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Siddiqui NU, Karaiskakis A, Goldman AL, Eagle WVI, Low TCH, Luo H, Smibert CA, Gavis ER, Lipshitz HD. Smaug regulates germ plasm assembly and primordial germ cell number in Drosophila embryos. SCIENCE ADVANCES 2024; 10:eadg7894. [PMID: 38608012 PMCID: PMC11014450 DOI: 10.1126/sciadv.adg7894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
During Drosophila oogenesis, the Oskar (OSK) RNA binding protein (RBP) determines the amount of germ plasm that assembles at the posterior pole of the oocyte. Here, we identify mechanisms that subsequently regulate germ plasm assembly in the early embryo. We show that the Smaug (SMG) RBP is transported into the germ plasm of the early embryo where it accumulates in the germ granules. SMG binds to and represses translation of the osk messenger RNA (mRNA) as well as the bruno 1 (bru1) mRNA, which encodes an RBP that we show promotes germ plasm production. Loss of SMG or mutation of SMG's binding sites in the osk or bru1 mRNA results in excess translation of these transcripts in the germ plasm, accumulation of excess germ plasm, and budding of excess primordial germ cells (PGCs). Therefore, SMG triggers a posttranscriptional regulatory pathway that attenuates the amount of germ plasm in embryos to modulate the number of PGCs.
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Affiliation(s)
- Najeeb U. Siddiqui
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
- Program in Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Angelo Karaiskakis
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Aaron L. Goldman
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
- Program in Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Whitby V. I. Eagle
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Timothy C. H. Low
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Hua Luo
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Craig A. Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Elizabeth R. Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Howard D. Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
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He W, Belsham DD. RNA-Binding Protein Motifs Predict microRNA Secretion and Cellular Retention in Hypothalamic and Other Cell Types. Biomedicines 2024; 12:857. [PMID: 38672211 PMCID: PMC11048351 DOI: 10.3390/biomedicines12040857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Cellular microRNAs (miRNAs) can be selectively secreted or retained, adding another layer to their critical role in regulating human health and disease. To date, select RNA-binding proteins (RBPs) have been proposed to be a mechanism underlying miRNA localization, but the overall relevance of RBPs in systematic miRNA sorting remains unclear. This study profiles intracellular and small extracellular vesicles' (sEVs) miRNAs in NPY-expressing hypothalamic neurons. These findings were corroborated by the publicly available sEV and intracellular miRNA profiles of white and brown adipocytes, endothelium, liver, and muscle from various databases. Using experimentally determined binding motifs of 93 RBPs, our enrichment analysis revealed that sEV-originating miRNAs contained significantly different RBP motifs than those of intracellularly retained miRNAs. Multiple RBP motifs were shared across cell types; for instance, RBM4 and SAMD4 are significantly enriched in neurons, hepatocytes, skeletal muscle, and endothelial cells. Homologs of both proteins physically interact with Argonaute1/2 proteins, suggesting that they play a role in miRNA sorting. Machine learning modelling also demonstrates that significantly enriched RBP motifs could predict cell-specific preferential miRNA sorting. Non-optimized machine learning modeling of the motifs using Random Forest and Naive Bayes in all cell types except WAT achieved an area under the receiver operating characteristic (ROC) curve of 0.77-0.84, indicating a high predictive accuracy. Given that the RBP motifs have a significant predictive power, these results underscore the critical role that RBPs play in miRNA sorting within mammalian cells and reinforce the importance of miRNA sequencing in preferential localization. For the future development of small RNA therapeutics, considering these RBP-RNA interactions could be crucial to maximize delivery effectiveness and minimize off-target effects.
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Affiliation(s)
- Wenyuan He
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Denise D. Belsham
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
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3
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Li D, Qi T, Chen J. SAMD4A serves as a negative prognostic marker for gastric cancer patients. Tissue Cell 2023; 84:102167. [PMID: 37515967 DOI: 10.1016/j.tice.2023.102167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 07/31/2023]
Abstract
INTRODUCTION The incidence and mortality of gastric cancer remain high in the world. We aim to explore the role of SAMD4A in gastric cancer. METHODS The expression of SAMD4A was up-regulated in gastric adenocarcinoma and the expression level of SAMD4A in gastric adenocarcinoma and adjacent normal tissues was verified by RT-qPCR. Immunohistochemical showed that SAMD4A was mainly located in the cytoplasm. RESULT The result showed that the expression of SAMD4A was positively correlated with the depth of invasion, the number of lymph node metastasis, and the clinical stage in patients with gastric adenocarcinoma. Survival analysis of GEPIA database showed that the overall survival of gastric adenocarcinoma patients with positive SAMD4A expression was lower than that of the negative group. Gastric cancer cell lines with knockdown of the SAMD4A gene were used to observe the differences in cell proliferation, invasion, and migration abilities between the knockdown group and the control group. The results showed that the proliferation, invasion, and migration abilities of the SAMD4A knockdown group were both weakened compared with the control group. This study is the first to find that the expression level of SAMD4A in gastric cancer is higher than that in the adjacent group and is associated with poor prognosis of patients. SAMD4A promotes the proliferation, invasion, and migration of gastric adenocarcinoma cells. CONCLUSION This indicates that SAMD4A plays an important role in the occurrence and development of gastric cancer, and is expected to be an effective indicator for the diagnosis and evaluation of the prognosis of gastric cancer.
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Affiliation(s)
- Deqin Li
- The Second Clinical Medical College, Binzhou Medical University, 264003 Yantai, China; Department of Oncology, Yantai Yuhuangding Hospital, Affiliated Hospital of Qingdao University, 264000 Yantai, China
| | - Tiantian Qi
- Department of Oncology, Weihai Municipal Hospital, 264299 Weihai, China
| | - Jian Chen
- Department of Oncology, Yantai Yuhuangding Hospital, Affiliated Hospital of Qingdao University, 264000 Yantai, China.
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Kubíková J, Ubartaitė G, Metz J, Jeske M. Structural basis for binding of Drosophila Smaug to the GPCR Smoothened and to the germline inducer Oskar. Proc Natl Acad Sci U S A 2023; 120:e2304385120. [PMID: 37523566 PMCID: PMC10410706 DOI: 10.1073/pnas.2304385120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/28/2023] [Indexed: 08/02/2023] Open
Abstract
Drosophila Smaug and its orthologs comprise a family of mRNA repressor proteins that exhibit various functions during animal development. Smaug proteins contain a characteristic RNA-binding sterile-α motif (SAM) domain and a conserved but uncharacterized N-terminal domain (NTD). Here, we resolved the crystal structure of the NTD of the human SAM domain-containing protein 4A (SAMD4A, a.k.a. Smaug1) to 1.6 Å resolution, which revealed its composition of a homodimerization D subdomain and a subdomain with similarity to a pseudo-HEAT-repeat analogous topology (PHAT) domain. Furthermore, we show that Drosophila Smaug directly interacts with the Drosophila germline inducer Oskar and with the Hedgehog signaling transducer Smoothened through its NTD. We determined the crystal structure of the NTD of Smaug in complex with a Smoothened α-helical peptide to 2.0 Å resolution. The peptide binds within a groove that is formed by both the D and PHAT subdomains. Structural modeling supported by experimental data suggested that an α-helix within the disordered region of Oskar binds to the NTD of Smaug in a mode similar to Smoothened. Together, our data uncover the NTD of Smaug as a peptide-binding domain.
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Affiliation(s)
- Jana Kubíková
- Biochemistry Center, Heidelberg University, Heidelberg69120, Germany
| | | | - Jutta Metz
- Biochemistry Center, Heidelberg University, Heidelberg69120, Germany
| | - Mandy Jeske
- Biochemistry Center, Heidelberg University, Heidelberg69120, Germany
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5
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Gao Y, Zhu Y, Sun Q, Chen D. Argonaute-dependent ribosome-associated protein quality control. Trends Cell Biol 2023; 33:260-272. [PMID: 35981909 DOI: 10.1016/j.tcb.2022.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022]
Abstract
Ribosome-associated protein quality control (RQC) is a protein surveillance mechanism that eliminates defective nascent polypeptides. The E3 ubiquitin ligase, Ltn1, is a key regulator of RQC that targets substrates for ubiquitination. Argonaute proteins (AGOs) are central players in miRNA-mediated gene silencing and have recently been shown to also regulate RQC by facilitating Ltn1. Therefore, AGOs directly coordinate post-transcriptional gene silencing and RQC, ensuring efficient gene silencing. We summarize the principles of RQC and the functions of AGOs in miRNA-mediated gene silencing, and discuss how AGOs associate with the endoplasmic reticulum (ER) to assist Ltn1 in controlling RQC. We highlight that RQC not only eliminates defective nascent polypeptides but also removes unwanted protein products when AGOs participate.
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Affiliation(s)
- Yajie Gao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Yuanxiang Zhu
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China.
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6
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Siddiqui NU, Karaiskakis A, Goldman AL, Eagle WV, Smibert CA, Gavis ER, Lipshitz HD. Smaug regulates germ plasm synthesis and primordial germ cell number in Drosophila embryos by repressing the oskar and bruno 1 mRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530189. [PMID: 36909513 PMCID: PMC10002672 DOI: 10.1101/2023.02.27.530189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
During Drosophila oogenesis, the Oskar (OSK) RNA-binding protein (RBP) determines the amount of germ plasm that assembles at the posterior pole of the oocyte. Here we identify the mechanisms that regulate the osk mRNA in the early embryo. We show that the Smaug (SMG) RBP is transported into the germ plasm of the early embryo where it accumulates in the germ granules. SMG binds to and represses translation of the osk mRNA itself as well as the bruno 1 (bru1) mRNA, which encodes an RBP that we show promotes germ plasm production. Loss of SMG or mutation of SMG's binding sites in the osk or bru1 mRNAs results in ectopic translation of these transcripts in the germ plasm and excess PGCs. SMG therefore triggers a post-transcriptional regulatory pathway that attenuates germ plasm synthesis in embryos, thus modulating the number of PGCs.
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Affiliation(s)
- Najeeb U. Siddiqui
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
- Program in Developmental & Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Angelo Karaiskakis
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Aaron L. Goldman
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
- Program in Developmental & Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Whitby V.I. Eagle
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Craig A. Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
| | - Elizabeth R. Gavis
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Howard D. Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
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7
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Wang XY, Zhang LN. RNA binding protein SAMD4: current knowledge and future perspectives. Cell Biosci 2023; 13:21. [PMID: 36732864 PMCID: PMC9893680 DOI: 10.1186/s13578-023-00968-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
SAMD4 protein family is a class of novel RNA-binding proteins that can mediate post-transcriptional regulation and translation repression in eukaryotes, which are highly conserved from yeast to humans during evolution. In mammalian cells, SAMD4 protein family consists of two members including SAMD4A/Smaug1 and SAMD4B/Smaug2, both of which contain common SAM domain that can specifically bind to different target mRNAs through stem-loop structures, also known as Smaug recognition elements (SREs), and regulate the mRNA stability, degradation and translation. In addition, SAMD4 can form the cytoplasmic mRNA silencing foci and regulate the translation of SRE-containing mRNAs in neurons. SAMD4 also can form the cytosolic membrane-less organelles (MLOs), termed as Smaug1 bodies, and regulate mitochondrial function. Importantly, many studies have identified that SAMD4 family members are involved in various pathological processes including myopathy, bone development, neural development, and cancer occurrence and progression. In this review, we mainly summarize the structural characteristics, biological functions and molecular regulatory mechanisms of SAMD4 protein family members, which will provide a basis for further research and clinical application of SAMD4 protein family.
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Affiliation(s)
- Xin-Ya Wang
- grid.28703.3e0000 0000 9040 3743Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, 100124 Beijing, People’s Republic of China
| | - Li-Na Zhang
- grid.28703.3e0000 0000 9040 3743Beijing International Science and Technology Cooperation Base of Antivirus Drug, Faculty of Environment and Life, Beijing University of Technology, 100124 Beijing, People’s Republic of China
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8
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Jungers CF, Djuranovic S. Modulation of miRISC-Mediated Gene Silencing in Eukaryotes. Front Mol Biosci 2022; 9:832916. [PMID: 35237661 PMCID: PMC8882679 DOI: 10.3389/fmolb.2022.832916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression is regulated at multiple levels in eukaryotic cells. Regulation at the post-transcriptional level is modulated by various trans-acting factors that bind to specific sequences in the messenger RNA (mRNA). The binding of different trans factors influences various aspects of the mRNA such as degradation rate, translation efficiency, splicing, localization, etc. MicroRNAs (miRNAs) are short endogenous ncRNAs that combine with the Argonaute to form the microRNA-induced silencing complex (miRISC), which uses base-pair complementation to silence the target transcript. RNA-binding proteins (RBPs) contribute to post-transcriptional control by influencing the mRNA stability and translation upon binding to cis-elements within the mRNA transcript. RBPs have been shown to impact gene expression through influencing the miRISC biogenesis, composition, or miRISC-mRNA target interaction. While there is clear evidence that those interactions between RBPs, miRNAs, miRISC and target mRNAs influence the efficiency of miRISC-mediated gene silencing, the exact mechanism for most of them remains unclear. This review summarizes our current knowledge on gene expression regulation through interactions of miRNAs and RBPs.
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9
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Cao WX, Karaiskakis A, Lin S, Angers S, Lipshitz HD. The F-box protein Bard (CG14317) targets the Smaug RNA-binding protein for destruction during the Drosophila maternal-to-zygotic transition. Genetics 2022; 220:iyab177. [PMID: 34757425 PMCID: PMC8733446 DOI: 10.1093/genetics/iyab177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/11/2021] [Indexed: 01/12/2023] Open
Abstract
During the maternal-to-zygotic transition (MZT), which encompasses the earliest stages of animal embryogenesis, a subset of maternally supplied gene products is cleared, thus permitting activation of zygotic gene expression. In the Drosophila melanogaster embryo, the RNA-binding protein Smaug (SMG) plays an essential role in progression through the MZT by translationally repressing and destabilizing a large number of maternal mRNAs. The SMG protein itself is rapidly cleared at the end of the MZT by a Skp/Cullin/F-box (SCF) E3-ligase complex. Clearance of SMG requires zygotic transcription and is required for an orderly MZT. Here, we show that an F-box protein, which we name Bard (encoded by CG14317), is required for degradation of SMG. Bard is expressed zygotically and physically interacts with SMG at the end of the MZT, coincident with binding of the maternal SCF proteins, SkpA and Cullin1, and with degradation of SMG. shRNA-mediated knock-down of Bard or deletion of the bard gene in the early embryo results in stabilization of SMG protein, a phenotype that is rescued by transgenes expressing Bard. Bard thus times the clearance of SMG at the end of the MZT.
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Affiliation(s)
- Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Angelo Karaiskakis
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Sichun Lin
- Department of Pharmaceutical Sciences & Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences & Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
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10
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When Down Is Up: Heterochromatin, Nuclear Organization and X Upregulation. Cells 2021; 10:cells10123416. [PMID: 34943924 PMCID: PMC8700316 DOI: 10.3390/cells10123416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 12/21/2022] Open
Abstract
Organisms with highly differentiated sex chromosomes face an imbalance in X-linked gene dosage. Male Drosophila solve this problem by increasing expression from virtually every gene on their single X chromosome, a process known as dosage compensation. This involves a ribonucleoprotein complex that is recruited to active, X-linked genes to remodel chromatin and increase expression. Interestingly, the male X chromosome is also enriched for several proteins associated with heterochromatin. Furthermore, the polytenized male X is selectively disrupted by the loss of factors involved in repression, silencing, heterochromatin formation or chromatin remodeling. Mutations in many of these factors preferentially reduce male survival or enhance the lethality of mutations that prevent normal recognition of the X chromosome. The involvement of primarily repressive factors in a process that elevates expression has long been puzzling. Interestingly, recent work suggests that the siRNA pathway, often associated with heterochromatin formation and repression, also helps the dosage compensation machinery identify the X chromosome. In light of this finding, we revisit the evidence that links nuclear organization and heterochromatin to regulation of the male X chromosome.
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11
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Fernández-Alvarez AJ, Thomas MG, Pascual ML, Habif M, Pimentel J, Corbat AA, Pessoa JP, La Spina PE, Boscaglia L, Plessis A, Carmo-Fonseca M, Grecco HE, Casado M, Boccaccio GL. Smaug1 membrane-less organelles respond to AMPK/mTOR and affect mitochondrial function‡. J Cell Sci 2021; 135:273619. [PMID: 34859817 DOI: 10.1242/jcs.253591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
Smaug is a conserved translational regulator that binds numerous mRNAs, including nuclear transcripts that encode mitochondrial enzymes. Smaug orthologs form cytosolic membrane-less organelles (MLOs) in several organisms and cell types. We have performed single-molecule FISH assays that revealed that SDHB and UQCRC1 mRNAs associate with Smaug1 bodies in U2OS cells. Loss of function of Smaug1 and Smaug2 affected both mitochondrial respiration and morphology of the mitochondrial network. Phenotype rescue by Smaug1 transfection depends on the presence of its RNA binding domain. Moreover, we identified specific Smaug1 domains involved in MLO formation, and found that impaired Smaug1 MLO condensation correlates with mitochondrial defects. Mitochondrial Complex I inhibition by rotenone -but not strong mitochondrial uncoupling by CCCP- rapidly induced Smaug1 MLOs dissolution. Metformin and rapamycin elicited similar effects, which were blocked by pharmacological inhibition of AMPK. Finally, we found that Smaug1 MLO dissolution weakens the interaction with target mRNAs, thus enabling their release. We propose that mitochondrial respiration and the AMPK/mTOR balance controls the condensation and dissolution of Smaug1 MLOs, thus regulating nuclear mRNAs that encode key mitochondrial proteins.
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Affiliation(s)
- Ana J Fernández-Alvarez
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - María Gabriela Thomas
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Malena L Pascual
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Martín Habif
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Jerónimo Pimentel
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Agustín A Corbat
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - João P Pessoa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Pablo E La Spina
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | | | - Anne Plessis
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Hernán E Grecco
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Marta Casado
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia 46010, Spain, and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid 28029, Spain
| | - Graciela L Boccaccio
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina.,Department of Molecular and Cellular Biology and Physiology (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, C1428EHA Buenos Aires, Argentina
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12
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Nazer E, Gómez Acuña L, Kornblihtt AR. Seeking the truth behind the myth: Argonaute tales from "nuclearland". Mol Cell 2021; 82:503-513. [PMID: 34856122 DOI: 10.1016/j.molcel.2021.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/19/2022]
Abstract
Argonaute proteins have been traditionally characterized as a highly evolutionary conserved family engaged in post-transcriptional gene silencing pathways. The Argonaute family is mainly grouped into the AGO and PIWI clades. The canonical role of Argonaute proteins relies on their ability to bind small-RNAs that recognize complementary sequences on target mRNAs to induce either mRNA degradation or translational repression. However, there is an increasing amount of evidence supporting that Argonaute proteins also exert multiple nuclear functions that subsequently regulate gene expression. In this line, genome-wide studies showed that members from the AGO clade regulate transcription, 3D chromatin organization, and splicing of active loci located within euchromatin. Here, we discuss recent work based on high-throughput technologies that have significantly contributed to shed light on the multivariate nuclear functions of AGO proteins in different model organisms. We also analyze data supporting that AGO proteins are able to execute these nuclear functions independently from small RNA pathways. Finally, we integrate these mechanistic insights with recent reports highlighting the clinical importance of AGO in breast and prostate cancer development.
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Affiliation(s)
- Ezequiel Nazer
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.
| | - Luciana Gómez Acuña
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
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13
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Dynamic Variations of 3'UTR Length Reprogram the mRNA Regulatory Landscape. Biomedicines 2021; 9:biomedicines9111560. [PMID: 34829789 PMCID: PMC8615635 DOI: 10.3390/biomedicines9111560] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/10/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022] Open
Abstract
This paper concerns 3′-untranslated regions (3′UTRs) of mRNAs, which are non-coding regulatory platforms that control stability, fate and the correct spatiotemporal translation of mRNAs. Many mRNAs have polymorphic 3′UTR regions. Controlling 3′UTR length and sequence facilitates the regulation of the accessibility of functional effectors (RNA binding proteins, miRNAs or other ncRNAs) to 3′UTR functional boxes and motifs and the establishment of different regulatory landscapes for mRNA function. In this context, shortening of 3′UTRs would loosen miRNA or protein-based mechanisms of mRNA degradation, while 3′UTR lengthening would strengthen accessibility to these effectors. Alterations in the mechanisms regulating 3′UTR length would result in widespread deregulation of gene expression that could eventually lead to diseases likely linked to the loss (or acquisition) of specific miRNA binding sites. Here, we will review the mechanisms that control 3′UTR length dynamics and their alterations in human disorders. We will discuss, from a mechanistic point of view centered on the molecular machineries involved, the generation of 3′UTR variability by the use of alternative polyadenylation and cleavage sites, of mutually exclusive terminal alternative exons (exon skipping) as well as by the process of exonization of Alu cassettes to generate new 3′UTRs with differential functional features.
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14
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Zhou M, Wang B, Li H, Han J, Li A, Lu W. RNA-binding protein SAMD4A inhibits breast tumor angiogenesis by modulating the balance of angiogenesis program. Cancer Sci 2021; 112:3835-3845. [PMID: 34219323 PMCID: PMC8409301 DOI: 10.1111/cas.15053] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
Tumor-induced angiogenesis is important for further progression of solid tumors. The initiation of tumor angiogenesis is dictated by a shift in the balance between proangiogenic and antiangiogenic gene expression programs. However, the potential mechanism controlling the expression of angiogenesis-related genes in the tumor cells, especially the process mediated by RNA-binding protein (RBP) remains unclear. SAMD4A is a conserved RBP across fly to mammals, and is believed to play an important role in controlling gene translation and stability. In this study, we identified the potential role of SAMD4A in modulating angiogenesis-related gene expression and tumor progression in breast cancer. SAMD4A expression was repressed in breast cancer tissues and cells and low SAMD4A expression in human breast tumor samples was strongly associated with poor survival of patients. Overexpression of SAMD4A inhibited breast tumor angiogenesis and caner progression, whereas knockdown of SAMD4A demonstrated a reversed effect. Mechanistically, SAMD4A was found to specifically destabilize the proangiogenic gene transcripts, including C-X-C motif chemokine ligand 5 (CXCL5), endoglin (ENG), interleukin 1β (IL1β), and angiopoietin 1 (ANGPT1), by directly interacting with the stem-loop structure in the 3' untranslated region (3'UTR) of these mRNAs through its sterile alpha motif (SAM) domain, resulting in the imbalance of angiogenic genes expression. Collectively, our results suggest that SAMD4A is a novel breast tumor suppressor that inhibits tumor angiogenesis by specifically downregulating the expression of proangiogenic genes, which might be a potential antiangiogenic target for breast cancer therapy.
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Affiliation(s)
- Meicen Zhou
- Department of Endocrinology, Beijing Jishuitan Hospital, The 4th Clinical Medical College of Peking University, Beijing, China
| | - Bing Wang
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hongwei Li
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianqun Han
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ailing Li
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wenbao Lu
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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15
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Cao WX, Kabelitz S, Gupta M, Yeung E, Lin S, Rammelt C, Ihling C, Pekovic F, Low TCH, Siddiqui NU, Cheng MHK, Angers S, Smibert CA, Wühr M, Wahle E, Lipshitz HD. Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition. Cell Rep 2021; 31:107783. [PMID: 32579915 PMCID: PMC7372737 DOI: 10.1016/j.celrep.2020.107783] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/06/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
In animal embryos, the maternal-to-zygotic transition (MZT) hands developmental control from maternal to zygotic gene products. We show that the maternal proteome represents more than half of the protein-coding capacity of Drosophila melanogaster’s genome, and that 2% of this proteome is rapidly degraded during the MZT. Cleared proteins include the post-transcriptional repressors Cup, Trailer hitch (TRAL), Maternal expression at 31B (ME31B), and Smaug (SMG). Although the ubiquitin-proteasome system is necessary for clearance of these repressors, distinct E3 ligase complexes target them: the C-terminal to Lis1 Homology (CTLH) complex targets Cup, TRAL, and ME31B for degradation early in the MZT and the Skp/Cullin/F-box-containing (SCF) complex targets SMG at the end of the MZT. Deleting the C-terminal 233 amino acids of SMG abrogates F-box protein interaction and confers immunity to degradation. Persistent SMG downregulates zygotic re-expression of mRNAs whose maternal contribution is degraded by SMG. Thus, clearance of SMG permits an orderly MZT. Cao et al. show that 2% of the proteome is degraded in early Drosophila embryos, including a repressive ribonucleoprotein complex. Two E3 ubiquitin ligases separately act on distinct components of this complex to phase their clearance. Failure to degrade a key component, the Smaug RNA-binding protein, disrupts an orderly maternal-to-zygotic transition.
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Affiliation(s)
- Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sarah Kabelitz
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Meera Gupta
- Department of Molecular Biology and the Lewis-Sigler Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Eyan Yeung
- Department of Molecular Biology and the Lewis-Sigler Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Sichun Lin
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Christian Ihling
- Institute of Pharmacy and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Filip Pekovic
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany
| | - Timothy C H Low
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Najeeb U Siddiqui
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Matthew H K Cheng
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Martin Wühr
- Department of Molecular Biology and the Lewis-Sigler Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology and Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06099 Halle, Germany.
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
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16
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Grützner J, Billenkamp F, Spanka DT, Rick T, Monzon V, Förstner KU, Klug G. The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover. Nucleic Acids Res 2021; 49:3003-3019. [PMID: 33706375 PMCID: PMC8034643 DOI: 10.1093/nar/gkab146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 02/10/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Many different protein domains are conserved among numerous species, but their function remains obscure. Proteins with DUF1127 domains number >17 000 in current databases, but a biological function has not yet been assigned to any of them. They are mostly found in alpha- and gammaproteobacteria, some of them plant and animal pathogens, symbionts or species used in industrial applications. Bioinformatic analyses revealed similarity of the DUF1127 domain of bacterial proteins to the RNA binding domain of eukaryotic Smaug proteins that are involved in RNA turnover and have a role in development from Drosophila to mammals. This study demonstrates that the 71 amino acid DUF1127 protein CcaF1 from the alphaproteobacterium Rhodobacter sphaeroides participates in maturation of the CcsR sRNAs that are processed from the 3' UTR of the ccaF mRNA and have a role in the oxidative stress defense. CcaF1 binds to many cellular RNAs of different type, several mRNAs with a function in cysteine / methionine / sulfur metabolism. It affects the stability of the CcsR RNAs and other non-coding RNAs and mRNAs. Thus, the widely distributed DUF1127 domain can mediate RNA-binding, affect stability of its binding partners and consequently modulate the bacterial transcriptome, thereby influencing different physiological processes.
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Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| | - Fabian Billenkamp
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
- Institute of Animal Nutrition, Friedrich Loeffler Institute, Bundesalle 37, D-38116 Braunschweig, Germany
| | - Daniel-Timon Spanka
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| | - Tim Rick
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| | | | - Konrad U Förstner
- ZB MED-Information Center of Life Science, Germany
- Institute of Information Science, TH Köln, University of Applied Science, Gustav-Heinemann-Ufer 54, D-50968 Köln, Cologne, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
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17
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The Importance of AGO 1 and 4 in Post-Transcriptional Gene Regulatory Function of tRF5-GluCTC, an Respiratory Syncytial Virus-Induced tRNA-Derived RNA Fragment. Int J Mol Sci 2020; 21:ijms21228766. [PMID: 33233493 PMCID: PMC7699471 DOI: 10.3390/ijms21228766] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/18/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection in infants, the elderly, and immune-compromised patients. It is also a significant contributor to upper respiratory tract infection in the pediatric population. However, its disease mechanisms are still largely unknown. We have recently shown that a tRNA-derived RNA fragment (tRF) from the 5′-end of mature tRNA encoding GluCTC (tRF5-GluCTC), a recently discovered non-coding RNA, is functionally important for RSV replication and host gene regulation at the post-transcriptional level. However, how tRF5-GluCTC carries out the gene regulation is not fully known. In this study, we found that tRF5-GluCTC has impaired gene trans-silencing function in cells deficient of AGO1 or 4, while AGO2 and 3 seem not involved in tRF5-GluCTC-mediated gene regulation. By pulling down individual AGO protein, we discovered that tRF5-GluCTC is detectable only in the AGO4 complex, confirming the essential role of AGO4 in gene regulation and also suggesting that AGO1 contributes to the gene trans-silencing activity of tRF5-GluCTC in an atypical way. We also found that the P protein of RSV is associated with both AGO1 and 4 and AGO4 deficiency leads to reduced infectious viral particles. In summary, this study demonstrates the importance of AGO1 and 4 in mediating the gene trans-silencing function of tRF5-GluCTC.
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18
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Laver JD, Ly J, Winn JK, Karaiskakis A, Lin S, Nie K, Benic G, Jaberi-Lashkari N, Cao WX, Khademi A, Westwood JT, Sidhu SS, Morris Q, Angers S, Smibert CA, Lipshitz HD. The RNA-Binding Protein Rasputin/G3BP Enhances the Stability and Translation of Its Target mRNAs. Cell Rep 2020; 30:3353-3367.e7. [PMID: 32160542 DOI: 10.1016/j.celrep.2020.02.066] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 01/13/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
G3BP RNA-binding proteins are important components of stress granules (SGs). Here, we analyze the role of the Drosophila G3BP Rasputin (RIN) in unstressed cells, where RIN is not SG associated. Immunoprecipitation followed by microarray analysis identifies over 550 mRNAs that copurify with RIN. The mRNAs found in SGs are long and translationally silent. In contrast, we find that RIN-bound mRNAs, which encode core components of the transcription, splicing, and translation machinery, are short, stable, and highly translated. We show that RIN is associated with polysomes and provide evidence for a direct role for RIN and its human homologs in stabilizing and upregulating the translation of their target mRNAs. We propose that when cells are stressed, the resulting incorporation of RIN/G3BPs into SGs sequesters them away from their short target mRNAs. This would downregulate the expression of these transcripts, even though they are not incorporated into stress granules.
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Affiliation(s)
- John D Laver
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Jimmy Ly
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Jamie K Winn
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Angelo Karaiskakis
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Sichun Lin
- Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Kun Nie
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Giulia Benic
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Nima Jaberi-Lashkari
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Alireza Khademi
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - J Timothy Westwood
- Department of Biology, University of Toronto, 3359 Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Vector Institute, 661 University Ave, Toronto, Ontario, Canada, M160 College Street, Toronto, ON M5G 1M1, Canada
| | - Stephane Angers
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
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19
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Vastenhouw NL, Cao WX, Lipshitz HD. The maternal-to-zygotic transition revisited. Development 2019; 146:146/11/dev161471. [PMID: 31189646 DOI: 10.1242/dev.161471] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The development of animal embryos is initially directed by maternal gene products. Then, during the maternal-to-zygotic transition (MZT), developmental control is handed to the zygotic genome. Extensive research in both vertebrate and invertebrate model organisms has revealed that the MZT can be subdivided into two phases, during which very different modes of gene regulation are implemented: initially, regulation is exclusively post-transcriptional and post-translational, following which gradual activation of the zygotic genome leads to predominance of transcriptional regulation. These changes in the gene expression program of embryos are precisely controlled and highly interconnected. Here, we review current understanding of the mechanisms that underlie handover of developmental control during the MZT.
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Affiliation(s)
- Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
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20
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Ma X, Zuo Z, Shao W, Jin Y, Meng Y. The expanding roles of Argonautes: RNA interference, splicing and beyond. Brief Funct Genomics 2019; 17:191-197. [PMID: 29240875 DOI: 10.1093/bfgp/elx045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Argonaute (AGO) protein family is highly conserved in eukaryotes and prokaryotes, reflecting its evolutionarily indispensible role in maintaining normal life cycle of the organisms. Small RNA-guided, AGO-dependent RNA interference (RNAi) is a well-studied pathway for gene expression regulation, which can be performed at transcriptional, posttranscriptional or translational level. In addition to RNAi, growing pieces of evidence point to a novel role of AGOs in pre-mRNA (messenger RNA precursor) splicing in animals. Many noncoding RNAs (ncRNAs) share common structural features with protein-coding genes, indicating that these ncRNAs might be subject to AGO-mediated splicing. Finally, we provide a comprehensive view that RNAi, transcription and RNA splicing are highly interactive processes, all of which involve several key factors such as AGOs. In this regard, the AGO proteins contribute to orchestrate an exquisite gene regulatory network in vivo. However, more research efforts are needed to reach a thorough understanding of the AGO activities.
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21
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Abstract
Small RNAs govern almost every biological process in eukaryotes associating with the Argonaute (AGO) proteins to form the RNA-induced silencing complex (mRISC). AGO proteins constitute the core of RISCs with different members having variety of protein-binding partners and biochemical properties. This review focuses on the AGO subfamily of the AGOs that are ubiquitously expressed and are associated with small RNAs. The structure, function and role of the AGO proteins in the cell is discussed in detail.
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Affiliation(s)
- Saife Niaz
- Department of Biotechnology, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
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22
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Bajczyk M, Bhat SS, Szewc L, Szweykowska-Kulinska Z, Jarmolowski A, Dolata J. Novel Nuclear Functions of Arabidopsis ARGONAUTE1: Beyond RNA Interference. PLANT PHYSIOLOGY 2019; 179:1030-1039. [PMID: 30606888 PMCID: PMC6393810 DOI: 10.1104/pp.18.01351] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/21/2018] [Indexed: 05/04/2023]
Abstract
Argonaute1 activity is not limited to the cytoplasm and has been found to be associated with the regulation of gene expression in the nucleus and to be tightly associated with chromatin and transcription.
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Affiliation(s)
- Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Susheel Sagar Bhat
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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23
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Camargo C, Wu K, Fishilevich E, Narva KE, Siegfried BD. Knockdown of RNA interference pathway genes in western corn rootworm, Diabrotica virgifera virgifera, identifies no fitness costs associated with Argonaute 2 or Dicer-2. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2018; 148:103-110. [PMID: 29891360 DOI: 10.1016/j.pestbp.2018.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/07/2018] [Accepted: 04/07/2018] [Indexed: 06/08/2023]
Abstract
The use of transgenic crops that induce silencing of essential genes using double-stranded RNA (dsRNA) through RNA interference (RNAi) in western corn rootworm, Diabrotica virgifera virgifera, is likely to be an important component of new technologies for the control of this important corn pest. Previous studies have demonstrated that the dsRNA response in D. v. virgifera depends on the presence of RNAi pathway genes including Dicer-2 and Argonaute 2, and that downregulation of these genes limits the lethality of environmental dsRNA. A potential resistance mechanism to lethal dsRNA may involve loss of function of RNAi pathway genes. Howver, the potential for resistance to evolve may depend on whether these pathway genes have essential functions such that the loss of function of core proteins in the RNAi pathway will have fitness costs in D. v. virgifera. Fitness costs associated with potential resistance mechanisms have a central role in determining how resistance can evolve to RNAi technologies in western corn rootworm. We evaluated the effect of dsRNA and microRNA pathway gene knockdown on the development of D. v. virgifera larvae through short-term and long-term exposures to dsRNA for Dicer and Argonaute genes. Downregulation of Argonaute 2, Dicer-2, Dicer-1 did not significantly affect larval survivorship or development through short and long-term exposure to dsRNA. However, downregulation of Argonaute 1 reduced larval survivorship and delayed development. The implications of these results as they relate to D. v. virgifera resistance to lethal dsRNA are discussed.
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Affiliation(s)
- Carolina Camargo
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Drive, Steinmetz Hall, Gainesville, FL 32611, United States
| | - Ke Wu
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Drive, Steinmetz Hall, Gainesville, FL 32611, United States
| | - Elane Fishilevich
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268, United States
| | - Kenneth E Narva
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268, United States
| | - Blair D Siegfried
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Drive, Steinmetz Hall, Gainesville, FL 32611, United States.
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24
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Werfel S, Leierseder S, Ruprecht B, Kuster B, Engelhardt S. Preferential microRNA targeting revealed by in vivo competitive binding and differential Argonaute immunoprecipitation. Nucleic Acids Res 2017; 45:10218-10228. [PMID: 28973447 PMCID: PMC5622317 DOI: 10.1093/nar/gkx640] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/21/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) have been described to simultaneously inhibit hundreds of targets, albeit to a modest extent. It was recently proposed that there could exist more specific, exceptionally strong binding to a subgroup of targets. However, it is unknown, whether this is the case and how such targets can be identified. Using Argonaute2-ribonucleoprotein immunoprecipitation and in vivo competitive binding assays, we demonstrate for miRNAs-21, -199–3p and let-7 exceptional regulation of a subset of targets, which are characterized by preferential miRNA binding. We confirm this finding by analysis of independent quantitative proteome and transcriptome datasets obtained after miRNA silencing. Our data suggest that mammalian miRNA activity is guided by preferential binding of a small set of 3′-untranslated regions, thereby shaping a steep gradient of regulation between potential targets. Our approach can be applied for transcriptome-wide identification of such targets independently of the presence of seed complementary sequences or other predictors.
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Affiliation(s)
- Stanislas Werfel
- Institut für Pharmakologie und Toxikologie, Technische Universität München (TUM), 80802 Munich, Germany.,DZHK (German Center for Cardiovascular Research), Munich Heart Alliance, 80802 Munich, Germany
| | - Simon Leierseder
- Institut für Pharmakologie und Toxikologie, Technische Universität München (TUM), 80802 Munich, Germany
| | - Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technische Universität München, 85354 Freising, Germany
| | - Stefan Engelhardt
- Institut für Pharmakologie und Toxikologie, Technische Universität München (TUM), 80802 Munich, Germany.,DZHK (German Center for Cardiovascular Research), Munich Heart Alliance, 80802 Munich, Germany
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25
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Lee HC, Jung SH, Hwang HJ, Kang D, De S, Dudekula DB, Martindale JL, Park B, Park SK, Lee EK, Lee JH, Jeong S, Han K, Park HJ, Ko YG, Gorospe M, Lee JS. WIG1 is crucial for AGO2-mediated ACOT7 mRNA silencing via miRNA-dependent and -independent mechanisms. Nucleic Acids Res 2017; 45:6894-6910. [PMID: 28472401 PMCID: PMC5499809 DOI: 10.1093/nar/gkx307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/28/2017] [Indexed: 12/14/2022] Open
Abstract
RNA-binding proteins (RBPs) are involved in mRNA splicing, maturation, transport, translation, storage and turnover. Here, we identified ACOT7 mRNA as a novel target of human WIG1. ACOT7 mRNA decay was triggered by the microRNA miR-9 in a WIG1-dependent manner via classic recruitment of Argonaute 2 (AGO2). Interestingly, AGO2 was also recruited to ACOT7 mRNA in a WIG1-dependent manner in the absence of miR-9, which indicates an alternative model whereby WIG1 controls AGO2-mediated gene silencing. The WIG1–AGO2 complex attenuated translation initiation via an interaction with translation initiation factor 5B (eIF5B). These results were confirmed using a WIG1 tethering system based on the MS2 bacteriophage coat protein and a reporter construct containing an MS2-binding site, and by immunoprecipitation of WIG1 and detection of WIG1-associated proteins using liquid chromatography-tandem mass spectrometry. We also identified WIG1-binding motifs using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation analyses. Altogether, our data indicate that WIG1 governs the miRNA-dependent and the miRNA-independent recruitment of AGO2 to lower the stability of and suppress the translation of ACOT7 mRNA.
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Affiliation(s)
- Hyung Chul Lee
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Seung Hee Jung
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Hyun Jung Hwang
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Donghee Kang
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Supriyo De
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Byungkyu Park
- Department of Computer Science and Engineering, Inha University, Incheon 22212, Korea
| | - Seung Kuk Park
- Department of Molecular Biology, Dankook University, Yongin 16890, Korea
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Sunjoo Jeong
- Department of Molecular Biology, Dankook University, Yongin 16890, Korea
| | - Kyungsook Han
- Department of Computer Science and Engineering, Inha University, Incheon 22212, Korea
| | - Heon Joo Park
- Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Department of Microbiology, Inha University College of Medicine, Incheon 22212, Korea
| | - Young-Gyu Ko
- Division of Life Sciences, Korea University, Seoul 02841, Korea
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jae-Seon Lee
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
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26
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Götze M, Dufourt J, Ihling C, Rammelt C, Pierson S, Sambrani N, Temme C, Sinz A, Simonelig M, Wahle E. Translational repression of the Drosophila nanos mRNA involves the RNA helicase Belle and RNA coating by Me31B and Trailer hitch. RNA (NEW YORK, N.Y.) 2017; 23:1552-1568. [PMID: 28701521 PMCID: PMC5602113 DOI: 10.1261/rna.062208.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/10/2017] [Indexed: 05/10/2023]
Abstract
Translational repression of maternal mRNAs is an essential regulatory mechanism during early embryonic development. Repression of the Drosophila nanos mRNA, required for the formation of the anterior-posterior body axis, depends on the protein Smaug binding to two Smaug recognition elements (SREs) in the nanos 3' UTR. In a comprehensive mass spectrometric analysis of the SRE-dependent repressor complex, we identified Smaug, Cup, Me31B, Trailer hitch, eIF4E, and PABPC, in agreement with earlier data. As a novel component, the RNA-dependent ATPase Belle (DDX3) was found, and its involvement in deadenylation and repression of nanos was confirmed in vivo. Smaug, Cup, and Belle bound stoichiometrically to the SREs, independently of RNA length. Binding of Me31B and Tral was also SRE-dependent, but their amounts were proportional to the length of the RNA and equimolar to each other. We suggest that "coating" of the RNA by a Me31B•Tral complex may be at the core of repression.
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Affiliation(s)
- Michael Götze
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Jérémy Dufourt
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Christian Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Stephanie Pierson
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Nagraj Sambrani
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Claudia Temme
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Martine Simonelig
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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27
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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28
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RNA-binding protein SAMD4 regulates skeleton development through translational inhibition of Mig6 expression. Cell Discov 2017; 3:16050. [PMID: 28163927 PMCID: PMC5259697 DOI: 10.1038/celldisc.2016.50] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/05/2016] [Indexed: 12/11/2022] Open
Abstract
Protein translation regulation has essential roles in inflammatory responses, cancer initiation and the pathogenesis of several neurodegenerative disorders. However, the role of the regulation of protein translation in mammalian skeleton development has been rarely elaborated. Here we report that the lack of the RNA-binding protein sterile alpha motif domain containing protein 4 (SAMD4) resulted in multiple developmental defects in mice, including delayed bone development and decreased osteogenesis. Samd4-deficient mesenchymal progenitors exhibit impaired osteoblast differentiation and function. Mechanism study demonstrates that SAMD4 binds the Mig6 mRNA and inhibits MIG6 protein synthesis. Consistent with this, Samd4-deficient cells have increased MIG6 protein level and knockdown of Mig6 rescues the impaired osteogenesis in Samd4-deficient cells. Furthermore, Samd4-deficient mice also display chondrocyte defects, which is consistent with the regulation of MIG6 protein level by SAMD4. These findings define SAMD4 as a previously unreported key regulator of osteoblastogenesis and bone development, implying that regulation of protein translation is an important mechanism governing skeletogenesis and that control of protein translation could have therapeutic potential in metabolic bone diseases, such as osteoporosis.
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29
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Abstract
Until the zygotic genome is activated, early development relies on the products deposited by the mother. Once the zygotic genome starts to be transcribed, most maternal products are not needed anymore by the developing embryo. This emancipation from the maternal genome occurs during the Zygotic Genome Activation (ZGA). Although the process by which the maternal content is replaced with zygotic products differs from species to species, there is a common theme to all of them: maternal transcripts are actively degraded. Here, a review of how the degradation of maternal RNAs is regulated during early development and discussions on some computational tools that may be of use in this research area are outlined.
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Affiliation(s)
- Antonio Marco
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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30
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The Smaug RNA-Binding Protein Is Essential for microRNA Synthesis During the Drosophila Maternal-to-Zygotic Transition. G3-GENES GENOMES GENETICS 2016; 6:3541-3551. [PMID: 27591754 PMCID: PMC5100853 DOI: 10.1534/g3.116.034199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Metazoan embryos undergo a maternal-to-zygotic transition (MZT) during which maternal gene products are eliminated and the zygotic genome becomes transcriptionally active. During this process, RNA-binding proteins (RBPs) and the microRNA-induced silencing complex (miRISC) target maternal mRNAs for degradation. In Drosophila, the Smaug (SMG), Brain tumor (BRAT), and Pumilio (PUM) RBPs bind to and direct the degradation of largely distinct subsets of maternal mRNAs. SMG has also been shown to be required for zygotic synthesis of mRNAs and several members of the miR-309 family of microRNAs (miRNAs) during the MZT. Here, we have carried out global analysis of small RNAs both in wild-type and in smg mutants. Our results show that 85% of all miRNA species encoded by the genome are present during the MZT. Whereas loss of SMG has no detectable effect on Piwi-interacting RNAs (piRNAs) or small interfering RNAs (siRNAs), zygotic production of more than 70 species of miRNAs fails or is delayed in smg mutants. SMG is also required for the synthesis and stability of a key miRISC component, Argonaute 1 (AGO1), but plays no role in accumulation of the Argonaute family proteins associated with piRNAs or siRNAs. In smg mutants, maternal mRNAs that are predicted targets of the SMG-dependent zygotic miRNAs fail to be cleared. BRAT and PUM share target mRNAs with these miRNAs but not with SMG itself. We hypothesize that SMG controls the MZT, not only through direct targeting of a subset of maternal mRNAs for degradation but, indirectly, through production and function of miRNAs and miRISC, which act together with BRAT and/or PUM to control clearance of a distinct subset of maternal mRNAs.
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31
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Bracken CP, Scott HS, Goodall GJ. A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet 2016; 17:719-732. [DOI: 10.1038/nrg.2016.134] [Citation(s) in RCA: 468] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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Poly(ADP-Ribosyl)ation of hnRNP A1 Protein Controls Translational Repression in Drosophila. Mol Cell Biol 2016; 36:2476-86. [PMID: 27402862 DOI: 10.1128/mcb.00207-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/27/2016] [Indexed: 01/14/2023] Open
Abstract
Poly(ADP-ribosyl)ation of heterogeneous nuclear ribonucleoproteins (hnRNPs) regulates the posttranscriptional fate of RNA during development. Drosophila hnRNP A1, Hrp38, is required for germ line stem cell maintenance and oocyte localization. The mRNA targets regulated by Hrp38 are mostly unknown. We identified 428 Hrp38-associated gene transcripts in the fly ovary, including mRNA of the translational repressor Nanos. We found that Hrp38 binds to the 3' untranslated region (UTR) of Nanos mRNA, which contains a translation control element. We have demonstrated that translation of the luciferase reporter bearing the Nanos 3' UTR is enhanced by dsRNA-mediated Hrp38 knockdown as well as by mutating potential Hrp38-binding sites. Our data show that poly(ADP-ribosyl)ation inhibits Hrp38 binding to the Nanos 3' UTR, increasing the translation in vivo and in vitro hrp38 and Parg null mutants showed an increased ectopic Nanos translation early in the embryo. We conclude that Hrp38 represses Nanos translation, whereas its poly(ADP-ribosyl)ation relieves the repression effect, allowing restricted Nanos expression in the posterior germ plasm during oogenesis and early embryogenesis.
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33
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A Smaug2-Based Translational Repression Complex Determines the Balance between Precursor Maintenance versus Differentiation during Mammalian Neurogenesis. J Neurosci 2016; 35:15666-81. [PMID: 26609159 DOI: 10.1523/jneurosci.2172-15.2015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED Here, we have asked about post-transcriptional mechanisms regulating murine developmental neurogenesis, focusing upon the RNA-binding proteins Smaug2 and Nanos1. We identify, in embryonic neural precursors of the murine cortex, a Smaug2 protein/nanos1 mRNA complex that is present in cytoplasmic granules with the translational repression proteins Dcp1 and 4E-T. We show that Smaug2 inhibits and Nanos1 promotes neurogenesis, with Smaug2 knockdown enhancing neurogenesis and depleting precursors, and Nanos1 knockdown inhibiting neurogenesis and maintaining precursors. Moreover, we show that Smaug2 likely regulates neurogenesis by silencing nanos1 mRNA. Specifically, Smaug2 knockdown inappropriately increases Nanos1 protein, and the Smaug2 knockdown-mediated neurogenesis is rescued by preventing this increase. Thus, Smaug2 and Nanos1 function as a bimodal translational repression switch to control neurogenesis, with Smaug2 acting in transcriptionally primed precursors to silence mRNAs important for neurogenesis, including nanos1 mRNA, and Nanos1 acting during the transition to neurons to repress the precursor state. SIGNIFICANCE STATEMENT The mechanisms instructing neural stem cells to generate the appropriate progeny are still poorly understood. Here, we show that the RNA-binding proteins Smaug2 and Nanos1 are critical regulators of this balance and provide evidence supporting the idea that neural precursors are transcriptionally primed to generate neurons but translational regulation maintains these precursors in a stem cell state until the appropriate developmental time.
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34
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Patel PH, Barbee SA, Blankenship JT. GW-Bodies and P-Bodies Constitute Two Separate Pools of Sequestered Non-Translating RNAs. PLoS One 2016; 11:e0150291. [PMID: 26930655 PMCID: PMC4773245 DOI: 10.1371/journal.pone.0150291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/11/2016] [Indexed: 01/05/2023] Open
Abstract
Non-translating RNAs that have undergone active translational repression are culled from the cytoplasm into P-bodies for decapping-dependent decay or for sequestration. Organisms that use microRNA-mediated RNA silencing have an additional pathway to remove RNAs from active translation. Consequently, proteins that govern microRNA-mediated silencing, such as GW182/Gw and AGO1, are often associated with the P-bodies of higher eukaryotic organisms. Due to the presence of Gw, these structures have been referred to as GW-bodies. However, several reports have indicated that GW-bodies have different dynamics to P-bodies. Here, we use live imaging to examine GW-body and P-body dynamics in the early Drosophila melanogaster embryo. While P-bodies are present throughout early embryonic development, cytoplasmic GW-bodies only form in significant numbers at the midblastula transition. Unlike P-bodies, which are predominantly cytoplasmic, GW-bodies are present in both nuclei and the cytoplasm. RNA decapping factors such as DCP1, Me31B, and Hpat are not associated with GW-bodies, indicating that P-bodies and GW-bodies are distinct structures. Furthermore, known Gw interactors such as AGO1 and the CCR4-NOT deadenylation complex, which have been shown to be important for Gw function, are also not present in GW-bodies. Use of translational inhibitors puromycin and cycloheximide, which respectively increase or decrease cellular pools of non-translating RNAs, alter GW-body size, underscoring that GW-bodies are composed of non-translating RNAs. Taken together, these data indicate that active translational silencing most likely does not occur in GW-bodies. Instead GW-bodies most likely function as repositories for translationally silenced RNAs. Finally, inhibition of zygotic gene transcription is unable to block the formation of either P-bodies or GW-bodies in the early embryo, suggesting that these structures are composed of maternal RNAs.
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Affiliation(s)
- Prajal H. Patel
- Department of Biological Sciences and Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, United States of America
| | - Scott A. Barbee
- Department of Biological Sciences and Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, United States of America
- Molecular and Cellular Biophysics Program, University of Denver, Denver, Colorado, United States of America
- * E-mail: (JTB); (SAB)
| | - J. Todd Blankenship
- Department of Biological Sciences and Eleanor Roosevelt Institute, University of Denver, Denver, Colorado, United States of America
- Molecular and Cellular Biophysics Program, University of Denver, Denver, Colorado, United States of America
- * E-mail: (JTB); (SAB)
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35
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Abstract
Germ granules are the hallmark of all germ cells. These membrane-less, electron-dense structures were first observed over 100 years ago. Today, their role in regulating and processing transcripts critical for the establishment, maintenance, and protection of germ cells is well established, and pathways outlining the biochemical mechanisms and physical properties associated with their biogenesis are emerging.
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Affiliation(s)
- Ruth Lehmann
- Howard Hughes Medical Institute (HHMI), Department of Cell Biology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, USA.
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36
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Sokolowski TR, Walczak AM, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. Phys Rev E 2016; 93:022404. [PMID: 26986359 PMCID: PMC5221721 DOI: 10.1103/physreve.93.022404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Indexed: 11/07/2022]
Abstract
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression.
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Affiliation(s)
- Thomas R. Sokolowski
- Institute of Science and Technology Austria, Am Campus 1, A-3400
Klosterneuburg, Austria
| | - Aleksandra M. Walczak
- CNRS-Laboratoire de Physique Théorique de
l’École Normale Supérieure, 24 rue Lhomond, F-75005 Paris,
France
| | - William Bialek
- Joseph Henry Laboratories of Physics, Lewis-Sigler Institute for
Integrative Genomics, Princeton University Princeton, New Jersey 08544, USA
| | - Gašper Tkačik
- Institute of Science and Technology Austria, Am Campus 1, A-3400
Klosterneuburg, Austria
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37
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Laver JD, Marsolais AJ, Smibert CA, Lipshitz HD. Regulation and Function of Maternal Gene Products During the Maternal-to-Zygotic Transition in Drosophila. Curr Top Dev Biol 2015; 113:43-84. [PMID: 26358870 DOI: 10.1016/bs.ctdb.2015.06.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Drosophila late-stage oocytes and early embryos are transcriptionally silent. Thus, control of gene expression during these developmental periods is posttranscriptional and posttranslational. Global changes in the transcriptome and proteome occur during oocyte maturation, after egg activation and fertilization, and upon zygotic genome activation. We review the scale, content, and dynamics of these global changes; the factors that regulate these changes; and the mechanisms by which they are accomplished. We highlight the intimate relationship between the clearance of maternal gene products and the activation of the embryo's own genome, and discuss the fact that each of these complementary components of the maternal-to-zygotic transition can be subdivided into several phases that serve different biological roles and are regulated by distinct factors.
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Affiliation(s)
- John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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38
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Yartseva V, Giraldez AJ. The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming. Curr Top Dev Biol 2015; 113:191-232. [PMID: 26358874 DOI: 10.1016/bs.ctdb.2015.07.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cellular transitions occur at all stages of organismal life from conception to adult regeneration. Changing cellular state involves three main features: activating gene expression necessary to install the new cellular state, modifying the chromatin status to stabilize the new gene expression program, and removing existing gene products to clear out the previous cellular program. The maternal-to-zygotic transition (MZT) is one of the most profound changes in the life of an organism. It involves gene expression remodeling at all levels, including the active clearance of the maternal oocyte program to adopt the embryonic totipotency. In this chapter, we provide an overview of molecular mechanisms driving maternal mRNA clearance during the MZT, describe the developmental consequences of losing components of this gene regulation, and illustrate how remodeling of gene expression during the MZT is common to other cellular transitions with parallels to cellular reprogramming.
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Affiliation(s)
- Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.
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39
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Barckmann B, Pierson S, Dufourt J, Papin C, Armenise C, Port F, Grentzinger T, Chambeyron S, Baronian G, Desvignes JP, Curk T, Simonelig M. Aubergine iCLIP Reveals piRNA-Dependent Decay of mRNAs Involved in Germ Cell Development in the Early Embryo. Cell Rep 2015; 12:1205-16. [PMID: 26257181 PMCID: PMC4626872 DOI: 10.1016/j.celrep.2015.07.030] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/17/2015] [Accepted: 07/14/2015] [Indexed: 11/25/2022] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway plays an essential role in the repression of transposons in the germline. Other functions of piRNAs such as post-transcriptional regulation of mRNAs are now emerging. Here, we perform iCLIP with the PIWI protein Aubergine (Aub) and identify hundreds of maternal mRNAs interacting with Aub in the early Drosophila embryo. Gene expression profiling reveals that a proportion of these mRNAs undergo Aub-dependent destabilization during the maternal-to-zygotic transition. Strikingly, Aub-dependent unstable mRNAs encode germ cell determinants. iCLIP with an Aub mutant that is unable to bind piRNAs confirms piRNA-dependent binding of Aub to mRNAs. Base pairing between piRNAs and mRNAs can induce mRNA cleavage and decay that are essential for embryonic development. These results suggest general regulation of maternal mRNAs by Aub and piRNAs, which plays a key developmental role in the embryo through decay and localization of mRNAs encoding germ cell determinants. Aub binds to maternal mRNAs in early Drosophila embryos Interaction between Aub and maternal mRNAs depends on piRNAs aub mutants are defective in mRNA decay during the MZT Aub-dependent unstable mRNAs encode germ cell determinants
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Affiliation(s)
- Bridlin Barckmann
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Stéphanie Pierson
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Jérémy Dufourt
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Catherine Papin
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Claudia Armenise
- RNA Silencing and Control of Transposition, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Fillip Port
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Thomas Grentzinger
- RNA Silencing and Control of Transposition, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Séverine Chambeyron
- RNA Silencing and Control of Transposition, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Grégory Baronian
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 5, France
| | - Jean-Pierre Desvignes
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 5, France
| | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Martine Simonelig
- mRNA Regulation and Development, Institut de Génétique Humaine, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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40
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Abstract
mRNA localisation coupled to translational regulation provides an important means of dictating when and where proteins function in a variety of model systems. This mechanism is particularly relevant in polarised or migrating cells. Although many of the models for how this is achieved were first proposed over 20 years ago, some of the molecular details are still poorly understood. Nevertheless, advanced imaging, biochemical and computational approaches have started to shed light on the cis-acting localisation signals and trans-acting factors that dictate the final destination of localised transcripts. In this Cell Science at a Glance article and accompanying poster, we provide an overview of mRNA localisation, from transcription to degradation, focusing on the microtubule-dependent active transport and anchoring mechanism, which we will use to explain the general paradigm. However, it is clear that there are diverse ways in which mRNAs become localised and target protein expression, and we highlight some of the similarities and differences between these mechanisms.
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Affiliation(s)
- Richard M Parton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alexander Davidson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Timothy T Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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Smalheiser NR, Gomes OLA. Mammalian Argonaute-DNA binding? Biol Direct 2014; 10:27. [PMID: 25472905 PMCID: PMC4258305 DOI: 10.1186/s13062-014-0027-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/19/2014] [Indexed: 12/21/2022] Open
Abstract
When a field shares the consensus that a particular phenomenon does NOT occur, this may reflect extensive experimental investigations with negative outcomes, or may represent the “common sense” position based on current knowledge and established ways of thinking. The current consensus of the RNA field is that eukaryotic Argonaute (Ago) proteins employ RNA guides and target other RNAs. The alternative -- that eukaryotic Ago has biologically important interactions with DNA in vivo – has not been seriously considered, in part because the only role contemplated for DNA was as a guide strand, and in part because it did not seem plausible that any natural source of suitable DNAs exists in eukaryotic cells. However, eukaryotic Argonaute domains bind DNA in the test tube, and several articles report that small inhibitory double-stranded DNAs do have the ability to silence target RNAs in a sequence-dependent (though poorly characterized) manner. A search of the literature identified potential DNA binding partners for Ago, including (among others) single-stranded DNAs residing in extracellular vesicles, and cytoplasmic satellite-repeat DNA fragments that are associated with the plasma membrane and transcribed by Pol II. It is interesting to note that both cytoplasmic and extracellular vesicle DNA are expressed at greatly elevated levels in cancer cells relative to normal cells. In such a pathological scenario, if not under normal conditions, there may be appreciable binding of Ago to DNA despite its lower affinity compared to RNA. If so, DNA might displace Ago from binding to its normal partners (miRNAs, siRNAs and other short ncRNAs), disrupting tightly controlled post-transcriptional gene silencing processes that are vital to correct functioning of a normal cell. The possible contribution to cancer pathogenesis is a strong motivator for further investigation of Ago-DNA binding. More generally, this case underscores the need for better informatics tools to allow investigators to analyze the state of a given scientific question at a high-level and to identify possible new research directions. Reviewers: This article was reviewed by Eugene Koonin, Kira S. Makarova, Alexander Maxwell Burroughs (nominated by L Aravind), and Isidore Rigoutsos. Open peer review: Reviewed by Eugene Koonin, Kira S. Makarova, Alexander Maxwell Burroughs (nominated by L Aravind), and Isidore Rigoutsos. For the full reviews, please go to the Reviewers’ comments section.
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Thomas MG, Pascual ML, Maschi D, Luchelli L, Boccaccio GL. Synaptic control of local translation: the plot thickens with new characters. Cell Mol Life Sci 2014; 71:2219-39. [PMID: 24212248 PMCID: PMC11113725 DOI: 10.1007/s00018-013-1506-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 10/11/2013] [Accepted: 10/21/2013] [Indexed: 12/18/2022]
Abstract
The production of proteins from mRNAs localized at the synapse ultimately controls the strength of synaptic transmission, thereby affecting behavior and cognitive functions. The regulated transcription, processing, and transport of mRNAs provide dynamic control of the dendritic transcriptome, which includes thousands of messengers encoding multiple cellular functions. Translation is locally modulated by synaptic activity through a complex network of RNA-binding proteins (RBPs) and various types of non-coding RNAs (ncRNAs) including BC-RNAs, microRNAs, piwi-interacting RNAs, and small interference RNAs. The RBPs FMRP and CPEB play a well-established role in synaptic translation, and additional regulatory factors are emerging. The mRNA repressors Smaug, Nanos, and Pumilio define a novel pathway for local translational control that affects dendritic branching and spines in both flies and mammals. Recent findings support a role for processing bodies and related synaptic mRNA-silencing foci (SyAS-foci) in the modulation of synaptic plasticity and memory formation. The SyAS-foci respond to different stimuli with changes in their integrity thus enabling regulated mRNA release followed by translation. CPEB, Pumilio, TDP-43, and FUS/TLS form multimers through low-complexity regions related to prion domains or polyQ expansions. The oligomerization of these repressor RBPs is mechanistically linked to the aggregation of abnormal proteins commonly associated with neurodegeneration. Here, we summarize the current knowledge on how specificity in mRNA translation is achieved through the concerted action of multiple pathways that involve regulatory ncRNAs and RBPs, the modification of translation factors, and mRNA-silencing foci dynamics.
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Affiliation(s)
- María Gabriela Thomas
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- IIBBA-CONICET, C1405BWE Buenos Aires, Argentina
| | - Malena Lucía Pascual
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- IIBBA-CONICET, C1405BWE Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Buenos Aires, Argentina
| | - Darío Maschi
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- Present Address: Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO USA
| | - Luciana Luchelli
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- IIBBA-CONICET, C1405BWE Buenos Aires, Argentina
| | - Graciela Lidia Boccaccio
- Instituto Leloir, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
- IIBBA-CONICET, C1405BWE Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Buenos Aires, Argentina
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43
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Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. Mol Cell 2014; 54:1042-1054. [PMID: 24857550 DOI: 10.1016/j.molcel.2014.03.049] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/24/2014] [Accepted: 03/26/2014] [Indexed: 12/22/2022]
Abstract
To exert regulatory function, miRNAs guide Argonaute (AGO) proteins to partially complementary sites on target RNAs. Crosslinking and immunoprecipitation (CLIP) assays are state-of-the-art to map AGO binding sites, but assigning the targeting miRNA to these sites relies on bioinformatics predictions and is therefore indirect. To directly and unambiguously identify miRNA:target site interactions, we modified our CLIP methodology in C. elegans to experimentally ligate miRNAs to their target sites. Unexpectedly, ligation reactions also occurred in the absence of the exogenous ligase. Our in vivo data set and reanalysis of published mammalian AGO-CLIP data for miRNA-chimeras yielded ∼17,000 miRNA:target site interactions. Analysis of interactions and extensive experimental validation of chimera-discovered targets of viral miRNAs suggest that our strategy identifies canonical, noncanonical, and nonconserved miRNA:targets. About 80% of miRNA interactions have perfect or partial seed complementarity. In summary, analysis of miRNA:target chimeras enables the systematic, context-specific, in vivo discovery of miRNA binding.
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Mutation of mouse Samd4 causes leanness, myopathy, uncoupled mitochondrial respiration, and dysregulated mTORC1 signaling. Proc Natl Acad Sci U S A 2014; 111:7367-72. [PMID: 24799716 DOI: 10.1073/pnas.1406511111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Sterile alpha motif domain containing protein 4 (Samd4) is an RNA binding protein that mediates translational repression. We identified a Samd4 missense mutation, designated supermodel, that caused leanness and kyphosis associated with myopathy and adipocyte defects in C57BL/6J mice. The supermodel mutation protected homozygous mice from high fat diet-induced obesity, likely by promoting enhanced energy expenditure through uncoupled mitochondrial respiration. Glucose tolerance was impaired due to diminished insulin release in homozygous mutant mice. The defects of metabolism in supermodel mice may be explained by dysregulated mechanistic target of rapamycin complex 1 (mTORC1) signaling, evidenced by hypophosphorylation of 4E-BP1 and S6 in muscle and adipose tissues of homozygous mice. Samd4 may interface with mTORC1 signaling through an interaction with 14-3-3 proteins and with Akt, which phosphorylates Samd4 in vitro.
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45
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Inefficient SRP interaction with a nascent chain triggers a mRNA quality control pathway. Cell 2014; 156:146-57. [PMID: 24439374 DOI: 10.1016/j.cell.2013.12.017] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 08/01/2013] [Accepted: 12/18/2013] [Indexed: 11/22/2022]
Abstract
Misfolded proteins are often cytotoxic, unless cellular systems prevent their accumulation. Data presented here uncover a mechanism by which defects in secretory proteins lead to a dramatic reduction in their mRNAs and protein expression. When mutant signal sequences fail to bind to the signal recognition particle (SRP) at the ribosome exit site, the nascent chain instead contacts Argonaute2 (Ago2), and the mutant mRNAs are specifically degraded. Severity of signal sequence mutations correlated with increased proximity of Ago2 to nascent chain and mRNA degradation. Ago2 knockdown inhibited degradation of the mutant mRNA, while overexpression of Ago2 or knockdown of SRP54 promoted degradation of secretory protein mRNA. The results reveal a previously unappreciated general mechanism of translational quality control, in which specific mRNA degradation preemptively regulates aberrant protein production (RAPP).
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46
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Chen L, Dumelie JG, Li X, Cheng MH, Yang Z, Laver JD, Siddiqui NU, Westwood JT, Morris Q, Lipshitz HD, Smibert CA. Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein. Genome Biol 2014; 15:R4. [PMID: 24393533 PMCID: PMC4053848 DOI: 10.1186/gb-2014-15-1-r4] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 01/07/2014] [Indexed: 12/12/2022] Open
Abstract
Background Smaug is an RNA-binding protein that induces the degradation and represses the translation of mRNAs in the early Drosophila embryo. Smaug has two identified direct target mRNAs that it differentially regulates: nanos and Hsp83. Smaug represses the translation of nanos mRNA but has only a modest effect on its stability, whereas it destabilizes Hsp83 mRNA but has no detectable effect on Hsp83 translation. Smaug is required to destabilize more than one thousand mRNAs in the early embryo, but whether these transcripts represent direct targets of Smaug is unclear and the extent of Smaug-mediated translational repression is unknown. Results To gain a panoramic view of Smaug function in the early embryo, we identified mRNAs that are bound to Smaug using RNA co-immunoprecipitation followed by hybridization to DNA microarrays. We also identified mRNAs that are translationally repressed by Smaug using polysome gradients and microarrays. Comparison of the bound mRNAs to those that are translationally repressed by Smaug and those that require Smaug for their degradation suggests that a large fraction of Smaug’s target mRNAs are both translationally repressed and degraded by Smaug. Smaug directly regulates components of the TRiC/CCT chaperonin, the proteasome regulatory particle and lipid droplets, as well as many metabolic enzymes, including several glycolytic enzymes. Conclusions Smaug plays a direct and global role in regulating the translation and stability of a large fraction of the mRNAs in the early Drosophila embryo, and has unanticipated functions in control of protein folding and degradation, lipid droplet function and metabolism.
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Abstract
Small-RNA-guided gene regulation has emerged as one of the fundamental principles in cell function, and the major protein players in this process are members of the Argonaute protein family. Argonaute proteins are highly specialized binding modules that accommodate the small RNA component - such as microRNAs (miRNAs), short interfering RNAs (siRNAs) or PIWI-associated RNAs (piRNAs) - and coordinate downstream gene-silencing events by interacting with other protein factors. Recent work has made progress in our understanding of classical Argonaute-mediated gene-silencing principles, such as the effects on mRNA translation and decay, but has also implicated Argonaute proteins in several other cellular processes, such as transcriptional regulation and splicing.
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48
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Pinder BD, Smibert CA. Smaug: an unexpected journey into the mechanisms of post-transcriptional regulation. Fly (Austin) 2013; 7:142-5. [PMID: 23519205 DOI: 10.4161/fly.24336] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Drosophila Smaug is a sequence-specific RNA-binding protein that can repress the translation and induce the degradation of target mRNAs in the early Drosophila embryo. Our recent work has uncovered a new mechanism of Smaug-mediated translational repression whereby it interacts with and recruits the Argonaute 1 (Ago1) protein to an mRNA. Argonaute proteins are typically recruited to mRNAs through an associated small RNA, such as a microRNA (miRNA). Surprisingly, we found that Smaug is able to recruit Ago1 to an mRNA in a miRNA-independent manner. This work suggests that other RNA-binding proteins are likely to employ a similar mechanism of miRNA-independent Ago recruitment to control mRNA expression. Our work also adds yet another mechanism to the list that Smaug can use to regulate its targets and here we discuss some of the issues that are raised by Smaug's multi-functional nature.
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Affiliation(s)
- Benjamin D Pinder
- Department of Biochemistry; University of Toronto; Toronto, ON Canada
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49
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Wahle E, Winkler GS. RNA decay machines: deadenylation by the Ccr4-not and Pan2-Pan3 complexes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:561-70. [PMID: 23337855 DOI: 10.1016/j.bbagrm.2013.01.003] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/14/2012] [Accepted: 01/09/2013] [Indexed: 12/20/2022]
Abstract
Shortening and removal of the 3' poly(A) tail of mature mRNA by poly(A)-specific 3' exonucleases (deadenylases) is the initial and often rate-limiting step in mRNA degradation. The majority of cytoplasmic deadenylase activity is associated with the Ccr4-Not and Pan2-Pan3 complexes. Two distinct catalytic subunits, Caf1/Pop2 and Ccr4, are associated with the Ccr4-Not complex, whereas the Pan2 enzymatic subunit forms a stable complex with Pan3. In this review, we discuss the composition and activity of these two deadenylases. In addition, we comment on generic and specific mechanisms of recruitment of Ccr4-Not and Pan2-Pan3 to mRNAs. Finally, we discuss specialised and redundant functions of the deadenylases and review the importance of Ccr4-Not subunits in the regulation of physiological processes. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.
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