Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications.
MicroRNAs (miRNAs) have important roles in various biological processes. miRNA cross-mapping is a prevalent phenomenon where miRNA sequence originating from one genomic region is mapped to another location. To have a better understanding of this phenomenon in the human genome, we performed a detaile...
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doaj-c62c29023e3b496980f7a64fffa15e902020-11-25T01:25:26ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-0165e2051710.1371/journal.pone.0020517Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications.Li GuoTingming LiangWanjun GuYuming XuYunfei BaiZuhong LuMicroRNAs (miRNAs) have important roles in various biological processes. miRNA cross-mapping is a prevalent phenomenon where miRNA sequence originating from one genomic region is mapped to another location. To have a better understanding of this phenomenon in the human genome, we performed a detailed analysis in this paper using public miRNA high-throughput sequencing data and all known human miRNAs. We observed widespread cross-mapping events between miRNA precursors (pre-miRNAs), other non-coding RNAs (ncRNAs) and the opposite strands of pre-miRNAs by analyzing the high-throughput sequencing data. Computational analysis on all known human miRNAs also confirmed that many of them could be involved in cross-mapping events. The processing or decay of both ncRNAs and pre-miRNA opposite strand transcripts may contribute to miRNA enrichment, although some might be miRNA-mimics due to miRNA mis-annotation. Comparing to canonical miRNAs, miRNAs involved in cross-mapping events between pre-miRNAs and other ncRNAs normally had shorter lengths (17-19 nt), lower prediction scores and were classified as pseudo miRNA precursors. Notably, 4.9% of all human miRNAs could be accurately mapped to the opposite strands of pre-miRNAs, which showed that both strands of the same genomic region had the potential to produce mature miRNAs and simultaneously implied some potential miRNA precursors. We proposed that the cross-mapping events are more complex than we previously thought. Sequence similarity between other ncRNAs and pre-miRNAs and the specific stem-loop structures of pre-miRNAs may provide evolutionary implications.http://europepmc.org/articles/PMC3102724?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Li Guo Tingming Liang Wanjun Gu Yuming Xu Yunfei Bai Zuhong Lu |
spellingShingle |
Li Guo Tingming Liang Wanjun Gu Yuming Xu Yunfei Bai Zuhong Lu Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. PLoS ONE |
author_facet |
Li Guo Tingming Liang Wanjun Gu Yuming Xu Yunfei Bai Zuhong Lu |
author_sort |
Li Guo |
title |
Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. |
title_short |
Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. |
title_full |
Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. |
title_fullStr |
Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. |
title_full_unstemmed |
Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. |
title_sort |
cross-mapping events in mirnas reveal potential mirna-mimics and evolutionary implications. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2011-01-01 |
description |
MicroRNAs (miRNAs) have important roles in various biological processes. miRNA cross-mapping is a prevalent phenomenon where miRNA sequence originating from one genomic region is mapped to another location. To have a better understanding of this phenomenon in the human genome, we performed a detailed analysis in this paper using public miRNA high-throughput sequencing data and all known human miRNAs. We observed widespread cross-mapping events between miRNA precursors (pre-miRNAs), other non-coding RNAs (ncRNAs) and the opposite strands of pre-miRNAs by analyzing the high-throughput sequencing data. Computational analysis on all known human miRNAs also confirmed that many of them could be involved in cross-mapping events. The processing or decay of both ncRNAs and pre-miRNA opposite strand transcripts may contribute to miRNA enrichment, although some might be miRNA-mimics due to miRNA mis-annotation. Comparing to canonical miRNAs, miRNAs involved in cross-mapping events between pre-miRNAs and other ncRNAs normally had shorter lengths (17-19 nt), lower prediction scores and were classified as pseudo miRNA precursors. Notably, 4.9% of all human miRNAs could be accurately mapped to the opposite strands of pre-miRNAs, which showed that both strands of the same genomic region had the potential to produce mature miRNAs and simultaneously implied some potential miRNA precursors. We proposed that the cross-mapping events are more complex than we previously thought. Sequence similarity between other ncRNAs and pre-miRNAs and the specific stem-loop structures of pre-miRNAs may provide evolutionary implications. |
url |
http://europepmc.org/articles/PMC3102724?pdf=render |
work_keys_str_mv |
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