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. 2015 Oct 27;10(10):e0138313.
doi: 10.1371/journal.pone.0138313. eCollection 2015.

A Database of microRNA Expression Patterns in Xenopus laevis

Ayisha Ahmed  1 , Nicole J Ward  1 , Simon Moxon  2 , Sara Lopez-Gomollon  1 , Camille Viaut  1 , Matthew L Tomlinson  1 , Ilya Patrushev  3 , Michael J Gilchrist  3 , Tamas Dalmay  1 , Dario Dotlic  1 , Andrea E Münsterberg  1 , Grant N Wheeler  1
Affiliations

A Database of microRNA Expression Patterns in Xenopus laevis

Ayisha Ahmed et al. PLoS One. .

Abstract

MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAs we have looked at show expression in the heart. Our results have been made freely available as a resource in both XenMARK and Xenbase.

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Conflict of interest statement

Competing Interests: Exiqon have provided some funding towards this project and were involved in the design of LNA probes. However, this does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Xenopus MicroRNAs show expression in a diverse number of developing organs and cell types.
Expression patterns of Xenopus laevis miRNAs are shown at varying stages. Arrowheads point to relevant expression. Views are lateral with anterior to left except (C, D and K) which is a ventral view with anterior to the left and (E) and (F) which are dorsal views with anterior to the bottom. MiR-34b, pancreas; miR-128, brain; miR-107, gut; miR-122, liver; miR-126, blood vessels; miR-200a, olfactory placodes; miR-455, liver; miR-30d, brain; miR-100, brain; miR-96, brain and olfactory placodes, miR-125, brain and gut, miR-200b, olfactory placode.
Fig 2
Fig 2. MicroRNA cluster 17–92 shows expression in different cell types of the developing eye.
(A) the miR-17-92 cluster. (B) WISH of stage 33 embryos showing the wholemount embryo and 30uM sections in the region of the eye of the miRNAs from the mir-17-92 cluster. Inset panels show a close up of the eye. L, Lens; NR, Neural Retina; RPE, Retinal Pigmented epithelium; LE, Lens Epithelia; SE, Surface Ectoderm.
Fig 3
Fig 3. Expression of Xenopus MicroRNAs in the developing somites.
Expression patterns of Xenopus laevis miRNA are shown at stage 33/34 both in wholemounts and transverse sections from the trunk. All embryos are lateral views with anterior to the left. (A) miRs-14, 17-5p, 499, 18b, 363-3p, 30a-5p, 302 and 220c show expression in the head and trunk. Sections show expression in the somites, neural tube and notochord. miR-499 and 302 also shows expression in the surface ectoderm. (B) miRs 1a, 1b and 206 show expression only in the trunk which is confined to the somites in sections. (C) miR-184 shows expression in the head and trunk. sections show expression in the nural tube and somites but bot the notochord. (D) mir-15b shows expression in the head and trunk. Sections show expression in the somites and dorsal neural tube. (E) mir133 family shows differential expression. Mir-133a and d show expression in the head and trunk and in the somites, neural tube and notochord. miR-133b and c show expression in the trunk and sections show only expression in the somites.
Fig 4
Fig 4. Identification and expression of novel Xenopus MicroRNAs.
(A) Predicted pre-miRNA structures of Xenopus laevis mir-GNW8, 9, 11, 12 and 13. The 5p and 3p miRNAs are highlighted on the predicted hairpin precursor with the most abundant sequence highlighted in green and the lower abundance sequence in pink (B) Normalised coverage plots showing the relative expression by number of reads of the 3p and 5p miRNAs from the libraries made from unfertilised egg, stage 7–8, stage 12, stages 18–20, stages 34–36 and stage 56 Xenopus laevis embryos. (C) Expression patterns of the novel miRNAs at stage 12/13 and stage 28/29.
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