1
|
Ramachandran S, Krogh N, Jørgensen TE, Johansen SD, Nielsen H, Babiak I. The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2'- O-Me sites. RNA (NEW YORK, N.Y.) 2020; 26:1919-1934. [PMID: 32912962 PMCID: PMC7668251 DOI: 10.1261/rna.076760.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/06/2020] [Indexed: 06/11/2023]
Abstract
During zebrafish development, an early type of rRNA is gradually replaced by a late type that is substantially different in sequence. We applied RiboMeth-seq to rRNA from developmental stages for profiling of 2'-O-Me, to learn if changes in methylation pattern were a component of the shift. We compiled a catalog of 2'-O-Me sites and cognate box C/D guide RNAs comprising 98 high-confidence sites, including 10 sites that were not known from other vertebrates, one of which was specific to late-type rRNA. We identified a subset of sites that changed in methylation status during development and found that some of these could be explained by availability of their cognate SNORDs. Sites that changed during development were enriched in the novel sites revealed in zebrafish. We propose that the early type of rRNA is a specialized form and that its structure and ribose methylation pattern may be an adaptation to features of development, including translation of specific maternal mRNAs.
Collapse
Affiliation(s)
- Sowmya Ramachandran
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2400 Copenhagen, Denmark
| | - Tor Erik Jørgensen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Steinar Daae Johansen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Henrik Nielsen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2400 Copenhagen, Denmark
| | - Igor Babiak
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| |
Collapse
|
2
|
Molla-Herman A, Angelova MT, Ginestet M, Carré C, Antoniewski C, Huynh JR. tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation. Front Genet 2020; 11:518949. [PMID: 33193603 PMCID: PMC7586317 DOI: 10.3389/fgene.2020.518949] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/03/2020] [Indexed: 01/16/2023] Open
Abstract
tRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing to cell proliferation control. However, the analysis of tRFs presents specific challenges and their biogenesis is not well understood. They are very heterogeneous and highly modified by numerous post-transcriptional modifications. Here we describe a bioinformatic pipeline (tRFs-Galaxy) to study tRFs populations and shed light onto tRNA fragments biogenesis in Drosophila melanogaster. Indeed, we used small RNAs Illumina sequencing datasets extracted from wild type and mutant ovaries affecting two different highly conserved steps of tRNA biogenesis: 5'pre-tRNA processing (RNase-P subunit Rpp30) and tRNA 2'-O-methylation (dTrm7_34 and dTrm7_32). Using our pipeline, we show how defects in tRNA biogenesis affect nuclear and mitochondrial tRFs populations and other small non-coding RNAs biogenesis, such as small nucleolar RNAs (snoRNAs). This tRF analysis workflow will advance the current understanding of tRFs biogenesis, which is crucial to better comprehend tRFs roles and their implication in human pathology.
Collapse
Affiliation(s)
- Anahi Molla-Herman
- Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, France
| | - Margarita T. Angelova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Maud Ginestet
- Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Christophe Antoniewski
- ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Jean-René Huynh
- Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, France
| |
Collapse
|
3
|
Drosophila dyskerin is required for somatic stem cell homeostasis. Sci Rep 2017; 7:347. [PMID: 28337032 PMCID: PMC5428438 DOI: 10.1038/s41598-017-00446-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/27/2017] [Indexed: 02/07/2023] Open
Abstract
Drosophila represents an excellent model to dissect the roles played by the evolutionary conserved family of eukaryotic dyskerins. These multifunctional proteins are involved in the formation of H/ACA snoRNP and telomerase complexes, both involved in essential cellular tasks. Since fly telomere integrity is guaranteed by a different mechanism, we used this organism to investigate the specific role played by dyskerin in somatic stem cell maintenance. To this aim, we focussed on Drosophila midgut, a hierarchically organized and well characterized model for stemness analysis. Surprisingly, the ubiquitous loss of the protein uniquely affects the formation of the larval stem cell niches, without altering other midgut cell types. The number of adult midgut precursor stem cells is dramatically reduced, and this effect is not caused by premature differentiation and is cell-autonomous. Moreover, a few dispersed precursors found in the depleted midguts can maintain stem identity and the ability to divide asymmetrically, nor show cell-growth defects or undergo apoptosis. Instead, their loss is mainly specifically dependent on defective amplification. These studies establish a strict link between dyskerin and somatic stem cell maintenance in a telomerase-lacking organism, indicating that loss of stemness can be regarded as a conserved, telomerase-independent effect of dyskerin dysfunction.
Collapse
|
4
|
Patra Bhattacharya D, Canzler S, Kehr S, Hertel J, Grosse I, Stadler PF. Phylogenetic distribution of plant snoRNA families. BMC Genomics 2016; 17:969. [PMID: 27881081 PMCID: PMC5122169 DOI: 10.1186/s12864-016-3301-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022] Open
Abstract
Background Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. Results In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. Conclusions The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3301-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Deblina Patra Bhattacharya
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany.,Institut für Informatik, Halle (Saale), D-06120, Germany
| | - Sebastian Canzler
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany
| | - Jana Hertel
- Young Investigators Group Bioinformatics & Transcriptomics, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, D-04318, Germany
| | - Ivo Grosse
- Institut für Informatik, Halle (Saale), D-06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany. .,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany. .,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, D-04103, Germany. .,Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, Leipzig, A-1090, Germany. .,Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Copenhagen, Denmark. .,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. .,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.
| |
Collapse
|
5
|
Agrisani A, Tafer H, Stadler PF, Furia M. Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster. Noncoding RNA 2015; 1:139-150. [PMID: 29861420 PMCID: PMC5932544 DOI: 10.3390/ncrna1020139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/06/2015] [Accepted: 07/09/2015] [Indexed: 12/12/2022] Open
Abstract
A computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors antisense to well-known protein-coding genes, and four of the candidates are produced from exon-coding regions. Only a minority of the new sequences appears to have canonical target sites in ribosomal or small nuclear RNAs. Taken together, these evolutionary young, poorly conserved, and genomically atypical sequences point at a class of snoRNA-like transcripts with predominantly regulatory functions in the fruit fly genome.
Collapse
Affiliation(s)
- Alberto Agrisani
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, I-80126 Napoli, Italy.
| | - Hakim Tafer
- Institut für Biotechnologie, Universität für Bodenkultur, Muthgasse 18, A-1190 Wien, Austria.
| | - Peter F Stadler
- Bioinformatics Group, Department Computer Science, German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig; University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany.
- Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.
- Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.
| | - Maria Furia
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, I-80126 Napoli, Italy.
| |
Collapse
|