Characterization of small RNAs in early zebrafish PGCs
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ABSTRACT:
PROVIDER: PRJNA663091 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12628229.fastq.gz | Fastqsanger.gz | |||
| SRR12628230.fastq.gz | Fastqsanger.gz | |||
| SRR12628231.fastq.gz | Fastqsanger.gz | |||
| SRR12628232.fastq.gz | Fastqsanger.gz | |||
| SRR12628233.fastq.gz | Fastqsanger.gz |
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Project description:Microscale small RNA high-throughput sequencing was used to study small RNA distribution in early zebrafish PGCs (primordial germ cells). We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected, miR-430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition, miR-92a-3p and miR-26a-5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR-92a-3p and miR-26a-5p can influence the number of zebrafish PGCs.
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Project description:During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small non-coding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs, the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the 5' and 3' ends of miRNAs with a large number of extra nucleotides added in a non-template directed manner. We also identified a large and diverse set of piRNAs expressed during early development, far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through-put sequencing
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Project description:Piwi proteins specify an animal-specific subclass of the Argonaute family, that in vertebrates are specifically expressed in germ cells. We demonstrate that zebrafish Piwi (Ziwi) is expressed in both the male and the female gonad, and is a component of a germline specifying structure, called nuage. Loss of Ziwi function results in a progressive loss of germ cells due to apoptosis during larval development. In animals that have only reduced Ziwi function, germ cells are maintained, but display abnormal levels of apoptosis in adults. In mammals, Piwi proteins have been found to associate with approximately 29-nucleotide long, testis specific RNA molecules, called piRNAs. Here we show that zebrafish piRNAs are present in both ovaries and testes. Furthermore, we show that piRNAs are modified at their 3’ end and that they are produced by a Dicer independent mechanism. Many ovarian piRNAs are derived from transposons, implicating a role for these molecules in the silencing of these repetitive elements in vertebrates. Keywords: high-throughput 454 sequencing sequencing of ~30 nt small RNAs from zebrafish ovaries and testes using 454 technology
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Project description:The requirement for primordial germ cells (PGCs) during sexual differentiation is variable among vertebrates. It has been shown that in zebrafish complete loss of PGCs in the embryos causes exclusive male development. Further, transplantation of a single PGC into a germline deficient zebrafish embryos generates male exclusively, suggesting PGC number might be important for the ovarian fate.To explore how PGC number might regulate sexual development in zebrafish, we experimentally manipulated its number by injecting dnd MO into embryos to generate fish containing a spectrum of PGC number. The experiment was designed to compare transcriptomes between the developing trunk regions of wild type and dnd morphants at different developmental stages. The dnd MO was microinjected into one cell stage embryos to generate zebrafish with a range of PGC numbers. Transcriptomes of developing trunk regions of wild type and dnd morphants at 14 dpf and 22 dpf were analyzed.
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