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| Status |
Public on Feb 04, 2017 |
| Title |
Systematic Identification and Characterization of Long Non-coding RNAs in Mouse Mature Sperm |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Increasingly, studies have shown that mature spermatozoa contain many transcripts including mRNAs and miRNAs. However, the expression profile of long noncoding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Here, we used highly purified RNA to investigate lncRNA expression profiles in mouse mature sperm by stranded-specific RNA-seq. We identified 20907 known and 4088 novel lncRNAs transcripts, and the existence of intact lncRNAs was confirmed by RT-PCR and fluorescence in situ hybridization on two representative lncRNAs. Compared with testes, 2873 upregulated and 6629 downregulated lncRNAs and 1237 upregulated and 2513 downregulated mRNAs were identified in sperm. Based on the “Cis and Trans” RNA-RNA interaction principle, we found 1793 targeted coding genes of differently expressed lncRNAs. In terms of GO analysis, differentially expressed lncRNAs targeted genes mainly related to nucleic acid metabolic, protein modification, chromatin and histone modification, sperm function, and spermatogenesis. In contrast, differentially expressed transcripts of mRNAs were highly enriched for nucleic acid metabolic, spermatogenesis, sperm function, and chromatin organization. Furthermore, KEGG pathway analysis showed that the differentially expressed lncRNAs were involved in mRNA surveillance and AMPK signaling pathways. Besides these two pathways, RNA transport splicesome was another pathway incorporated with the differentially expressed mRNA. In summary, this study provides a preliminary database valuable for identifying lncRNAs critical in the late stage of spermatogenesis or important for sperm function regulation.
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| Overall design |
LncRNA profiles of mice (3-5 months) were generated by stranded-specific RNA-seq, using Illumina HiSeqTM 4000 with PE100.
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| Contributor(s) |
Zhang X, Zeng X |
| Citation(s) |
28291811 |
| Submission date |
Oct 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaoning Zhang |
| E-mail(s) |
zhangxiaoning@ncu.edu.cn
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| Organization name |
Nanchang University
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| Street address |
999 Xuefu R.D., Nanchang
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| City |
Nanchang |
| ZIP/Postal code |
330031 |
| Country |
China |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE88739 |
Dysregulation of long non-coding RNAs in mouse testis and sperm after exposure to cadmium |
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| Relations |
| BioProject |
PRJNA348417 |
| SRA |
SRP091539 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE88732_RAW.tar |
2.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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