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 gen...

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Main Authors:	Chen, Beibei, Zhang, Bo, Luo, Huaxia, Yuan, Jiao, Skogerbø, Geir, Chen, Runsheng
Format:	Online
Language:	English
Published:	Hindawi Publishing Corporation 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296955/

id	pubmed-3296955
recordtype	oai_dc
spelling	pubmed-32969552012-04-13 Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells Chen, Beibei Zhang, Bo Luo, Huaxia Yuan, Jiao Skogerbø, Geir Chen, Runsheng Research Article 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. Hindawi Publishing Corporation 2012 2012-02-12 /pmc/articles/PMC3296955/ /pubmed/22505932 http://dx.doi.org/10.1155/2012/672462 Text en Copyright © 2012 Beibei Chen et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Chen, Beibei Zhang, Bo Luo, Huaxia Yuan, Jiao Skogerbø, Geir Chen, Runsheng
spellingShingle	Chen, Beibei Zhang, Bo Luo, Huaxia Yuan, Jiao Skogerbø, Geir Chen, Runsheng Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells
author_facet	Chen, Beibei Zhang, Bo Luo, Huaxia Yuan, Jiao Skogerbø, Geir Chen, Runsheng
author_sort	Chen, Beibei
title	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_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_sort	distinct microrna subcellular size and expression patterns in human cancer cells
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.
publisher	Hindawi Publishing Corporation
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296955/
_version_	1611511438253228032

Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells

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