Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells
Introduction. Small noncoding RNAs have important regulatory functions in different cell pathways. It is believed that most of them mainly play role in gene post-transcriptional regulation in the cytoplasm. Recent evidence suggests miRNA and siRNA activity in the nucleus. Here, we show distinct geno...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2012-01-01
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| Series: | International Journal of Cell Biology |
| Online Access: | http://dx.doi.org/10.1155/2012/672462 |
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| _version_ | 1832562795691900928 |
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| author | Beibei Chen Bo Zhang Huaxia Luo Jiao Yuan Geir Skogerbø Runsheng Chen |
| author_facet | Beibei Chen Bo Zhang Huaxia Luo Jiao Yuan Geir Skogerbø Runsheng Chen |
| author_sort | Beibei Chen |
| collection | DOAJ |
| description | Introduction. Small noncoding RNAs have important regulatory functions in different cell pathways. It is believed that most of them mainly play role in gene post-transcriptional regulation in the cytoplasm. Recent evidence suggests miRNA and siRNA activity in the nucleus. Here, we show distinct genome-wide sub-cellular localization distribution profiles of small noncoding RNAs in human breast cancer cells. Methods. We separated breast cancer cell nuclei from cytoplasm, and identified small RNA sequences using a high-throughput sequencing platform. To determine the relationship between miRNA sub-cellular distribution and cancer progression, we used microarray analysis to examine the miRNA expression levels in nucleus and cytoplasm of three human cell lines, one normal breast cell line and two breast cancer cell lines. Logistic regression and SVM were used for further analysis. Results. The sub-cellular distribution of small noncoding RNAs shows that numerous miRNAs and their isoforms (isomiR) not only locate to the cytoplasm but also appeare in the nucleus. Subsequent microarray analyses indicated that the miRNA nuclear-cytoplasmic-ratio is a significant characteristic of different cancer cell lines. Conclusions. Our results indicate that the sub-cellular distribution is important for miRNA function, and that the characterization of the small RNAs sub-cellular localizome may contribute to cancer research and diagnosis. |
| format | Article |
| id | doaj-art-25df0ace177445b48e153f0a68ac16af |
| institution | Kabale University |
| issn | 1687-8876 1687-8884 |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Cell Biology |
| spelling | doaj-art-25df0ace177445b48e153f0a68ac16af2025-02-03T01:21:48ZengWileyInternational Journal of Cell Biology1687-88761687-88842012-01-01201210.1155/2012/672462672462Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer CellsBeibei Chen0Bo Zhang1Huaxia Luo2Jiao Yuan3Geir Skogerbø4Runsheng Chen5Laboratory of Bioinformation and Noncoding RNA and Center for Systems Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ChinaLaboratory of Bioinformation and Noncoding RNA and Center for Systems Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ChinaLaboratory of Bioinformation and Noncoding RNA and Center for Systems Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ChinaLaboratory of Bioinformation and Noncoding RNA and Center for Systems Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ChinaLaboratory of Bioinformation and Noncoding RNA and Center for Systems Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ChinaLaboratory of Bioinformation and Noncoding RNA and Center for Systems Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, ChinaIntroduction. Small noncoding RNAs have important regulatory functions in different cell pathways. It is believed that most of them mainly play role in gene post-transcriptional regulation in the cytoplasm. Recent evidence suggests miRNA and siRNA activity in the nucleus. Here, we show distinct genome-wide sub-cellular localization distribution profiles of small noncoding RNAs in human breast cancer cells. Methods. We separated breast cancer cell nuclei from cytoplasm, and identified small RNA sequences using a high-throughput sequencing platform. To determine the relationship between miRNA sub-cellular distribution and cancer progression, we used microarray analysis to examine the miRNA expression levels in nucleus and cytoplasm of three human cell lines, one normal breast cell line and two breast cancer cell lines. Logistic regression and SVM were used for further analysis. Results. The sub-cellular distribution of small noncoding RNAs shows that numerous miRNAs and their isoforms (isomiR) not only locate to the cytoplasm but also appeare in the nucleus. Subsequent microarray analyses indicated that the miRNA nuclear-cytoplasmic-ratio is a significant characteristic of different cancer cell lines. Conclusions. Our results indicate that the sub-cellular distribution is important for miRNA function, and that the characterization of the small RNAs sub-cellular localizome may contribute to cancer research and diagnosis.http://dx.doi.org/10.1155/2012/672462 |
| spellingShingle | Beibei Chen Bo Zhang Huaxia Luo Jiao Yuan Geir Skogerbø Runsheng Chen Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells International Journal of Cell Biology |
| title | Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells |
| title_full | Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells |
| title_fullStr | Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells |
| title_full_unstemmed | Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells |
| title_short | Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells |
| title_sort | distinct microrna subcellular size and expression patterns in human cancer cells |
| url | http://dx.doi.org/10.1155/2012/672462 |
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