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Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

ABSTRACT: Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

PROVIDER: PRJNA565724 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10123820_subreads.fastq.gz	Fastqsanger.gz
	SRR10123821_subreads.fastq.gz	Fastqsanger.gz
	SRR10123822_subreads.fastq.gz	Fastqsanger.gz
	SRR10123823_subreads.fastq.gz	Fastqsanger.gz
	SRR10123824_subreads.fastq.gz	Fastqsanger.gz

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Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

Project description:Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the composition of long RNAs has been limited by the lack of sensitive, high-throughput experimental techniques that can distinguish intact RNAs from fragmented RNAs, known to abound in sperm. Here, we integrate single-molecule long-read sequencing with short-read sequencing to detect sperm intact RNAs (spiRNAs). We identify 3,440 spiRNA species in mice and 4,100 in humans. The spiRNA profile consists of both mRNAs and long non-coding RNAs, is evolutionarily conserved between mice and humans, and displays an enrichment in mRNAs encoding for ribosome. In sum, we characterize the landscape of intact long RNAs in sperm, paving the way for future studies on their biogenesis and functions. Our experimental and bioinformatics approaches can be applied to other tissues and organisms to detect intact transcripts.

2021-01-11 | GSE137490 | GEO

Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm.

Project description:Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the composition of long RNAs, has been limited by the lack of sensitive, high-throughput experimental techniques that can distinguish intact RNAs from fragmented RNAs, known to abound in sperm. Here, we integrate single-molecule long-read sequencing with short-read sequencing to detect sperm intact RNAs (spiRNAs). We identify 3440 spiRNA species in mice and 4100 in humans. The spiRNA profile consists of both mRNAs and long non-coding RNAs, is evolutionarily conserved between mice and humans, and displays an enrichment in mRNAs encoding for ribosome. In sum, we characterize the landscape of intact long RNAs in sperm, paving the way for future studies on their biogenesis and functions. Our experimental and bioinformatics approaches can be applied to other tissues and organisms to detect intact transcripts.

| S-EPMC7921563 | biostudies-literature

single molecule and long-read RNA-seq

Project description:A single molecule and long-read view of the diverse human transcriptome

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Systematic Identification and Characterization of Long Non-coding RNAs in Mouse Mature Sperm

Project description: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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Project description:Growing evidences have shown that many transcripts have been discovered in sperm and small noncoding RNAs, such as miRNA and tsRNA, of sperm paly an important role in the transgenerational transmission of paternal lifetime experiences. However, the expression profile of long noncoding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Furthermore, Abnormal expression of lncRNA whether or not related with the asthenozoospermic is completely unknown. In the present study, highly purified RNA was served to investigate lncRNA expression profiles in human mature sperm by stranded-specific RNA-seq. We identified 38,307 known and 27,472 novel lncRNA genes, and the existence of intact LncRNA transcripts was confirmed by RT-PCR and fluorescence in situ hybridization (FISH) on two representative LncRNAs. Many lncRNAs exclusive were expressed in testis and sperm. 880 lncRNA sequences were conserved between human and mouse with > 80% overlap. Compared with normal population, the lncRNA profiles in asthenozoospermic patients’ sperm showed significant difference with 2437 up-regulation and 306 down-regulation of lncRNA. This study will provide a preliminary database valuable for identifying lncRNAs critical on sperm function regulation or important for screening the lncRNA markers of asthenozoospermia.

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Sperm modulate uterine immune parameters relevant to embryo implantation and reproductive success

Project description:Seminal fluid factors modulate the female immune response at conception to facilitate embryo implantation and reproductive success. Whether sperm affect this response has not been clear. We evaluated global gene expression by microarray in the mouse uterus after mating with intact or vasectomized males. Intact males induced greater changes in gene transcription, prominently affecting pro-inflammatory cytokine and immune regulatory genes, with TLR4 signaling identified as a top-ranked upstream driver. Recruitment of neutrophils and expansion of peripheral regulatory T cells were elevated by seminal fluid of intact males. In vitro, epididymal sperm induced IL6, CXCL2, and CSF3 in uterine epithelial cells of wild-type, but not Tlr4 null females. Collectively these experiments show that sperm assist in promoting female immune tolerance by eliciting uterine cytokine expression through TLR4-dependent signaling. The findings indicate a biological role for sperm beyond oocyte fertilization, in modulating immune mechanisms involved in female control of reproductive investment. We used microarrays to detail the global programme of gene expression in mice following exposure to different components of seminal fluid

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