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RNF17 referees ping-pong in mouse testes

ABSTRACT: In mammals, piRNA populations are dynamic throughout male germ cell development. Embryonic piRNAs consist of both primary and secondary species and are mainly directed toward transposons. In meiotic cells, however, the piRNA population is transposon-poor and restricted to primary piRNAs derived from pachytene piRNA clusters. The mechanism controlling which piRNAs are present at each developmental stage is poorly understood. Here we show that RNF17 shapes adult meiotic piRNA content by suppressing the production of secondary piRNAs. In the absence of RNF17, ping-pong (secondary amplification) occurs inappropriately in meiotic cells – aberrantly targeting protein-coding genes and lncRNAs. Our data indicate that RNF17 comprises one component of a “refereeing” mechanism that prevents deleterious activity of the meiotic piRNA pathway by ensuring the selective loading of PIWI proteins with products of meiotic piRNA clusters. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Vasily Vagin

PROVIDER: E-GEOD-53919 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNF17 referees ping-pong in mouse testes [RIP-seq]

Project description:In mammals, piRNA populations are dynamic throughout male germ cell development. Embryonic piRNAs consist of both primary and secondary species and are mainly directed toward transposons. In meiotic cells, however, the piRNA population is transposon-poor and restricted to primary piRNAs derived from pachytene piRNA clusters1-6. The mechanism controlling which piRNAs are present at each developmental stage is poorly understood. Here we show that RNF17 shapes adult meiotic piRNA content by suppressing the production of secondary piRNAs. In the absence of RNF17, ping-pong (secondary amplification) occurs inappropriately in meiotic cells – aberrantly targeting protein-coding genes and lncRNAs. Our data indicate that RNF17 comprises one component of a “refereeing” mechanism that prevents deleterious activity of the meiotic piRNA pathway by ensuring the selective loading of PIWI proteins with products of meiotic piRNA clusters. Examination of small RNAs isolated from MIWI and MILI IPs of heterozygous and homozygous RNF17 adult testes

2014-12-17 | E-GEOD-57241 | biostudies-arrayexpress

RNF17 referees ping-pong in mouse testes [smallRNAseq]

Project description:In mammals, piRNA populations are dynamic throughout male germ cell development. Embryonic piRNAs consist of both primary and secondary species and are mainly directed toward transposons. In meiotic cells, however, the piRNA population is transposon-poor and restricted to primary piRNAs derived from pachytene piRNA clusters. The mechanism controlling which piRNAs are present at each developmental stage is poorly understood. Here we show that RNF17 shapes adult meiotic piRNA content by suppressing the production of secondary piRNAs. In the absence of RNF17, ping-pong (secondary amplification) occurs inappropriately in meiotic cells – aberrantly targeting protein-coding genes and lncRNAs. Our data indicate that RNF17 comprises one component of a “refereeing” mechanism that prevents deleterious activity of the meiotic piRNA pathway by ensuring the selective loading of PIWI proteins with products of meiotic piRNA clusters. Examination of small RNA profile in heterozygous and homozygous RNF17 adult testes, pachytene or round spermatid sorted cells

2014-12-17 | E-GEOD-53917 | biostudies-arrayexpress

The Atlas of Chromatoid Body Components [small RNA-seq]

Project description:The genome of male germ cells is actively transcribed during spermatogenesis to produce phase-specific protein coding mRNAs and a considerable amount of different non-coding RNAs. Ribonucleoprotein (RNP) granule-mediated RNA regulation provides a powerful means to secure the quality and correct expression of the requisite transcripts. Haploid spermatids are characterized by a unique, unusually large cytoplasmic granule, the chromatoid body (CB), that emerges during the switch between the meiotic and post-meiotic phases of spermatogenesis. To better understand the role of the CB in male germ cell differentiation, we isolated CBs from mouse testes and revealed its full RNA and protein composition. We showed that the CB is mainly composed of RNA-binding proteins and other proteins involved RNA regulation. The CB was loaded with RNA, including pachytene piRNAs, a diverse set of mRNAs and a number of uncharacterized long non-coding transcripts. The CB was demonstrated to accumulate nascent RNA during all the steps of round spermatid differentiation. Our results revealed the CB as a large germ cell -specific RNP platform that is involved in the control of the highly complex transcriptome of haploid male germ cells. Small RNA profiling of purified chromatoid body, each steps of chromatoid body purification, and sortred round spermatid cells

2014-01-24 | E-GEOD-54287 | biostudies-arrayexpress

Pachytene piRNAs target endogenous mRNAs for silencing during meiosis

Project description:During embryonic germ cell development in mice, transposon-enriched, piwi-interacting RNAs (piRNAs) guide MILI and MIWI2 to direct silencing of potentially active mobile element families. In contrast, we know much less about the function of the highly abundant and extremely diverse class of piRNAs, which partner with MIWI and MILI during meiosis. Both MIWI and its catalytic activity are required for successful spermatogenesis, strongly indicating that piRNA-guided cleavage is critical for germ cell development. To gain an understanding of meiotic piRNA targets, we augmented the mouse piRNA repertoire by introducing an entire human meiotic piRNA cluster. This triggered a spermatogenesis defect, presumably by inappropriately targeting the piRNA machinery to mouse RNAs essential for germ cell development. Through an analysis of such de novo targets, we derived a signature for pachytene piRNA target recognition. This enabled identification of both transposable elements and meiotically expressed protein coding genes as targets of native piRNAs. Cleavage of genic targets begins at the pachytene stage when meiotic piRNAs first appear. As such, target mRNA levels attenuate starting from the pachytene stage and are further repressed throughout meiosis. Target mRNA-piRNA pairs also show evidence of an ongoing cleavage-dependent amplification cycle, which is not normally a strong feature of meiotic piRNAs. Our data support the idea that meiotic piRNA populations must be strongly selected to enable successful spermatogenesis, both driving the response away from essential genes and directing the pathway toward mRNA targets that are regulated by small RNAs in meiotic cells. 48 samples

2015-05-22 | E-GEOD-64138 | biostudies-arrayexpress

RNF17 referees ping-pong in mouse testes [5'RACE]

Project description:In mammals, piRNA populations are dynamic throughout male germ cell development. Embryonic piRNAs consist of both primary and secondary species and are mainly directed toward transposons. In meiotic cells, however, the piRNA population is transposon-poor and restricted to primary piRNAs derived from pachytene piRNA clusters. The mechanism controlling which piRNAs are present at each developmental stage is poorly understood. Here we show that RNF17 shapes adult meiotic piRNA content by suppressing the production of secondary piRNAs. In the absence of RNF17, ping-pong (secondary amplification) occurs inappropriately in meiotic cells – aberrantly targeting protein-coding genes and lncRNAs. Our data indicate that RNF17 comprises one component of a “refereeing” mechanism that prevents deleterious activity of the meiotic piRNA pathway by ensuring the selective loading of PIWI proteins with products of meiotic piRNA clusters. Examination of 5'RACE in heterozygous and homozygous RNF17 adult testes or MIWI/MILI immunoprecipitates

2014-12-17 | E-GEOD-53915 | biostudies-arrayexpress

Characterization of active piRNAs and an piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12 (small RNA)

Project description:We have found that oncogenic Ras combined with loss of the Hippo tumour-suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells, coincident with oncogenic transformation. In these cells, Piwi becomes loaded with piRNAs derived from generative loci, which are normally restricted to either the germline or the somatic follicle cells. Negating the pathway leads to increases in the expression of a wide variety of transposons and also to altered expression of some protein coding genes. This correlates with a reduction in the proliferation of the transformed cells in culture, suggesting that at least in this context, the piRNA pathway may play a functional role in cancer. Small RNAs cloned from whole cells, piwi-bound small RNAs and long RNA-Seq were performed in wts-RNAi;RasV12 cells to identify piRNAs and gene expression and compared to RasV12 cells, somatic OSS cells, and germline UAS-wts-RNAi;UAS-RasV12 control ovaries. After knock-down of several components of the piRNA machinery in WRR-1 cells (piwi, zuchini, armitage, aubergine, argonaute3) and GFP and/or dsRED control knock-downs, small RNAs were cloned and gene expression profiles (RNA-Seq) were established.

2016-08-01 | E-GEOD-83871 | biostudies-arrayexpress

The Atlas of Chromatoid Body Components

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-01-24 | E-GEOD-54288 | biostudies-arrayexpress

RNF17 referees ping-pong in mouse testes [RNAseq]

Project description:In mammals, piRNA populations are dynamic throughout male germ cell development. Embryonic piRNAs consist of both primary and secondary species and are mainly directed toward transposons. In meiotic cells, however, the piRNA population is transposon-poor and restricted to primary piRNAs derived from pachytene piRNA clusters. The mechanism controlling which piRNAs are present at each developmental stage is poorly understood. Here we show that RNF17 shapes adult meiotic piRNA content by suppressing the production of secondary piRNAs. In the absence of RNF17, ping-pong (secondary amplification) occurs inappropriately in meiotic cells – aberrantly targeting protein-coding genes and lncRNAs. Our data indicate that RNF17 comprises one component of a “refereeing” mechanism that prevents deleterious activity of the meiotic piRNA pathway by ensuring the selective loading of PIWI proteins with products of meiotic piRNA clusters. Examination of transcriptom in heterozygous and homozygous RNF17 adult testes and RNF17 immunoprecipitates

2014-12-17 | E-GEOD-53913 | biostudies-arrayexpress

C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts

Project description:Piwi Argonautes and Piwi-interacting RNAs (piRNAs) mediate genome defense by targeting transposons. However, many piRNA species lack obvious sequence complementarity to transposons or other loci. For example, only one C. elegans transposon is a known piRNA target. Here we show that, in mutants lacking the Piwi Argonaute PRG-1 and associated piRNAs (21U-RNAs), many silent loci in the germline exhibit increased levels of mRNA expression and depletion of an amplified RNAdependent RNA polymerase (RdRP)-derived species of small RNA termed 22G-RNAs. Sequences depleted of 22G-RNAs are enriched nearby potential target sites that base pair imperfectly but extensively to 21U-RNAs. We show that PRG-1 is required to initiate, but not to maintain, silencing of transgenes engineered to contain complementarity to endogenous 21U-RNAs. Our findings support a model in which C. elegans piRNAs utilize their enormous repertoire of targeting capacity to scan the germline transcriptome for foreign sequences, while endogenous germline-expressed genes are actively protected from piRNA-induced silencing. Examine small RNA population changes in prg-1 and rescued strains

2012-09-01 | E-GEOD-38723 | biostudies-arrayexpress

Profiling and comparison of miRNA populations in male and female tissues from Drosophila melanogaster at various stages

Project description:By surveying miRNA populations in each sex, we identified sets of miRNAs differentially expressed in male and female tissues across various stages of development. Small RNAs cloning of dissected male and female tissues from Drosophila melanogaster at various stages

2014-08-01 | E-GEOD-57029 | biostudies-arrayexpress

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