L, Grigoriev A . Computational meta-analysis of ribosomal RNA fragments: potential targets and interaction mechanisms. Nucleic Acids Res. 2021; 49(7):4085-4103. PMC: 8053083. DOI: 10.1093/nar/gkab190. View

Moss T, Langlois F, Gagnon-Kugler T, Stefanovsky V . A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis. Cell Mol Life Sci. 2006; 64(1):29-49. PMC: 11136161. DOI: 10.1007/s00018-006-6278-1. View

Wei H, Zhou B, Zhang F, Tu Y, Hu Y, Zhang B . Profiling and identification of small rDNA-derived RNAs and their potential biological functions. PLoS One. 2013; 8(2):e56842. PMC: 3572043. DOI: 10.1371/journal.pone.0056842. View

Wilson D, Cate J . The structure and function of the eukaryotic ribosome. Cold Spring Harb Perspect Biol. 2012; 4(5). PMC: 3331703. DOI: 10.1101/cshperspect.a011536. View

10.

Yu S, Lemos B . A Portrait of Ribosomal DNA Contacts with Hi-C Reveals 5S and 45S rDNA Anchoring Points in the Folded Human Genome. Genome Biol Evol. 2016; 8(11):3545-3558. PMC: 5203791. DOI: 10.1093/gbe/evw257. View

11.

Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G . A draft human pangenome reference. Nature. 2023; 617(7960):312-324. PMC: 10172123. DOI: 10.1038/s41586-023-05896-x. View

12.

Goffova I, Fajkus J . The rDNA Loci-Intersections of Replication, Transcription, and Repair Pathways. Int J Mol Sci. 2021; 22(3). PMC: 7865372. DOI: 10.3390/ijms22031302. View

13.

Telonis A, Loher P, Magee R, Pliatsika V, Londin E, Kirino Y . tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities. Cancer Res. 2019; 79(12):3034-3049. PMC: 6571059. DOI: 10.1158/0008-5472.CAN-19-0789. View

14.

Telonis A, Loher P, Jing Y, Londin E, Rigoutsos I . Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity. Nucleic Acids Res. 2015; 43(19):9158-75. PMC: 4627084. DOI: 10.1093/nar/gkv922. View

15.

Anderson S, Bankier A, Barrell B, de Bruijn M, Coulson A, Drouin J . Sequence and organization of the human mitochondrial genome. Nature. 1981; 290(5806):457-65. DOI: 10.1038/290457a0. View

16.

Kuscu C, Kumar P, Kiran M, Su Z, Malik A, Dutta A . tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. RNA. 2018; 24(8):1093-1105. PMC: 6049499. DOI: 10.1261/rna.066126.118. View

17.

Telonis A, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y . Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015; 6(28):24797-822. PMC: 4694795. DOI: 10.18632/oncotarget.4695. View

18.

Zhou Y, Peng H, Cui Q, Zhou Y . tRFTar: Prediction of tRF-target gene interactions via systemic re-analysis of Argonaute CLIP-seq datasets. Methods. 2020; 187:57-67. DOI: 10.1016/j.ymeth.2020.10.006. View

19.

Magee R, Rigoutsos I . On the expanding roles of tRNA fragments in modulating cell behavior. Nucleic Acids Res. 2020; 48(17):9433-9448. PMC: 7515703. DOI: 10.1093/nar/gkaa657. View

20.

Telonis A, Magee R, Loher P, Chervoneva I, Londin E, Rigoutsos I . Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types. Nucleic Acids Res. 2017; 45(6):2973-2985. PMC: 5389567. DOI: 10.1093/nar/gkx082. View