In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach.
Abstract: The importance of microRNAs at the post-transcriptional regulation level has recently been recognized in both animals and plants. We used the simple but effective sequential method of first Blasting known animal miRNAs against the horse genome and then using the located candidates to search for novel miRNAs by RNA folding method in the vicinity (+ -500 bp) of the candidates. Here, a total of 407 novel horse miRNA genes including 354 mature miRNAs were identified, of these, 75 miRNAs were grouped into 32 families based on seed sequence identity. MiRNA genes tend to be present as clusters in some chromosomes, and 146 miRNA genes accounted for 36% of the total were observed as part of polycistronic transcripts. Detailed analysis of sequence characteristics in novel horse and all previous known animal miRNAs were carried out. Our study will provide a reference point for further study on miRNAs identification in animals and improve the understanding of genome in horse.
Publication Date: 2009-05-03 PubMed ID: 19406225DOI: 10.1016/j.ygeno.2009.04.006Google Scholar: Lookup
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- Comparative Study
- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The research abstract discusses the use of an integrated computational method to detect and identify characteristics of 407 new microRNA (miRNA) genes in the genome of Equus caballus, or the horse. The study also provides information about the distribution, families, and sequence characteristics of these miRNAs, which contribute to the regulation of genes in the horse’s genome.
Research Methodology
- The researchers utilized a sequential computational method that begins with blasting known animal miRNAs against the horse genome. ‘Blasting’ here involves comparing the genetic sequences of known miRNAs from a host of different animals to the complete set of genes in the horse genome. This comparison helped researchers to locate potential matches or candidates for miRNAs in the horse genome.
- The located candidates were then used as a reference point to further search for new miRNAs. The study specifically focused on areas near these candidate sites (within + or – 500 base pairs).
- The final step in the process was conducting RNA folding method for prediction of secondary structures of the potential miRNA. This further aids in their identification. The folding and structural alignment occured in RNA programs where the on-screen results were manually inspected.
Key Findings
- A total of 407 new horse miRNA genes were identified in this study.
- Out of these, 354 are mature miRNAs and 75 miRNAs are grouped into 32 families based on seed sequence identity. Seed sequences are portions of RNA that interact directly with the target gene and are fundamental in aligning the miRNA to its target sites.
- The researchers found that miRNA genes tend to be present as clusters in some chromosomes.
- 146 miRNA genes, accounting for 36% of the total, were observed as part of polycistronic transcripts. Polycistronic transcription involves a single genetic event that leads to the creation of multiple separate proteins.
- A detailed analysis of sequence characteristics in these newly discovered horse miRNAs and all previously known animal miRNAs was carried out.
Significance of the Study
- This study contributes to the wider understanding of miRNAs, critical regulators of gene expression after transcription.
- The sheer number of novel miRNA genes identified in this study demonstrates the vast potential for miRNA discovery yet to be unlocked.
- The research provides a richer understanding of the horse genome and provides reference material for further study of miRNAs in animals.
Cite This Article
APA
Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He T, Zheng Y.
(2009).
In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach.
Genomics, 94(2), 125-131.
https://doi.org/10.1016/j.ygeno.2009.04.006 Publication
Researcher Affiliations
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
MeSH Terms
- Animals
- Chromosomes, Mammalian
- Computers
- Genome
- Horses / genetics
- MicroRNAs / genetics
- Transcription, Genetic
Citations
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