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Xu W, Liu J, Qi H, Si R, Zhao Z, Tao Z, Bai Y, Hu S, Sun X, Cong Y, Zhang H, Fan D, Xiao L, Wang Y, Li Y, Du Z. A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis. Nat Commun 2024; 15:2783. [PMID: 38555276 PMCID: PMC10981687 DOI: 10.1038/s41467-024-47055-4] [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: 01/08/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024] Open
Abstract
Elucidating the expression of microRNAs in developing single cells is critical for functional discovery. Here, we construct scCAMERA (single-cell cartography of microRNA expression based on reporter assay), utilizing promoter-driven fluorescent reporters in conjunction with imaging and lineage tracing. The cartography delineates the transcriptional activity of 54 conserved microRNAs in lineage-resolved single cells throughout C. elegans embryogenesis. The combinatorial expression of microRNAs partitions cells into fine clusters reflecting their function and anatomy. Notably, the expression of individual microRNAs exhibits high cell specificity and divergence among family members. Guided by cellular expression patterns, we identify developmental functions of specific microRNAs, including miR-1 in pharynx development and physiology, miR-232 in excretory canal morphogenesis by repressing NHR-25/NR5A, and a functional synergy between miR-232 and miR-234 in canal development, demonstrating the broad utility of scCAMERA. Furthermore, integrative analysis reveals that tissue-specific fate determinants activate microRNAs to repress protein production from leaky transcripts associated with alternative, especially neuronal, fates, thereby enhancing the fidelity of developmental fate differentiation. Collectively, our study offers rich opportunities for multidimensional expression-informed analysis of microRNA biology in metazoans.
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Affiliation(s)
- Weina Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyi Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huan Qi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ruolin Si
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhiguang Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiju Tao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Yuchuan Bai
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shipeng Hu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xiaohan Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yulin Cong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haoye Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Duchangjiang Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Long Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yangyang Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yongbin Li
- College of Life Sciences, Capital Normal University, Beijing, China.
| | - Zhuo Du
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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2
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Patel R, Galagali H, Kim JK, Frand AR. Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans. eLife 2022; 11:e80010. [PMID: 35968765 PMCID: PMC9377799 DOI: 10.7554/elife.80010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Animal development requires coordination among cyclic processes, sequential cell fate specifications, and once-a-lifetime morphogenic events, but the underlying timing mechanisms are not well understood. Caenorhabditis elegans undergoes four molts at regular 8 to 10 hour intervals. The pace of the cycle is governed by PERIOD/lin-42 and other as-yet unknown factors. Cessation of the cycle in young adults is controlled by the let-7 family of microRNAs and downstream transcription factors in the heterochronic pathway. Here, we characterize a negative feedback loop between NHR-23, the worm homolog of mammalian retinoid-related orphan receptors (RORs), and the let-7 family of microRNAs that regulates both the frequency and finite number of molts. The molting cycle is decelerated in nhr-23 knockdowns and accelerated in let-7(-) mutants, but timed similarly in let-7(-) nhr-23(-) double mutants and wild-type animals. NHR-23 binds response elements (ROREs) in the let-7 promoter and activates transcription. In turn, let-7 dampens nhr-23 expression across development via a complementary let-7-binding site (LCS) in the nhr-23 3' UTR. The molecular interactions between NHR-23 and let-7 hold true for other let-7 family microRNAs. Either derepression of nhr-23 transcripts by LCS deletion or high gene dosage of nhr-23 leads to protracted behavioral quiescence and extra molts in adults. NHR-23 and let-7 also coregulate scores of genes required for execution of the molts, including lin-42. In addition, ROREs and LCSs isolated from mammalian ROR and let-7 genes function in C. elegans, suggesting conservation of this feedback mechanism. We propose that this feedback loop unites the molting timer and the heterochronic gene regulatory network, possibly by functioning as a cycle counter.
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Affiliation(s)
- Ruhi Patel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Himani Galagali
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Alison R Frand
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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3
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Simion V, Loussouarn C, Laurent Y, Roncali L, Gosset D, Reverchon F, Rousseau A, Martin F, Midoux P, Pichon C, Garcion E, Baril P. LentiRILES, a miRNA-ON sensor system for monitoring the functionality of miRNA in cancer biology and therapy. RNA Biol 2021; 18:198-214. [PMID: 34570661 DOI: 10.1080/15476286.2021.1978202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A major unresolved challenge in miRNA biology is the capacity to monitor the spatiotemporal activity of miRNAs expressed in animal disease models. We recently reported that the miRNA-ON monitoring system called RILES (RNAi-inducible expression Luciferase system) implanted in lentivirus expression system (LentiRILES) offers unique opportunity to decipher the kinetics of miRNA activity in vitro, in relation with their intracellular trafficking in glioblastoma cells. In this study, we describe in detail the method for the production of LentiRILES stable cell lines and employed it in several applications in the field of miRNA biology and therapy. We show that LentiRILES is a robust, highly specific and sensitive miRNA sensor system that can be used in vitro as a single-cell miRNA monitoring method, cell-based screening platform for miRNA therapeutics and as a tool to analyse the structure-function relationship of the miRNA duplex. Furthermore, we report the kinetics of miRNA activity upon the intracranial delivery of miRNA mimics in an orthotopic animal model of glioblastoma. This information is exploited to evaluate the tumour suppressive function of miRNA-200c as locoregional therapeutic modality to treat glioblastoma. Our data provide evidence that LentiRILES is a robust system, well suited to resolve the activity of endogenous and exogenously expressed miRNAs from basic research to gene and cell therapy.
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Affiliation(s)
- Viorel Simion
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Claire Loussouarn
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - Yoan Laurent
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Loris Roncali
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - David Gosset
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Flora Reverchon
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Audrey Rousseau
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - Francisco Martin
- GENYO, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Patrick Midoux
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Chantal Pichon
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Emmanuel Garcion
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - Patrick Baril
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
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Nelson C, Ambros V. Trans-splicing of the C. elegans let-7 primary transcript developmentally regulates let-7 microRNA biogenesis and let-7 family microRNA activity. Development 2019; 146:dev172031. [PMID: 30770392 PMCID: PMC6432665 DOI: 10.1242/dev.172031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/11/2019] [Indexed: 12/19/2022]
Abstract
The sequence and roles in developmental progression of the microRNA let-7 are conserved. In general, transcription of the let-7 primary transcript (pri-let-7) occurs early in development, whereas processing of the mature let-7 microRNA arises during cellular differentiation. In Caenorhabditiselegans and other animals, the RNA-binding protein LIN-28 post-transcriptionally inhibits let-7 biogenesis at early developmental stages, but the mechanisms by which LIN-28 does this are not fully understood. Nor is it understood how the developmental regulation of let-7 might influence the expression or activities of other microRNAs of the same seed family. Here, we show that pri-let-7 is trans-spliced to the SL1 splice leader downstream of the let-7 precursor stem-loop, which produces a short polyadenylated downstream mRNA, and that this trans-splicing event negatively impacts the biogenesis of mature let-7 microRNA in cis Moreover, this trans-spliced mRNA contains sequences that are complementary to multiple members of the let-7 seed family (let-7fam) and negatively regulates let-7fam function in trans Thus, this study provides evidence for a mechanism by which splicing of a microRNA primary transcript can negatively regulate said microRNA in cis as well as other microRNAs in trans.
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Affiliation(s)
- Charles Nelson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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5
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Zhao L, Dong S, Zhao Y, Shao H, Krasteva N, Wu Q, Wang D. Dysregulation of let-7 by PEG modified graphene oxide in nematodes with deficit in epidermal barrier. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 169:1-7. [PMID: 30412893 DOI: 10.1016/j.ecoenv.2018.10.106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 06/08/2023]
Abstract
In nematode Caenorhabditis elegans, epidermal RNA interference (RNAi) knockdown of bli-1 encoding a cuticular collagen caused the toxicity induction of GO-PEG (PEG surface modified graphene oxide). In this study, we further found that epidermal RNAi knockdown of bli-1 increased expression of a microRNA let-7, and let-7 mutation suppressed the susceptibility of bli-1(RNAi) nematodes to GO-PEG toxicity. let-7 regulated the toxicity induction of GO-PEG by suppressing expression and function of its direct targets (HBL-1 and LIN-41). Like the nematodes with epidermal RNAi knockdown of bli-1, epidermal RNAi knockdown of hbl-1 or lin-41 also induced functional abnormality in epidermal barrier. Therefore, a signaling cascade of BLI-1-let-7-HBL-1/LIN-41 was raised to be involved in GO-PEG toxicity induction. Our data imply the dysregulation of let-7-mediated molecular machinery for developmental timing control by GO-PEG in nematodes with deficit in epidermal barrier caused by bli-1(RNAi).
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Affiliation(s)
- Li Zhao
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Shuangshuang Dong
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Yunli Zhao
- Department of Preventive Medicine, Bengbu Medical College, Bengbu 233030, China
| | - Huimin Shao
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Natalia Krasteva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Science, Sofia 1113, Bulgaria
| | - Qiuli Wu
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Dayong Wang
- Key Laboratory of Environmental Medicine Engineering in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China.
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6
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The Doubletime Homolog KIN-20 Mainly Regulates let-7 Independently of Its Effects on the Period Homolog LIN-42 in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2018; 8:2617-2629. [PMID: 29880558 PMCID: PMC6071595 DOI: 10.1534/g3.118.200392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Caenorhabditis elegans (C. elegans) heterochronic pathway, which regulates developmental timing, is thought to be an ancestral form of the circadian clock in other organisms. An essential member of this clock is the Period protein whose homolog, lin-42, in C. elegans is an important heterochronic gene. LIN-42 functions as a transcriptional repressor of multiple genes including the conserved lin-4 and let-7 microRNAs. Like other Period proteins, levels of LIN-42 oscillate throughout development. In other organisms this cycling is controlled in part by phosphorylation. KIN-20 is the C. elegans homolog of the Drosophila Period protein kinase Doubletime. Worms containing a large deletion in kin-20 have a significantly smaller brood size and develop slower than wild type C. elegans Here we analyze the effect of kin-20 on lin-42 phenotypes and microRNA expression. We find that kin-20 RNAi enhances loss-of-function lin-42 mutant phenotypes and that kin-20 mutant worms express lower levels of LIN-42 We also show that kin-20 is important for post-transcriptional regulation of mature let-7 and lin-4 microRNA expression. In addition, the increased level of let-7 found in lin-42(n1089) mutant worms is not maintained after kin-20 RNAi treatment. Instead, let-7 is further repressed when levels of kin-20 and lin-42 are both decreased. Altogether these results suggest that though kin-20 regulates lin-42 and let-7 microRNA, it mainly affects let-7 microRNA expression independently of lin-42 These findings further our understanding of the mechanisms by which these conserved circadian rhythmic genes interact to ultimately regulate rhythmic processes, developmental timing and microRNA biogenesis in C. elegans.
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7
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Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs. Genetics 2018; 209:651-673. [PMID: 29967059 PMCID: PMC6028246 DOI: 10.1534/genetics.118.300291] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are small, noncoding RNAs that regulate gene expression at the post-transcriptional level in essentially all aspects of Caenorhabditis elegans biology. More than 140 genes that encode microRNAs in C. elegans regulate development, behavior, metabolism, and responses to physiological and environmental changes. Genetic analysis of C. elegans microRNA genes continues to enhance our fundamental understanding of how microRNAs are integrated into broader gene regulatory networks to control diverse biological processes, including growth, cell division, cell fate determination, behavior, longevity, and stress responses. As many of these microRNA sequences and the related processing machinery are conserved over nearly a billion years of animal phylogeny, the assignment of their functions via worm genetics may inform the functions of their orthologs in other animals, including humans. In vivo investigations are especially important for microRNAs because in silico extrapolation of their functions using mRNA target prediction programs can easily assign microRNAs to incorrect genetic pathways. At this mezzanine level of microRNA bioinformatic sophistication, genetic analysis continues to be the gold standard for pathway assignments.
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8
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Liu C, Mhashilkar AS, Chabanon J, Xu S, Lustigman S, Adams JH, Unnasch TR. Development of a toolkit for piggyBac-mediated integrative transfection of the human filarial parasite Brugia malayi. PLoS Negl Trop Dis 2018; 12:e0006509. [PMID: 29782496 PMCID: PMC5983866 DOI: 10.1371/journal.pntd.0006509] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/01/2018] [Accepted: 05/08/2018] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The human filarial parasites cause diseases that are among the most important causes of morbidity in the developing world. The elimination programs targeting these infections rely on a limited number of drugs, making the identification of new chemotherapeutic agents a high priority. The study of these parasites has lagged due to the lack of reverse genetic methods. METHODOLOGY/PRINCIPAL FINDINGS We report a novel co-culture method that results in developmentally competent infective larvae of one of the human filarial parasites (Brugia malayi) and describe a method to efficiently transfect the larval stages of this parasite. We describe the production of constructs that result in integrative transfection using the piggyBac transposon system, and a selectable marker that can be used to identify transgenic parasites. We describe the production and use of dual reporter plasmids containing both a secreted luciferase selectable marker and fluorescent protein reporters that will be useful to study temporal and spatial patterns of gene expression. CONCLUSIONS/SIGNIFICANCE The methods and constructs reported here will permit the efficient production of integrated transgenic filarial parasite lines, allowing reverse genetic technologies to be applied to all life cycle stages of the parasite.
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Affiliation(s)
- Canhui Liu
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Amruta S. Mhashilkar
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Johan Chabanon
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Shulin Xu
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Sara Lustigman
- Molecular Parasitology, New York Blood Center, New York, NY, United States of America
| | - John H. Adams
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
| | - Thomas R. Unnasch
- Center for Global Health Infectious Disease Research, Department of Global Health, University of South Florida, Tampa, FL, United States of America
- * E-mail:
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9
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Pham T, Day SM, Glassford WJ, Williams TM, Rebeiz M. The evolutionary origination of a novel expression pattern through an extreme heterochronic shift. Evol Dev 2017; 19:43-55. [PMID: 28116844 DOI: 10.1111/ede.12215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The evolutionary origins of morphological structures are thought to often depend upon the redeployment of old genes into new developmental settings. Although many examples of cis-regulatory divergence have shown how pre-existing patterns of gene expression have been altered, only a small number of case studies have traced the origins of cis-regulatory elements that drive new expression domains. Here, we elucidate the evolutionary history of a novel expression pattern of the yellow gene within the Zaprionus genus of fruit flies. We observed a unique pattern of yellow transcript accumulation in the wing disc during the third larval instar, a stage that precedes its typical expression pattern associated with cuticular melanization by about a week. The region of the Zaprionus wing disc that expresses yellow subsequently develops into a portion of the thorax, a tissue for which yellow expression has been reported for several fruit fly species. Tests of GFP reporter transgenes containing the Zaprionus yellow regulatory region revealed that the wing disc pattern arose by changes in the cis-regulatory region of yellow. Moreover, the wing disc enhancer activity of yellow depends upon a short conserved sequence with ancestral thoracic functions, suggesting that the pupal thorax regulatory sequence was genetically reprogrammed to drive expression that commences much earlier during development. These results highlight how novel domains of gene expression may arise by extreme shifts in timing during the origins of novel traits.
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Affiliation(s)
- Thomas Pham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephanie M Day
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - William J Glassford
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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10
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Jovelin R, Krizus A, Taghizada B, Gray JC, Phillips PC, Claycomb JM, Cutter AD. Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis. RNA (NEW YORK, N.Y.) 2016; 22:968-978. [PMID: 27140965 PMCID: PMC4911920 DOI: 10.1261/rna.055392.115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) comprise a class of short noncoding RNA molecules that play diverse developmental and physiological roles by controlling mRNA abundance and protein output of the vast majority of transcripts. Despite the importance of miRNAs in regulating gene function, we still lack a complete understanding of how miRNAs themselves are transcriptionally regulated. To fill this gap, we predicted regulatory sequences by searching for abundant short motifs located upstream of miRNAs in eight species of Caenorhabditis nematodes. We identified three conserved motifs across the Caenorhabditis phylogeny that show clear signatures of purifying selection from comparative genomics, patterns of nucleotide changes in motifs of orthologous miRNAs, and correlation between motif incidence and miRNA expression. We then validated our predictions with transgenic green fluorescent protein reporters and site-directed mutagenesis for a subset of motifs located in an enhancer region upstream of let-7 We demonstrate that a CT-dinucleotide motif is sufficient for proper expression of GFP in the seam cells of adult C. elegans, and that two other motifs play incremental roles in combination with the CT-rich motif. Thus, functional tests of sequence motifs identified through analysis of molecular evolutionary signatures provide a powerful path for efficiently characterizing the transcriptional regulation of miRNA genes.
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Affiliation(s)
- Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Aldis Krizus
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Bakhtiyar Taghizada
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Jeremy C Gray
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Oregon 97403, USA
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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11
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A novel function for the DEAD-box RNA helicase DDX-23 in primary microRNA processing in Caenorhabditis elegans. Dev Biol 2016; 409:459-72. [DOI: 10.1016/j.ydbio.2015.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 12/24/2022]
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12
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Mondol V, Ahn BC, Pasquinelli AE. Splicing remodels the let-7 primary microRNA to facilitate Drosha processing in Caenorhabditis elegans. RNA (NEW YORK, N.Y.) 2015; 21:1396-1403. [PMID: 26081559 PMCID: PMC4509930 DOI: 10.1261/rna.052118.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/11/2015] [Indexed: 06/04/2023]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that use partial base-pairing to recognize and regulate the expression of messenger RNAs (mRNAs). Mature miRNAs arise from longer primary transcripts (pri-miRNAs) that are processed to a shorter hairpin precursor miRNA (pre-miRNA) by the Microprocessor complex. In Caenorhabditis elegans the primary let-7 (pri-let-7) transcript undergoes trans-splicing, where pri-let-7 is cleaved at a 3' splice site and the splice-leader-1 (SL1) sequence is appended at the 5' end. Here we investigate the role of this splicing event in the biogenesis of let-7 miRNA. We hypothesized that splicing changes the secondary structure of the pri-let-7 transcript, creating a more favorable substrate for recognition by the Microprocessor. Supporting this idea, we detected conspicuous structural differences between unspliced and SL1-spliced pri-let-7 transcripts using in vitro ribonuclease (RNase) assays. Through the generation of transgenic worm strains, we found that the RNA secondary structure produced by splicing, as opposed to the act of splicing itself, optimizes processing of pri-let-7 by the Microprocessor in vivo. We also observed that the endogenous spliced, but not the unspliced, pri-let-7 transcripts bind to the Microprocessor and accumulate upon its depletion. We conclude that splicing is a key step in generating pri-let-7 transcripts with a structure that enables downstream processing events to produce appropriate levels of mature let-7.
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Affiliation(s)
- Vanessa Mondol
- Division of Biology, University of California, San Diego, La Jolla, California 92093-0349, USA
| | - Byoung Chan Ahn
- Division of Biology, University of California, San Diego, La Jolla, California 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, California 92093-0349, USA
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13
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Ecsedi M, Rausch M, Großhans H. The let-7 microRNA directs vulval development through a single target. Dev Cell 2015; 32:335-44. [PMID: 25669883 DOI: 10.1016/j.devcel.2014.12.018] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/31/2014] [Accepted: 12/18/2014] [Indexed: 11/16/2022]
Abstract
The let-7 microRNA (miRNA) regulates stemness in animals ranging from worms to humans. However, the cause of the dramatic vulval rupturing phenotype of let-7 mutant C. elegans has remained unknown. Consistent with the notion that miRNAs function by coordinately tuning the expression of many targets, bursting may result from joint dysregulation of several targets, possibly in the epidermis. Alternatively, overexpression of LET-60/RAS, a key vulva development gene and a phylogenetically conserved target of let-7, may be responsible. Here, we show that let-7 functions in the vulval-uterine system to ensure vulval integrity but that regulation of most targets of let-7, including LET-60/RAS, is dispensable. Using CRISPR-Cas9 to edit endogenous let-7 target sites, we found that regulation of LIN-41/TRIM71 alone is necessary and sufficient to prevent vulval rupturing. Hence, let-7 does not function to reduce gene expression noise broadly, but to direct vulval development through extensive regulation of a single, defined target.
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Affiliation(s)
- Matyas Ecsedi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Magdalene Rausch
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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Caenorhabditis elegans period homolog lin-42 regulates the timing of heterochronic miRNA expression. Proc Natl Acad Sci U S A 2014; 111:15450-5. [PMID: 25319259 DOI: 10.1073/pnas.1414856111] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNAs that regulate gene expression posttranscriptionally via the 3' UTR of target mRNAs and were first identified in the Caenorhabditis elegans heterochronic pathway. miRNAs have since been found in many organisms and have broad functions, including control of differentiation and pluripotency in humans. lin-4 and let-7-family miRNAs regulate developmental timing in C. elegans, and their proper temporal expression ensures cell lineage patterns are correctly timed and sequentially executed. Although much is known about miRNA biogenesis, less is understood about how miRNA expression is timed and regulated. lin-42, the worm homolog of the circadian rhythm gene period of flies and mammals, is another core component of the heterochronic gene pathway. lin-42 mutants have a precocious phenotype, in which later-stage programs are executed too early, but the placement of lin-42 in the timing pathway is unclear. Here, we demonstrate that lin-42 negatively regulates heterochronic miRNA transcription. let-7 and the related miRNA miR-48 accumulate precociously in lin-42 mutants. This defect reflects transcriptional misregulation because enhanced expression of both primary miRNA transcripts (pri-miRNAs) and a let-7 promoter::gfp fusion are observed. The pri-miRNA levels oscillate during larval development, in a pattern reminiscent of lin-42 expression. Importantly, we show that lin-42 is not required for this cycling; instead, peak amplitude is increased. Genetic analyses further confirm that lin-42 acts through let-7 family miRNAs. Taken together, these data show that a key function of lin-42 in developmental timing is to dampen pri-miRNAs levels, preventing their premature expression as mature miRNAs.
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15
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Perales R, King DM, Aguirre-Chen C, Hammell CM. LIN-42, the Caenorhabditis elegans PERIOD homolog, negatively regulates microRNA transcription. PLoS Genet 2014; 10:e1004486. [PMID: 25032706 PMCID: PMC4102445 DOI: 10.1371/journal.pgen.1004486] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 05/19/2014] [Indexed: 02/06/2023] Open
Abstract
During C. elegans development, microRNAs (miRNAs) function as molecular switches that define temporal gene expression and cell lineage patterns in a dosage-dependent manner. It is critical, therefore, that the expression of miRNAs be tightly regulated so that target mRNA expression is properly controlled. The molecular mechanisms that function to optimize or control miRNA levels during development are unknown. Here we find that mutations in lin-42, the C. elegans homolog of the circadian-related period gene, suppress multiple dosage-dependent miRNA phenotypes including those involved in developmental timing and neuronal cell fate determination. Analysis of mature miRNA levels in lin-42 mutants indicates that lin-42 functions to attenuate miRNA expression. Through the analysis of transcriptional reporters, we show that the upstream cis-acting regulatory regions of several miRNA genes are sufficient to promote highly dynamic transcription that is coupled to the molting cycles of post-embryonic development. Immunoprecipitation of LIN-42 complexes indicates that LIN-42 binds the putative cis-regulatory regions of both non-coding and protein-coding genes and likely plays a role in regulating their transcription. Consistent with this hypothesis, analysis of miRNA transcriptional reporters in lin-42 mutants indicates that lin-42 regulates miRNA transcription. Surprisingly, strong loss-of-function mutations in lin-42 do not abolish the oscillatory expression patterns of lin-4 and let-7 transcription but lead to increased expression of these genes. We propose that lin-42 functions to negatively regulate the transcriptional output of multiple miRNAs and mRNAs and therefore coordinates the expression levels of genes that dictate temporal cell fate with other regulatory programs that promote rhythmic gene expression. MicroRNAs play pervasive roles in controlling gene expression throughout animal development. Given that individual microRNAs are predicted to regulate hundreds of mRNAs and that most mRNA transcripts are microRNA targets, it is essential that the expression levels of microRNAs be tightly regulated. With the goal of unveiling factors that regulate the expression of microRNAs that control developmental timing, we identified lin-42, the C. elegans homolog of the human and Drosophila period gene implicated in circadian gene regulation, as a negative regulator of microRNA expression. By analyzing the transcriptional expression patterns of representative microRNAs, we found that the transcription of many microRNAs is normally highly dynamic and coupled aspects of post-embryonic growth and behavior. We suggest that lin-42 functions to modulate the transcriptional output of temporally-regulated microRNAs and mRNAs in order to maintain optimal expression of these genes throughout development.
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Affiliation(s)
- Roberto Perales
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dana M. King
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Cristina Aguirre-Chen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Christopher M. Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- * E-mail:
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16
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Chu YD, Wang WC, Chen SAA, Hsu YT, Yeh MW, Slack FJ, Chan SP. RACK-1 regulates let-7 microRNA expression and terminal cell differentiation in Caenorhabditis elegans. Cell Cycle 2014; 13:1995-2009. [PMID: 24776851 PMCID: PMC4111763 DOI: 10.4161/cc.29017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The let-7 microRNA (miRNA) regulates cell cycle exit and terminal differentiation in the C. elegans heterochronic gene pathway. Low expression of let-7 results in retarded vulva and hypodermal cell development in C. elegans and has been associated with several human cancers. Previously, the versatile scaffold protein receptor for activated C kinase 1 (RACK1) was proposed to facilitate recruitment of the miRNA-induced silencing complex (miRISC) to the polysome and to be required for miRNA function in C. elegans and humans. Here, we show that depletion of C. elegans RACK-1 by RNAi increases let-7 miRNA levels and suppresses the retarded terminal differentiation of lateral hypodermal seam cells in mutants carrying the hypomorphic let-7(n2853) allele or lacking the let-7 family miRNA genes mir-48 and mir-241. Depletion of RACK-1 also increases the levels of precursor let-7 miRNA. When Dicer is knocked down and pre-miRNA processing is inhibited, depletion of RACK-1 still leads to increased levels of pre-let-7, suggesting that RACK-1 affects a biogenesis mechanism upstream of Dicer. No changes in the activity of the let-7 promoter or the levels of primary let-7 miRNA are associated with depletion of RACK-1, suggesting that RACK-1 affects let-7 miRNA biogenesis at the post-transcriptional level. Interestingly, rack-1 knockdown also increases the levels of a few other precursor miRNAs. Our results reveal that RACK-1 controls the biogenesis of a subset of miRNAs, including let-7, and in this way plays a role in the heterochronic gene pathway during C. elegans development.
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Affiliation(s)
- Yu-De Chu
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan
| | - Wei-Chieh Wang
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan
| | - Shi-An A Chen
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan; Genome and Systems Biology Degree Program; College of Life Science; National Taiwan University; Taipei, Taiwan
| | - Yen-Ting Hsu
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan
| | - Meng-Wei Yeh
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan
| | - Frank J Slack
- Department of Molecular, Cellular, and Developmental Biology; Yale University; New Haven, CT USA
| | - Shih-Peng Chan
- Graduate Institute of Microbiology; College of Medicine; National Taiwan University; Taipei, Taiwan; Genome and Systems Biology Degree Program; College of Life Science; National Taiwan University; Taipei, Taiwan; Department of Molecular, Cellular, and Developmental Biology; Yale University; New Haven, CT USA
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17
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Nowak JS, Choudhury NR, de Lima Alves F, Rappsilber J, Michlewski G. Lin28a regulates neuronal differentiation and controls miR-9 production. Nat Commun 2014; 5:3687. [PMID: 24722317 PMCID: PMC4035284 DOI: 10.1038/ncomms4687] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 03/18/2014] [Indexed: 01/23/2023] Open
Abstract
microRNAs shape the identity and function of cells by regulating gene expression. It is known that brain-specific miR-9 is controlled transcriptionally; however, it is unknown whether post-transcriptional processes contribute to establishing its levels. Here, we show that miR-9 is regulated transcriptionally and post-transcriptionally during neuronal differentiation of the embryonic carcinoma cell line P19. We demonstrate that miR-9 is more efficiently processed in differentiated than undifferentiated cells. We reveal that Lin28a affects miR-9 by inducing the degradation of its precursor through a uridylation-independent mechanism. Furthermore, we show that constitutively expressed untagged but not GFP-tagged Lin28a decreases differentiation capacity of P19 cells, which coincides with reduced miR-9 levels. Finally, using an inducible system we demonstrate that Lin28a can also reduce miR-9 levels in differentiated P19 cells. Together, our results shed light on the role of Lin28a in neuronal differentiation and increase our understanding of the mechanisms regulating the level of brain-specific microRNAs.
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Affiliation(s)
- Jakub S Nowak
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
| | - Nila Roy Choudhury
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
| | - Flavia de Lima Alves
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
| | - Juri Rappsilber
- 1] Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK [2] Department of Biotechnology, Technische Universität Berlin, 13353 Berlin, Germany
| | - Gracjan Michlewski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
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18
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Van Wynsberghe PM, Finnegan EF, Stark T, Angelus EP, Homan KE, Yeo GW, Pasquinelli AE. The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans. Dev Biol 2014; 390:126-35. [PMID: 24699545 DOI: 10.1016/j.ydbio.2014.03.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 11/18/2022]
Abstract
MicroRNAs (miRNAs) are small RNAs that post-transcriptionally regulate gene expression in many multicellular organisms. They are encoded in the genome and transcribed into primary (pri-) miRNAs before two processing steps that ultimately produce the mature miRNA. In order to generate the appropriate amount of a particular miRNA in the correct location at the correct time, proper regulation of miRNA biogenesis is essential. Here we identify the Period protein homolog LIN-42 as a new regulator of miRNA biogenesis in Caenorhabditis elegans. We mapped a spontaneous suppressor of the normally lethal let-7(n2853) allele to the lin-42 gene. Mutations in this allele (ap201) or a second lin-42 allele (n1089) caused increased mature let-7 miRNA levels at most time points when mature let-7 miRNA is normally expressed. Levels of pri-let-7 and a let-7 transcriptional reporter were also increased in lin-42(n1089) worms. These results indicate that LIN-42 normally represses pri-let-7 transcription and thus the accumulation of let-7 miRNA. This inhibition is not specific to let-7, as pri- and mature levels of lin-4 and miR-35 were also increased in lin-42 mutants. Furthermore, small RNA-seq analysis showed widespread increases in the levels of mature miRNAs in lin-42 mutants. Thus, we propose that the period protein homolog LIN-42 is a global regulator of miRNA biogenesis.
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Affiliation(s)
- Priscilla M Van Wynsberghe
- Division of Biology, University of California at San Diego, La Jolla, CA 92093-0349, USA; Department of Biology, Colgate University, Hamilton, NY 13323, USA.
| | - Emily F Finnegan
- Division of Biology, University of California at San Diego, La Jolla, CA 92093-0349, USA
| | - Thomas Stark
- Division of Biology, University of California at San Diego, La Jolla, CA 92093-0349, USA; Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, University of California at San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Evan P Angelus
- Department of Biology, Colgate University, Hamilton, NY 13323, USA
| | - Kathryn E Homan
- Department of Biology, Colgate University, Hamilton, NY 13323, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, University of California at San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California at San Diego, La Jolla, CA 92093-0349, USA.
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19
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Abstract
The let-7 miRNA (microRNA) is an essential regulator of development from nematode worms to humans. Altered expression of let-7 results in larval arrest or lethality in Caenorhabditis elegans. Likewise, under- or over-expression of let-7 in human cells can result in cellular overproliferation or halted cell division respectively. Thus the biogenesis of this critical miRNA is controlled at multiple levels. An unexpected mechanism for regulating the initial processing of let-7 was recently found to involve the let-7 miRNA itself. The mature let-7 miRNA along with its effector protein, Argonaute, were shown to bind to a site in the primary transcripts produced by the let-7 gene. This interaction enhances processing through a novel auto-regulatory feedback loop. This discovery highlights a new role for the miRNA complex in regulating miRNA biogenesis and enriches the classes of RNAs targeted by Argonaute.
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