Assessing 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data

Maciej Szymanski; Wojciech M Karlowski

doi:10.18388/abp.2016_1367

Maciej Szymanski Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan
Wojciech M Karlowski Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan

DOI: https://doi.org/10.18388/abp.2016_1367

Keywords: 5S ribosomal RNA, RNA, next generation sequencing

Abstract

Ribosomal 5S rRNAs in eukaryotes are products of multigene families organized within clusters of repeating units. Accumulation of genomic data from a variety of organisms demonstrated that the potential 5S rRNA coding sequences show a large number of variants, often incompatible with folding into correct secondary structure. Here we present results of an analysis of the large set of short RNA sequences generated by next generation sequencing techniques to address the problem of heterogeneity of the 5S rRNA transcripts in Arabidopsis and identification of potentially functional rRNA-derived fragments.

References

Barciszewska MZ, Erdmann VA, Barciszewski J (1994) A new type of RNA editing. 5S ribosomal DNA transcripts are edited to mature 5S rRNA. Biochem Mol Biol Int 34: 437-448.

Baum BR, Edwards T, Johnson DA (2013) What does the 5S rRNA multigene family tell us about the origin of the annual Triticeae (Poaceae)? Genome 56: 245-266. doi: 10.1139/gen-2012-0195.

Baum BR, Johnson DA Baum BR, Johnson DA (1994) The molecular diversity of the 5S rRNA gene in barley (Hordeum vulgare). Genome 37: 992-998.

Bellavia D, Dimarco E, Naselli F, Caradonna F (2013) DNA-methylation dependent regulation of embryo-specific 5S ribosomal DNA cluster transcription in adult tissues of sea urchin Paracentrotus lividus. Genomics 102: 397-402. doi: 10.1016/j.ygeno.2013.08.001.

Campell BR, Song Y, Posch TE, Cullis CA, Town CD (1992) Sequence and organization of 5S ribosomal RNA-encoding genes of Arabidopsis thaliana. Gene 112: 225-228.

Ciganda M, Williams N (2011) Eukaryotic 5S rRNA biogenesis. Wiley Interdiscip Rev RNA 2: 523-533. doi: 10.1002/wrna.74

Cloix, C., Tutois, S., Yukawa, Y., Mathieu, O., Cuvillier, C., Espagnol, M.C., Picard, G. and Tourmente, S (2002) Analysis of the 5S RNA pool in Arabidopsis thaliana: RNAs are heterogeneous and only two of the genomic 5S loci produce mature 5S RNA. Genome Res 12: 132-144. doi: 10.1101/gr.181301

Dimarco E, Cascone E, Bellavia D, Caradonna F (2012) Functional variants of 5S rRNA in the ribosomes of common sea urchin Paracentrotus lividus. Gene 508: 21-25.

Ford PJ, Southern EM (1973) Different sequences for 5S RNA in kidney cells and ovaries of Xenopus laevis. Nat New Biol 241: 7-12.

Fransz P, Armstrong S, Alonso-Blanco C, Fisher T C, Torres-Ruiz R A, Jones G (1998) Cytogenetics for the model system Arabidopsis thaliana. Plant J 13: 867-876.

Hariharan N, Reddy PS, Padayatty JD (1987) 5S-rRNA genes in rice embryos. Plant Mol Biol 9: 443-451.

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.

Mathieu O, Jasencakova Z, Vaillant I, Gendrel AV, Colot V, Schubert I, Tourmente S (2003) Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis. Plant Cell 15: 2929-2939.

Murata M, Heslop-Harrison JS, Motoyoshi F (1997) Physical mapping of the 5S ribosomal RNA genes in Arabidopsis thaliana by multi-color fluorescence in situ hybridization with cosmid clones. Plant J 12: 31-37.

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD (2015) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res 43: D130-137. doi: 10.1093/nar/gku1063.

Peterson RC, Doering JL, Brown DD (1980) Characterization of two xenopus somatic 5S DNAs and one minor oocyte-specific 5S DNA. Cell 20: 131–141.

Sloan KE, Bohnsack MT, Watkins NJ (2013) The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress. Cell Rep 5: 237-247. doi: 10.1016/j.celrep.2013.08.049.

Szymanski M, Barciszewska M, Erdmann VA, Barciszewski J (1995) Are 5S ribosomal RNA primary transcripts edited? Biochem Mol Biol Int 37: 413-422.

Szymański M, Barciszewska MZ, Erdmann VA, Barciszewski J (2003) 5 S rRNA: structure and interactions. Biochem J 371: 641-651.

Szymanski M, Zielezinski A, Barciszewski J, Erdmann VA, Karlowski WM (2016) 5SRNAdb: an information resource for 5S ribosomal RNAs. Nucleic Acids Res 44:D180-3. doi: 10.1093/nar/gkv1081.

Vaillant I, Tutois S, Jasencakova Z, Douet J, Schubert I, Tourmente S (2008) Hypomethylation and hypermethylation of the tandem repetitive 5S rRNA genes in Arabidopsis. Plant J 54: 299-309. doi: 10.1111/j.1365-313X.2008.03413.x.