Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. elegans and Drosophila
MicroRNAs (miRNAs) are a class of 20 to 23 nucleotide small RNAs that regulate gene expression post-transcriptionally in animals and plants. Annotation of miRNAs by the miRBase database has largely relied on computational approaches. As a result, many miRBase entries lack experimental validation, an...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2011-05-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00025/full |
| _version_ | 1818036503208525824 |
|---|---|
| author | Xiangfeng eWang Xiangfeng eWang Shirley eLiu |
| author_facet | Xiangfeng eWang Xiangfeng eWang Shirley eLiu |
| author_sort | Xiangfeng eWang |
| collection | DOAJ |
| description | MicroRNAs (miRNAs) are a class of 20 to 23 nucleotide small RNAs that regulate gene expression post-transcriptionally in animals and plants. Annotation of miRNAs by the miRBase database has largely relied on computational approaches. As a result, many miRBase entries lack experimental validation, and discrepancies between miRBase annotation and actual miRNA sequences are often observed. In this study, we integrated the small RNA sequencing (smRNA-seq) datasets in Caenorhabditis elegans and Drosophila melanogaster and devised an analytical pipeline coupled with detailed manual inspection to curate miRNA annotation systematically in miRBase. Our analysis reveals 19 (17.0%) and 51 (31.3%) miRNAs entries with detectable smRNA-seq reads have mature sequence discrepancies in C. elegans and D. melanogaster, respectively. These discrepancies frequently occur either for conserved miRNA families whose mature sequences were predicted according to their homologous counterparts in other species or for miRNAs whose precursor miRNA (pre-miRNA) hairpins produce an abundance of multiple miRNA isoforms or variants. Our analysis shows that while Drosophila pre-miRNAs, on average, produce less than 60% accurate mature miRNA reads in addition to their 5’ and 3’ variant isoforms, the precision of miRNA processing in C. elegans is much higher, at over 90%. Based on the revised miRNA sequences, we analyzed expression patterns of the more conserved (MC) and less conserved (LC) miRNAs and found that, whereas MC miRNAs are often co-expressed at multiple developmental stages, LC miRNAs tend to be expressed specifically at fewer stages. |
| first_indexed | 2024-12-10T07:11:59Z |
| format | Article |
| id | doaj.art-41dd387dc65d43e29f83b18ccb2c63e6 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-10T07:11:59Z |
| publishDate | 2011-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-41dd387dc65d43e29f83b18ccb2c63e62022-12-22T01:58:02ZengFrontiers Media S.A.Frontiers in Genetics1664-80212011-05-01210.3389/fgene.2011.0002511107Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. elegans and DrosophilaXiangfeng eWang0Xiangfeng eWang1Shirley eLiu2 Dana-Farber Cancer InstituteUniversity of Arizona Dana-Farber Cancer InstituteMicroRNAs (miRNAs) are a class of 20 to 23 nucleotide small RNAs that regulate gene expression post-transcriptionally in animals and plants. Annotation of miRNAs by the miRBase database has largely relied on computational approaches. As a result, many miRBase entries lack experimental validation, and discrepancies between miRBase annotation and actual miRNA sequences are often observed. In this study, we integrated the small RNA sequencing (smRNA-seq) datasets in Caenorhabditis elegans and Drosophila melanogaster and devised an analytical pipeline coupled with detailed manual inspection to curate miRNA annotation systematically in miRBase. Our analysis reveals 19 (17.0%) and 51 (31.3%) miRNAs entries with detectable smRNA-seq reads have mature sequence discrepancies in C. elegans and D. melanogaster, respectively. These discrepancies frequently occur either for conserved miRNA families whose mature sequences were predicted according to their homologous counterparts in other species or for miRNAs whose precursor miRNA (pre-miRNA) hairpins produce an abundance of multiple miRNA isoforms or variants. Our analysis shows that while Drosophila pre-miRNAs, on average, produce less than 60% accurate mature miRNA reads in addition to their 5’ and 3’ variant isoforms, the precision of miRNA processing in C. elegans is much higher, at over 90%. Based on the revised miRNA sequences, we analyzed expression patterns of the more conserved (MC) and less conserved (LC) miRNAs and found that, whereas MC miRNAs are often co-expressed at multiple developmental stages, LC miRNAs tend to be expressed specifically at fewer stages.http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00025/fullmicroRNADeep sequencingmiRBase curation |
| spellingShingle | Xiangfeng eWang Xiangfeng eWang Shirley eLiu Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. elegans and Drosophila Frontiers in Genetics microRNA Deep sequencing miRBase curation |
| title | Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. elegans and Drosophila |
| title_full | Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. elegans and Drosophila |
| title_fullStr | Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. elegans and Drosophila |
| title_full_unstemmed | Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. elegans and Drosophila |
| title_short | Systematic curation of miRBase annotation using integrated small RNA high-throughput sequencing data for C. elegans and Drosophila |
| title_sort | systematic curation of mirbase annotation using integrated small rna high throughput sequencing data for c elegans and drosophila |
| topic | microRNA Deep sequencing miRBase curation |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00025/full |
| work_keys_str_mv | AT xiangfengewang systematiccurationofmirbaseannotationusingintegratedsmallrnahighthroughputsequencingdataforcelegansanddrosophila AT xiangfengewang systematiccurationofmirbaseannotationusingintegratedsmallrnahighthroughputsequencingdataforcelegansanddrosophila AT shirleyeliu systematiccurationofmirbaseannotationusingintegratedsmallrnahighthroughputsequencingdataforcelegansanddrosophila |