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Series GSE53252 Query DataSets for GSE53252
Status Public on Oct 24, 2015
Title 3’ and 5’ end modifications in plant microRNA post biogenesis: evidences from NGS of small RNAs [Oryza sativa]
Organism Oryza sativa
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Backgropund:In a major paradigm shift in the last decade, the knowledge about a whole class of non-coding RNAs known as miRNAs has emerged, which have proved these to be important regulators of a wide range of cellular processes by the way of modulation of gene expression. It is reported that some of these miRNAs are modified by addition or deletion of nucleotides at their ends, after biogenesis. However, the biogenesis and functions of these modifications are not well studied in eukaryotes, especially in plants. In this study, we examined the miRNA modifications in different tissues of the various plants, namely rice, tomato and Arabidopsis and identified some common features of such modifications.
Results:We have analyzed different aspects of miRNA modifications in plants. To achieve this end, we developed a PERL script to find the modifications in the sequences using small RNA deep sequencing data. The modification occurs in both mature and passenger (star) strands, as well as at both the 5' and 3' ends of miRNAs. Interestingly, we found a position-specific nucleotide biased modification, as evident by increased number of modification at the 5' end with the presence of Cytosine (nucleotide 'C') at the 3’end of the miRNA sequence. The level of modifications is not strictly dependent on the abundance of miRNA. Our study showed that the modification events are independent of plant species, tissue and physiological conditions. Our analysis also indicates that the RNAi enzyme, namely, the RNA dependent RNA polymerase 6 (RDR6) may not have any role in Arabidopsis miRNA modifications. Some of these modified miRNAs are bound to AGO1, suggesting their possible roles in biological processes.
Conclusions:This is a first report that reveals that 5' nucleotide additions are preferred for mature miRNA sequences with 3’ terminal ‘C’ nucleotide. Our analysis also indicates that the miRNAs modifications involving addition of nucleotides to the 5’ or 3’ end are independent of RDR6 activity and are not restricted by plant species, physiological conditions and tissue types. The results also indicate that such modifications might be important for biological processes.
Overall design Total 14 samples were analyzed, each in a pair of control and heat stress.
Contributor(s) Mukherjee SK, sanan-Mishra N, Gupta D, Saraf S
Citation(s) 26471296
Submission date Dec 12, 2013
Last update date May 15, 2019
Contact name Dinesh Gupta
Organization name ICGEB
Department Structural and Computational Biology
Lab Bioinformatics
Street address Aruna Asaf Ali Marg
City New Delhi
State/province Delhi
ZIP/Postal code 110067
Country India
Platforms (1)
GPL9316 Illumina Genome Analyzer II (Oryza sativa)
Samples (14)
GSM1288566 s5
GSM1288567 s6
GSM1288568 s8
This SubSeries is part of SuperSeries:
GSE53688 3' and 5' end modifications in plant microRNA post biogenesis: evidences from NGS of small RNAs
BioProject PRJNA232641
SRA SRP034747

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Supplementary file Size Download File type/resource
GSE53252_RAW.tar 413.2 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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