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E-GEOD-62874 - The Partitioning of RNAs in sperm

Status
Released on 8 July 2015, last updated on 19 August 2015
Organism
Mus musculus
Samples (6)
Protocols (2)
Description
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. RNA-seq analysis of whole mouse sperm and fractionated nuclei
Experiment type
RNA-seq of coding RNA 
Contacts
Graham Johnson <geo@ncbi.nlm.nih.gov>, Graham D Johnson, Stephen A Krawet
Citation
Chromatin and extracellular vesicle associated sperm RNAs. Johnson GD, Mackie P, Jodar M, Moskovtsev S, Krawetz SA.
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-62874.idf.txt
Sample and data relationshipE-GEOD-62874.sdrf.txt
Additional data (1)E-GEOD-62874.additional.1.zip
Links