Back to Search
Start Over
Computational Characterization of ncRNA Fragments in Various Tissues of the Brassica rapa Plant
- Source :
- Non-Coding RNA; Volume 3; Issue 2; Pages: 17, Non-Coding RNA
- Publication Year :
- 2017
- Publisher :
- Multidisciplinary Digital Publishing Institute, 2017.
-
Abstract
- Recently, a novel type of non-coding RNA (ncRNA), known as ncRNA fragments or ncRFs, has been characterised in various organisms, including plants. The biogenesis mechanism, function and abundance of ncRFs stemming from various ncRNAs are poorly understood, especially in plants. In this work, we have computationally analysed the composition of ncRNAs and the fragments that derive from them in various tissues of Brassica rapa plants, including leaves, meristem tissue, pollen, unfertilized and fertilized ova, embryo and endosperm. Detailed analysis of transfer RNA (tRNA) fragments (tRFs), ribosomal RNA (rRNA) fragments (rRFs), small nucleolar RNA (snoRNA) fragments (snoRFs) and small nuclear RNA (snRNA) fragments (snRFs) showed a predominance of tRFs, with the 26 nucleotides (nt) fraction being the largest. Mapping ncRF reads to full-length mature ncRNAs showed a strong bias for one or both termini. tRFs mapped predominantly to the 5′ end, whereas snRFs mapped to the 3′ end, suggesting that there may be specific biogenesis and retention mechanisms. In the case of tRFs, specific isoacceptors were enriched, including tRNAGly(UCC) and tRFAsp(GUC). The analysis showed that the processing of 26-nt tRF5′ occurred by cleavage at the last unpaired nucleotide of the loop between the D arm and the anticodon arm. Further support for the functionality of ncRFs comes from the analysis of binding between ncRFs and their potential targets. A higher average percentage of binding at the first half of fragments was observed, with the highest percentage being at 2–6 nt. To summarise, our analysis showed that ncRFs in B. rapa are abundantly produced in a tissue-specific manner, with bias toward a terminus, the bias toward the size of generated fragments and the bias toward the targeting of specific biological processes.
- Subjects :
- 0106 biological sciences
0301 basic medicine
ncRNA fragments
non-coding RNA
D arm
embryo
snoRF
unpollinated ovules
Biology
01 natural sciences
Biochemistry
Article
endosperm
03 medical and health sciences
pollinated ovules
Genetics
rRF
tRF
Small nucleolar RNA
Molecular Biology
snRF
apical meristem
Brassica rapa
RNA
Ribosomal RNA
ncRFs
Non-coding RNA
ncRNA
leaves
pollen
030104 developmental biology
Transfer RNA
Biogenesis
Small nuclear RNA
010606 plant biology & botany
Subjects
Details
- Language :
- English
- ISSN :
- 2311553X
- Database :
- OpenAIRE
- Journal :
- Non-Coding RNA; Volume 3; Issue 2; Pages: 17
- Accession number :
- edsair.doi.dedup.....0b6cbb9c8282a1632e47a7e14e0e7146
- Full Text :
- https://doi.org/10.3390/ncrna3020017