Smg6 interacting partners in mouse
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Elite
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): Testis
SUBMITTER: 
Lin Ma
LAB HEAD: Noora Kotaja
PROVIDER: PXD037090 | Pride | 2022-10-01
REPOSITORIES: Pride
Similar Datasets
Project description:Nonsense-mediated RNA decay (NMD) is a conserved RNA turnover pathway. Here we report that the sole endonuclease in the NMD pathway, SMG6, is essential for the male germline. Germ-cell conditional knockout (cKO) of Smg6 causes complete arrest of spermatogenesis at the early haploid cell stage. Smg6-cKO round spermatids accumulate NMD target mRNAs with long 3’ untranslated regions (UTRs) and fail to eliminate transcripts normally expressed during meiosis, the previous step in spermatogenesis. SMG6 and PIWI-interacting (pi) RNA pathway components are highly enriched in the chromatoid body (CB), a specialized cytoplasmic granule in male germ cells. This led to the intriguing possibility that the CB is a site where SMG6 and the piRNA pathway co-operate to regulate RNA metabolism. Several findings supported this hypothesis: (i) SMG6 and the piRNA-binding protein PIWIL1 have almost identical temporal expression and localization patterns, (ii) SMG6 and PIWIL1 physically interact, (iii) scores of genes upregulated in Smg6-cKO round spermatids overlap with those upregulated in Piwil1-KO round spermatids, and (iv) the phenotypic defects caused by SMG6 loss phenocopies the defects caused by PIWIL1 loss. Together, our results demonstrate that SMG6 is an essential regulator of the male germline transcriptome and highlight the CB as a molecular platform coordinating RNA regulatory pathways to control sperm production and fertility.
2022-09-27 | GSE182518 | GEO
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. Transcriptome profling of purified chromatoid body, each steps of chromatoid body purification, and sortred round spermatid cells
2014-01-24 | E-GEOD-54286 | biostudies-arrayexpress
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
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.
2014-01-24 | GSE54287 | GEO
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.
2014-01-24 | GSE54286 | GEO
Project description:In metazoans, the endoribonuclease SMG6 is thought to cleave many endogenous mRNAs targeted for nonsense-mediated mRNA decay (NMD). However, most evidence as to the identity of endogenous SMG6 substrates is indirect, and little is known about their cleavage sites. Here, we report the efficacy of an RNA degradome approach called parallel analysis of RNA ends (PARE) for identifying NMD intermediates in human cells. By specifically sequencing the 5’ ends of intermediates dependent on SMG6 and the critical NMD factor UPF1, hundreds of endogenous transcripts that are direct targets of SMG6 have been revealed. A preferred sequence motif spanning most SMG6 cleavage sites has been identified and validated by mutational analysis. For many SMG6 substrates, depletion of SMG6 leads to decapping of the RNAs. These findings provide key insights into NMD and targeting by SMG6 while also demonstrating the potential of PARE for analyzing other ribonucleases with diverse endogenous substrates.
2014-12-01 | GSE61398 | GEO
Project description:Nonsense-mediated mRNA decay (NMD) controls gene expression by eliminating mRNAs with premature or aberrant translation termination. Degradation of NMD substrates is initiated by the central NMD factor UPF1, which recruits the endonuclease SMG6 and the deadenylation-promoting SMG5/7 complex. Here we map transcriptome-wide sites of SMG6-mediated endocleavage via 3′ fragment capture and degradome sequencing.
2017-06-01 | E-MTAB-3625 | biostudies-arrayexpress
Project description:Germ granules are large cytoplasmic ribonucleoprotein complexes that emerge in the germline to participate in RNA regulation. The two most prominent germ granules are the intermitochondrial cement (IMC) in meiotic spermatocytes and the chromatoid body (CB) in haploid round spermatids, both functionally linked to the PIWI-interacting RNA (piRNA) pathway. In this study, we clarified the IMC function by identifying proteins that form complexes with a well-known IMC protein PIWIL2/MILI in the mouse testis. The PIWIL2 interactome included several proteins with known functions in piRNA biogenesis. We further characterized the expression and localization of two of the identified proteins, Exonuclease 3′–5′ domain-containing proteins EXD1 and EXD2, and confirmed their localization to the IMC. We showed that EXD2 interacts with PIWIL2, and that the mutation of Exd2 exonuclease domain in mice induces misregulation of piRNA levels originating from specific pachytene piRNA clusters, but does not disrupt male fertility. Altogether, this study highlights the central role of the IMC as a platform for piRNA biogenesis, and suggests that EXD1 and EXD2 function in the IMC-mediated RNA regulation in postnatal male germ cells.
2023-12-21 | GSE194043 | GEO
Project description:Nonsense-mediated mRNA decay (NMD) pathway promotes the degradation of several mRNA species, including transcripts containing a premature termination codon. Here,we measured global mRNA half-lives in NMD deficient and wild-type (WT) embryonic stem cells (ESCs). This allowed us to discriminate which transcripts are affected by NMD. Several transcripts had an impaired half-life in Smg5 and Smg6 KO ESCs compared to WT. They belong to different pathways and cellular processing indicating that NMD regulates multiple processes in the cells. Finally, majority of the transcripts had an impairment on the half-life in both Smg5 and Smg6 KO ESCs indicating that endo- and exonucleolityc branches of the NMD pathway target the same mRNAs.
2022-02-02 | GSE153455 | GEO
Project description:Nonsense-mediated mRNA decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or mis-splicing. Additional roles for NMD in determining mRNA stability in regular gene expression have emerged as well, yet it is poorly known which functions the pathway has in regular mammalian physiology in vivo. Here, we report a novel conditional Smg6 mouse allele that allows converting wild-type SMG6 to a nuclease-mutant version of the protein. We analyzed the consequences of an inactive NMD pathway on the function of the circadian clock whose mechanism is known to depend on high turnover rates of their oscillating mRNAs and proteins. Fibroblast and liver clocks show strong lengthening of free-running circadian periods under Smg6 mutant conditions. We identify a specific core clock component, Cry2, as directly NMD-regulated through its long 3' UTR. Our findings indicate that NMD has been co-opted as an mRNA decay pathway to limit the temporal availability of CRY2, one of the key transcriptional repressors in the rhythm-generating feedback loop, expanding the known scope of NMD regulation in vivo.
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