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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 08, 2015 |
| Title |
The Partitioning of RNAs in sperm |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
A diverse pool of RNAs remain encapsulated within the transcriptionally and translationally silent spermatozoon. These transcripts persist within the male gamete despite the dramatic reduction in cellular volume achieved through expulsion of the cytoplasm and quite possibly the nucleoplasm. The precise location of RNAs retained within the sperm cell remains largely unknown. However, early evidence suggested that many are embedded within the nucleus (1). To discern the global pattern of transcript compartmentalization in sperm, total RNA was extracted from whole mouse spermatozoa and detergent demembranated nuclei fractionated through a sucrose gradient. Isolated RNAs were subjected to RNA-sequencing (RNA-seq) and their abundance used to infer localization. Transcripts enriched in the unfractionated cells were related to the production and function of mitochondria and surprisingly, exosomes. The absence of these extracellular vesicles associated RNAs within the inner-nuclear compartment was suggestive of an origin other than sperm. This contributes to the growing evidence for sperm-bound exosomes rich in RNA. In comparison, the majority of the remaining sperm RNAs were associated with the nucleus. This included the abundant fragmented ribosomal transcripts which likely persist between the nuclear envelope and the perinuclear theca. The spermatozoal inner-nuclear compartment was also enriched in repetitive transcribed sequences. This included LINE elements and simple repeat sequences both of which have been shown to contribute to chromatin structure in other cell types suggesting that they may serve parallel roles in the spermatozoon.
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| Overall design |
RNA-seq analysis of whole mouse sperm and fractionated nuclei
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| Contributor(s) |
Johnson GD, Krawet SA |
| Citation(s) |
26071953, 26224537 |
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| Submission date |
Oct 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Graham Johnson |
| Organization name |
WSUSOM
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| Department |
CMMG
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| Lab |
Krawetz
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| Street address |
275 E. Hancock
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| City |
Detroit |
| State/province |
Michigan |
| ZIP/Postal code |
48201 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA265872 |
| SRA |
SRP049420 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE62874_Genomic_Coordinates_of_Novel_Transcripts.txt.gz |
28.0 Kb |
(ftp)(http) |
TXT |
| GSE62874_adj_w_subcount.txt.gz |
90.1 Kb |
(ftp)(http) |
TXT |
| GSE62874_nuc1_subcount.txt.gz |
97.7 Kb |
(ftp)(http) |
TXT |
| GSE62874_nuc2_subcount.txt.gz |
95.5 Kb |
(ftp)(http) |
TXT |
| GSE62874_unadjusted_RPKMs.txt.gz |
454.2 Kb |
(ftp)(http) |
TXT |
| GSE62874_w_subcount.txt.gz |
99.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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