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miRNA arm selection and isomiR distribution in gastric cancer.

Li SC, Liao YL, Ho MR, Tsai KW, Lai CH, Lin WC - BMC Genomics (2012)

Bottom Line: Arm selections and isomiR patterns are significantly varied in human cancers by using deep sequencing NGS data.Our results provided a novel research topic in miRNA regulation study.With advanced bioinformatics and molecular biology studies, more robust conclusions and insight into miRNA regulation can be achieved in the near future.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan.

ABSTRACT

Background: MicroRNAs (miRNAs) are small non-protein-coding RNAs. miRNA genes need several biogenesis steps to form function miRNAs. However, the precise mechanism and biology involved in the mature miRNA molecules are not clearly investigated. In this study, we conducted in-depth analyses to examine the arm selection and isomiRs using NGS platform.

Methods: We sequenced small RNAs from one pair of normal and gastric tumor tissues with Solexa platform. By analyzing the NGS data, we quantified the expression profiles of miRNAs and isomiRs in gastric tissues. Then, we measured the expression ratios of 5p arm to 3p arm of the same pre-miRNAs. And, we used Kolmogorov-Smirnov (KS) test to examine isomiR pattern difference between tissues.

Results: Our result showed the 5p arm and 3p arm miRNA derived from the same pre-miRNAs have different tissue expression preference, one preferred normal tissue and the other preferred tumor tissue, which strongly implied that there could be other mechanism controlling mature miRNA selection in addition to the known hydrogen-bonding selection rule. Furthermore, by using the KS test, we demonstrated that some isomiR types preferentially occur in normal gastric tissue but other types prefer tumor gastric tissue.

Conclusions: Arm selections and isomiR patterns are significantly varied in human cancers by using deep sequencing NGS data. Our results provided a novel research topic in miRNA regulation study. With advanced bioinformatics and molecular biology studies, more robust conclusions and insight into miRNA regulation can be achieved in the near future.

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Related in: MedlinePlus

The expression ratios of 5p arm miRNA to 3p arm miRNA. Several pre-miRNAs have significantly different ratios, demonstrating the arm selection preferences within the pre-miRNAs are significantly different between gastric normal and gastric tumor tissue.
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Figure 3: The expression ratios of 5p arm miRNA to 3p arm miRNA. Several pre-miRNAs have significantly different ratios, demonstrating the arm selection preferences within the pre-miRNAs are significantly different between gastric normal and gastric tumor tissue.

Mentions: By an empirical criterion of fold change difference larger than three, 36 out of 166 examined pre-miRNAs show different expression ratios of 5p to 3p in normal and tumor gastric tissue. As shown in Figure 3, several pre-miRNAs have significantly different ratios, demonstrating that the arm selection preferences within the pre-miRNAs are significantly different between gastric normal and gastric tumor tissue. For more detailed examination, we listed the information of the 36 significant pre-miRNAs in Table 3 and Additional file 5. As illustrated in Table 3, the fold change can even reach up to more than 20. Among the significant altered pre-miRNAs, hsa-mir-17 is a very interesting case, at which 5p arm has almost two times higher expression level than 3p arm in normal tissue. However, in tumor tissue, the 5p arm becomes about 1.4 times higher than in normal tissue but the 3p arm becomes 5.3 times lower, which results in the large difference in expression ratio of 5p to 3p. Even with large difference in expression ratio of 5p to 3p, the major arm of hsa-mir-17 in normal and tumor tissue is the same one, the 5p arm. In another interesting case of hsa-mir-423, the major arm and minor arm in normal tissue are individually 5p arm and 3p arm, obeying the annotation of miRBase. However, in tumor tissue, the major arm and minor arm are individually the 3p arm and 5p arm, totally reverse to miRBase annotation. In this case, the preferential arm in normal and tumor tissue shift from 5p to 3p.


miRNA arm selection and isomiR distribution in gastric cancer.

Li SC, Liao YL, Ho MR, Tsai KW, Lai CH, Lin WC - BMC Genomics (2012)

The expression ratios of 5p arm miRNA to 3p arm miRNA. Several pre-miRNAs have significantly different ratios, demonstrating the arm selection preferences within the pre-miRNAs are significantly different between gastric normal and gastric tumor tissue.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3303722&req=5

Figure 3: The expression ratios of 5p arm miRNA to 3p arm miRNA. Several pre-miRNAs have significantly different ratios, demonstrating the arm selection preferences within the pre-miRNAs are significantly different between gastric normal and gastric tumor tissue.
Mentions: By an empirical criterion of fold change difference larger than three, 36 out of 166 examined pre-miRNAs show different expression ratios of 5p to 3p in normal and tumor gastric tissue. As shown in Figure 3, several pre-miRNAs have significantly different ratios, demonstrating that the arm selection preferences within the pre-miRNAs are significantly different between gastric normal and gastric tumor tissue. For more detailed examination, we listed the information of the 36 significant pre-miRNAs in Table 3 and Additional file 5. As illustrated in Table 3, the fold change can even reach up to more than 20. Among the significant altered pre-miRNAs, hsa-mir-17 is a very interesting case, at which 5p arm has almost two times higher expression level than 3p arm in normal tissue. However, in tumor tissue, the 5p arm becomes about 1.4 times higher than in normal tissue but the 3p arm becomes 5.3 times lower, which results in the large difference in expression ratio of 5p to 3p. Even with large difference in expression ratio of 5p to 3p, the major arm of hsa-mir-17 in normal and tumor tissue is the same one, the 5p arm. In another interesting case of hsa-mir-423, the major arm and minor arm in normal tissue are individually 5p arm and 3p arm, obeying the annotation of miRBase. However, in tumor tissue, the major arm and minor arm are individually the 3p arm and 5p arm, totally reverse to miRBase annotation. In this case, the preferential arm in normal and tumor tissue shift from 5p to 3p.

Bottom Line: Arm selections and isomiR patterns are significantly varied in human cancers by using deep sequencing NGS data.Our results provided a novel research topic in miRNA regulation study.With advanced bioinformatics and molecular biology studies, more robust conclusions and insight into miRNA regulation can be achieved in the near future.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan.

ABSTRACT

Background: MicroRNAs (miRNAs) are small non-protein-coding RNAs. miRNA genes need several biogenesis steps to form function miRNAs. However, the precise mechanism and biology involved in the mature miRNA molecules are not clearly investigated. In this study, we conducted in-depth analyses to examine the arm selection and isomiRs using NGS platform.

Methods: We sequenced small RNAs from one pair of normal and gastric tumor tissues with Solexa platform. By analyzing the NGS data, we quantified the expression profiles of miRNAs and isomiRs in gastric tissues. Then, we measured the expression ratios of 5p arm to 3p arm of the same pre-miRNAs. And, we used Kolmogorov-Smirnov (KS) test to examine isomiR pattern difference between tissues.

Results: Our result showed the 5p arm and 3p arm miRNA derived from the same pre-miRNAs have different tissue expression preference, one preferred normal tissue and the other preferred tumor tissue, which strongly implied that there could be other mechanism controlling mature miRNA selection in addition to the known hydrogen-bonding selection rule. Furthermore, by using the KS test, we demonstrated that some isomiR types preferentially occur in normal gastric tissue but other types prefer tumor gastric tissue.

Conclusions: Arm selections and isomiR patterns are significantly varied in human cancers by using deep sequencing NGS data. Our results provided a novel research topic in miRNA regulation study. With advanced bioinformatics and molecular biology studies, more robust conclusions and insight into miRNA regulation can be achieved in the near future.

Show MeSH
Related in: MedlinePlus