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Fragmentation and Matching of Human MicroRNA Sequences in 3'utr
Michael S Parker1, Ambikaipakan Balasubramaniam2, Floyd R Sallee3
1Department of Microbiology and Molecular Cell Sciences, University of Memphis, Memphis TN 38152, United States.
Aims:
Definition of sense and antisense microRNA matches in 3'utr.
Background:
Matches of mature microRNAs (m-miRs) in human 3'utr could be traced to mutations producing fragments of original m-miR sequences without physical separation. (The m-miR matches in 5'utr and cds should be by far fewer, but could follow similar patterns).
Objective:
To ascertain if the sense and antisense m-miR fragments in 3'utr occur at similar or different levels.
Methods:
Frequency of sense and antisense m-miR matches in 3'utr was examined in the range of 7-22 nucleotides.
Results:
The fragmentation occurs at gene level by mutation within one of the paired m-miRs, which upon transcription results in increased interactive capability for both former pre-micro (premir) RNA stem partners. The non-mutated stem partner can persist in 3'utr sequences, as is apparent from significant presence of miR-619-5p and miR-5096 and some conservation of 20 other simian- specific m-miR sequences. However, most of m-mir sequences in 3'utr are extensively fragmented, with low preservation of long matches. In flanks of individual m-miR embeds the mutated pre-mir positions are to a degree defined specifically.
Conclusion:
The m-mir matches of various sizes in 3'utr apparently reflect accumulation, on a phylogenetic time scale, of in-sequence point mutations. Across human 3'utr this fragmentation is significantly less for evolutionarily recent human m-miRs that originate in simians compared to human m-miRs first appearing in lower primates, and especially to human m-miRs introduced in nonprimates.
Insights
Sense and antisense microRNA fragments in 3' untranslated regions (3' UTRs) arise from gene mutations. Fragmentation levels vary based on evolutionary origin, with newer microRNAs showing less fragmentation.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Mature microRNAs (m-miRs) can match in human 3' UTRs through mutations, generating fragments without physical separation.
- These fragments may arise from altered pre-microRNA (premir) stem structures due to mutations.
Purpose of the Study:
- To determine if sense and antisense m-miR fragments in 3' UTRs occur at similar or different frequencies.
- To analyze the size distribution of these fragmented m-miR sequences.
Main Methods:
- Examined the frequency of sense and antisense m-miR matches in 3' UTRs within a 7–22 nucleotide range.
- Analyzed fragmentation patterns and conservation of m-miR sequences.
Main Results:
- Fragmentation occurs at the gene level due to mutations in paired m-miRs, increasing interactive capabilities.
- Specific m-miRs like miR-619-5p and miR-5096 persist, alongside conserved simian-specific sequences, but most are fragmented.
- Fragmentation levels correlate with evolutionary history, with less fragmentation in recent human m-miRs.
Conclusions:
- Accumulation of point mutations on a phylogenetic timescale leads to fragmented m-miR matches in 3' UTRs.
- Evolutionary origin significantly impacts m-miR fragmentation in human 3' UTRs, with primate-derived m-miRs showing less fragmentation than non-primate ones.
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