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Lorenzo-Orts L, Pauli A. The molecular mechanisms underpinning maternal mRNA dormancy. Biochem Soc Trans 2024; 52:861-871. [PMID: 38477334 PMCID: PMC11088918 DOI: 10.1042/bst20231122] [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: 12/14/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
A large number of mRNAs of maternal origin are produced during oogenesis and deposited in the oocyte. Since transcription stops at the onset of meiosis during oogenesis and does not resume until later in embryogenesis, maternal mRNAs are the only templates for protein synthesis during this period. To ensure that a protein is made in the right place at the right time, the translation of maternal mRNAs must be activated at a specific stage of development. Here we summarize our current understanding of the sophisticated mechanisms that contribute to the temporal repression of maternal mRNAs, termed maternal mRNA dormancy. We discuss mechanisms at the level of the RNA itself, such as the regulation of polyadenine tail length and RNA modifications, as well as at the level of RNA-binding proteins, which often block the assembly of translation initiation complexes at the 5' end of an mRNA or recruit mRNAs to specific subcellular compartments. We also review microRNAs and other mechanisms that contribute to repressing translation, such as ribosome dormancy. Importantly, the mechanisms responsible for mRNA dormancy during the oocyte-to-embryo transition are also relevant to cellular quiescence in other biological contexts.
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Affiliation(s)
- Laura Lorenzo-Orts
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
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2
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Wu J, Niu L, Yang K, Xu J, Zhang D, Ling J, Xia P, Wu Y, Liu X, Liu J, Zhang J, Yu P. The role and mechanism of RNA-binding proteins in bone metabolism and osteoporosis. Ageing Res Rev 2024; 96:102234. [PMID: 38367813 DOI: 10.1016/j.arr.2024.102234] [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: 10/11/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Osteoporosis is a prevalent chronic metabolic bone disease that poses a significant risk of fractures or mortality in elderly individuals. Its pathophysiological basis is often attributed to postmenopausal estrogen deficiency and natural aging, making the progression of primary osteoporosis among elderly people, especially older women, seemingly inevitable. The treatment and prevention of osteoporosis progression have been extensively discussed. Recently, as researchers delve deeper into the molecular biological mechanisms of bone remodeling, they have come to realize the crucial role of posttranscriptional gene control in bone metabolism homeostasis. RNA-binding proteins, as essential actors in posttranscriptional activities, may exert influence on osteoporosis progression by regulating the RNA life cycle. This review compiles recent findings on the involvement of RNA-binding proteins in abnormal bone metabolism in osteoporosis and describes the impact of some key RNA-binding proteins on bone metabolism regulation. Additionally, we explore the potential and rationale for modulating RNA-binding proteins as a means of treating osteoporosis, with an overview of drugs that target these proteins.
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Affiliation(s)
- Jiaqiang Wu
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, 332000, China; The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China; Department of General Surgery, First Medical Center of the Chinese PLA General Hospital, Beijing, China
| | - Liyan Niu
- HuanKui College of Nanchang University, Nanchang 330006, China
| | - Kangping Yang
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Jingdong Xu
- Queen Mary College of Nanchang University, Nanchang 330006, China
| | - Deju Zhang
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China
| | - Jitao Ling
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China
| | - Panpan Xia
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China
| | - Yuting Wu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China
| | - Xiao Liu
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianping Liu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China
| | - Jing Zhang
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, 332000, China; Department of Anesthesiology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
| | - Peng Yu
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, Jiangxi, 332000, China; Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 1, Minde Road, Donghu District, Nanchang 330006, China; Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang 330006, China.
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3
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Santoni M, Meneau F, Sekhsoukh N, Castella S, Le T, Miot M, Daldello EM. Unraveling the interplay between PKA inhibition and Cdk1 activation during oocyte meiotic maturation. Cell Rep 2024; 43:113782. [PMID: 38358892 DOI: 10.1016/j.celrep.2024.113782] [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: 09/03/2023] [Revised: 12/19/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
Oocytes are arrested in prophase I. In vertebrates, meiotic resumption is triggered by hormonal stimulation that results in cAMP-dependent protein kinase (PKA) downregulation leading to Cdk1 activation. Yet the pathways connecting PKA to Cdk1 remain unclear. Here, we identify molecular events triggered by PKA downregulation occurring upstream of Cdk1 activation. We describe a two-step regulation controlling cyclin B1 and Mos accumulation, which depends on both translation and stabilization. Cyclin B1 accumulation is triggered by PKA inhibition upstream of Cdk1 activation, while its translation requires Cdk1 activity. Conversely, Mos translation initiates in response to the hormone, but the protein accumulates only downstream of Cdk1. Furthermore, two successive translation waves take place, the first controlled by PKA inhibition and the second by Cdk1 activation. Notably, Arpp19, an essential PKA effector, does not regulate the early PKA-dependent events. This study elucidates how PKA downregulation orchestrates multiple pathways that converge toward Cdk1 activation and induce the oocyte G2/M transition.
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Affiliation(s)
- Martina Santoni
- Sorbonne Université-CNRS, Laboratoire de Biologie du Développement Institut de Biologie Paris Seine, LBD-IBPS, 75005 Paris, France
| | - Ferdinand Meneau
- Sorbonne Université-CNRS, Laboratoire de Biologie du Développement Institut de Biologie Paris Seine, LBD-IBPS, 75005 Paris, France
| | - Nabil Sekhsoukh
- Sorbonne Université-CNRS, Laboratoire de Biologie du Développement Institut de Biologie Paris Seine, LBD-IBPS, 75005 Paris, France
| | - Sandrine Castella
- Sorbonne Université-CNRS, Laboratoire de Biologie du Développement Institut de Biologie Paris Seine, LBD-IBPS, 75005 Paris, France
| | - Tran Le
- Sorbonne Université-CNRS, Laboratoire de Biologie du Développement Institut de Biologie Paris Seine, LBD-IBPS, 75005 Paris, France
| | - Marika Miot
- Sorbonne Université-CNRS, Laboratoire de Biologie du Développement Institut de Biologie Paris Seine, LBD-IBPS, 75005 Paris, France
| | - Enrico Maria Daldello
- Sorbonne Université-CNRS, Laboratoire de Biologie du Développement Institut de Biologie Paris Seine, LBD-IBPS, 75005 Paris, France.
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4
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Berg C, Sieber M, Sun J. Finishing the egg. Genetics 2024; 226:iyad183. [PMID: 38000906 PMCID: PMC10763546 DOI: 10.1093/genetics/iyad183] [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: 07/05/2023] [Accepted: 09/27/2023] [Indexed: 11/26/2023] Open
Abstract
Gamete development is a fundamental process that is highly conserved from early eukaryotes to mammals. As germ cells develop, they must coordinate a dynamic series of cellular processes that support growth, cell specification, patterning, the loading of maternal factors (RNAs, proteins, and nutrients), differentiation of structures to enable fertilization and ensure embryonic survival, and other processes that make a functional oocyte. To achieve these goals, germ cells integrate a complex milieu of environmental and developmental signals to produce fertilizable eggs. Over the past 50 years, Drosophila oogenesis has risen to the forefront as a system to interrogate the sophisticated mechanisms that drive oocyte development. Studies in Drosophila have defined mechanisms in germ cells that control meiosis, protect genome integrity, facilitate mRNA trafficking, and support the maternal loading of nutrients. Work in this system has provided key insights into the mechanisms that establish egg chamber polarity and patterning as well as the mechanisms that drive ovulation and egg activation. Using the power of Drosophila genetics, the field has begun to define the molecular mechanisms that coordinate environmental stresses and nutrient availability with oocyte development. Importantly, the majority of these reproductive mechanisms are highly conserved throughout evolution, and many play critical roles in the development of somatic tissues as well. In this chapter, we summarize the recent progress in several key areas that impact egg chamber development and ovulation. First, we discuss the mechanisms that drive nutrient storage and trafficking during oocyte maturation and vitellogenesis. Second, we examine the processes that regulate follicle cell patterning and how that patterning impacts the construction of the egg shell and the establishment of embryonic polarity. Finally, we examine regulatory factors that control ovulation, egg activation, and successful fertilization.
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Affiliation(s)
- Celeste Berg
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-5065USA
| | - Matthew Sieber
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390USA
| | - Jianjun Sun
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT 06269USA
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Rand MD, Tennessen JM, Mackay TFC, Anholt RRH. Perspectives on the Drosophila melanogaster Model for Advances in Toxicological Science. Curr Protoc 2023; 3:e870. [PMID: 37639638 PMCID: PMC10463236 DOI: 10.1002/cpz1.870] [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] [Indexed: 08/31/2023]
Abstract
The use of Drosophila melanogaster for studies of toxicology has grown considerably in the last decade. The Drosophila model has long been appreciated as a versatile and powerful model for developmental biology and genetics because of its ease of handling, short life cycle, low cost of maintenance, molecular genetic accessibility, and availability of a wide range of publicly available strains and data resources. These features, together with recent unique developments in genomics and metabolomics, make the fly model especially relevant and timely for the development of new approach methodologies and movements toward precision toxicology. Here, we offer a perspective on how flies can be leveraged to identify risk factors relevant to environmental exposures and human health. First, we review and discuss fundamental toxicologic principles for experimental design with Drosophila. Next, we describe quantitative and systems genetics approaches to resolve the genetic architecture and candidate pathways controlling susceptibility to toxicants. Finally, we summarize the current state and future promise of the emerging field of Drosophila metabolomics for elaborating toxic mechanisms. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Matthew D. Rand
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | | | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
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Zhang H, Ji S, Zhang K, Chen Y, Ming J, Kong F, Wang L, Wang S, Zou Z, Xiong Z, Xu K, Lin Z, Huang B, Liu L, Fan Q, Jin S, Deng H, Xie W. Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition. Genome Biol 2023; 24:166. [PMID: 37443062 PMCID: PMC10347836 DOI: 10.1186/s13059-023-02997-8] [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: 09/14/2022] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic genome activation. How the transcriptome, translatome, and proteome are coordinated during this critical developmental window remains poorly understood. RESULTS Utilizing a highly sensitive and quantitative mass spectrometry approach, we obtain high-quality proteome data spanning seven mouse stages, from full-grown oocyte (FGO) to blastocyst, using 100 oocytes/embryos at each stage. Integrative analyses reveal distinct proteome reprogramming compared to that of the transcriptome or translatome. FGO to 8-cell proteomes are dominated by FGO-stockpiled proteins, while the transcriptome and translatome are more dynamic. FGO-originated proteins frequently persist to blastocyst while corresponding transcripts are already downregulated or decayed. Improved concordance between protein and translation or transcription is observed for genes starting translation upon meiotic resumption, as well as those transcribed and translated only in embryos. Concordance between protein and transcription/translation is also observed for proteins with short half-lives. We built a kinetic model that predicts protein dynamics by incorporating both initial protein abundance in FGOs and translation kinetics across developmental stages. CONCLUSIONS Through integrative analyses of datasets generated by ultrasensitive methods, our study reveals that the proteome shows distinct dynamics compared to the translatome and transcriptome during mouse OET. We propose that the remarkably stable oocyte-originated proteome may help save resources to accommodate the demanding needs of growing embryos. This study will advance our understanding of mammalian OET and the fundamental principles governing gene expression.
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Affiliation(s)
- Hongmei Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Shuyan Ji
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuling Chen
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jia Ming
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Shun Wang
- School of Mathematics and Statistics, Wuhan University, Wuhan, China
- Hubei Key Laboratory of Computational Science, Wuhan University, Wuhan, China
| | - Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Zhuqing Xiong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bo Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310002, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Suoqin Jin
- School of Mathematics and Statistics, Wuhan University, Wuhan, China
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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Harry ND, Zakas C. Maternal patterns of inheritance alter transcript expression in eggs. BMC Genomics 2023; 24:191. [PMID: 37038099 PMCID: PMC10084599 DOI: 10.1186/s12864-023-09291-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/01/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Modifications to early development can lead to evolutionary diversification. The early stages of development are under maternal control, as mothers produce eggs loaded with nutrients, proteins and mRNAs that direct early embryogenesis. Maternally provided mRNAs are the only expressed genes in initial stages of development and are tightly regulated. Differences in maternal mRNA provisioning could lead to phenotypic changes in embryogenesis and ultimately evolutionary changes in development. However, the extent that maternal mRNA expression in eggs can vary is unknown for most developmental models. Here, we use a species with dimorphic development- where females make eggs and larvae of different sizes and life-history modes-to investigate the extent of variation in maternal mRNA provisioning to the egg. RESULTS We find that there is significant variation in gene expression across eggs of different development modes, and that there are both qualitative and quantitative differences in mRNA expression. We separate parental effects from allelic effects, and find that both mechanisms contribute to mRNA expression differences. We also find that offspring of intraspecific crosses differentially provision their eggs based on the parental cross direction (a parental effect), which has not been previously demonstrated in reproductive traits like oogenesis. CONCLUSION We find that maternally controlled initiation of development is functionally distinct between eggs of different sizes and maternal genotypes. Both allele-specific effects and parent-of-origin effects contribute to gene expression differences in eggs. The latter indicates an intergenerational effect where a parent's genotype can affect gene expression in an egg made by the next generation.
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Affiliation(s)
- Nathan D Harry
- Department of Biological Sciences, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA
| | - Christina Zakas
- Department of Biological Sciences, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA.
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8
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Identification of chicken LOC420478 as Bucky ball equivalent and potential germ plasm organizer in birds. Sci Rep 2022; 12:16858. [PMID: 36207377 PMCID: PMC9546911 DOI: 10.1038/s41598-022-21239-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
Bucky ball was identified as germ plasm organizer in zebrafish and has proven crucial for Balbiani body condensation. A synteny comparison identified an uncharacterized gene locus in the chicken genome as predicted avian counterpart. Here, we present experimental evidence that this gene locus indeed encodes a ‘Bucky ball’ equivalent in matured oocytes and early embryos of chicken. Heterologous expression of Bucky ball fusion proteins both from zebrafish and chicken with a fluorescent reporter revealed unique patterns indicative for liquid–liquid phase separation of intrinsically disordered proteins. Immuno-labeling detected Bucky ball from oocytes to blastoderms with diffuse distribution in matured oocytes, aggregation in first cleavage furrows, and co-localization to the chicken vasa homolog (CVH). Later, Bucky ball translocated to the cytoplasm of first established cells, and showed nuclear translocation during the major zygotic activation together with CVH. Remarkably, during the phase of area pellucida formation, Bucky ball translocated back into the cytoplasm at stage EGK VI, whereas CVH remained within the nuclei. The condensation of Bucky ball and co-localization with CVH in cleavage furrows and nuclei of the centrally located cells strongly suggests chicken Bucky ball as a germ plasm organizer in birds, and indicate a special importance of the major zygotic activation for germline specification.
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Li W, Liu X, Tan LF. Binding properties of [Ru(phen)2(11-R-dppz)]2+ (R = F or CN) with poly(A)•poly(U) duplex RNA. J Inorg Biochem 2022; 232:111833. [DOI: 10.1016/j.jinorgbio.2022.111833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
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Fang J, Lerit DA. Orb-dependent polyadenylation contributes to PLP expression and centrosome scaffold assembly. Development 2022; 149:275606. [DOI: 10.1242/dev.200426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/25/2022] [Indexed: 01/09/2023]
Abstract
ABSTRACT
As the microtubule-organizing centers of most cells, centrosomes engineer the bipolar mitotic spindle required for error-free mitosis. Drosophila Pericentrin-like protein (PLP) directs formation of a pericentriolar material (PCM) scaffold required for PCM organization and microtubule-organizing center function. Here, we investigate the post-transcriptional regulation of Plp mRNA. We identify conserved binding sites for cytoplasmic polyadenylation element binding (CPEB) proteins within the Plp 3′-untranslated region and examine the role of the CPEB ortholog Oo18 RNA-binding protein (Orb) in Plp mRNA regulation. Our data show that Orb interacts biochemically with Plp mRNA to promote polyadenylation and PLP protein expression. Loss of orb, but not orb2, diminishes PLP levels in embryonic extracts. Consequently, PLP localization to centrosomes and its function in PCM scaffolding are compromised in orb mutant embryos, resulting in genomic instability and embryonic lethality. Moreover, we find that PLP overexpression restores centrosome scaffolding and rescues the cell division defects caused by orb depletion. Our data suggest that Orb modulates PLP expression at the level of Plp mRNA polyadenylation and demonstrates that the post-transcriptional regulation of core, conserved centrosomal mRNAs is crucial for centrosome function.
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Affiliation(s)
- Junnan Fang
- Emory University School of Medicine Department of Cell Biology , , Atlanta, GA 30322 , USA
| | - Dorothy A. Lerit
- Emory University School of Medicine Department of Cell Biology , , Atlanta, GA 30322 , USA
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11
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Shang J, He L, Wang J, Tong A, Xiang Y. In Situ Visualizing Nascent RNA by Exploring DNA-Templated Oxidative Amination of 4-Thiouridine. Bioconjug Chem 2022; 33:164-171. [PMID: 34910465 DOI: 10.1021/acs.bioconjchem.1c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tracking and mapping the nascent RNA molecules in cells is essential for deciphering embryonic development and neuronal differentiation. Here, we utilized 4-thiouridine (s4U) as a metabolic tag to label nascent RNA and developed a fluorescence imaging method based on the DNA-templated oxidative amination (DTOA) reaction of s4U. The DTOA reaction occurred between amine-modified DNA and s4U-containing RNA with high sequence specificity and chemical selectivity. Target nascent mRNAs in HeLa cells, including those encoding green fluorescent proteins (GFPs) and endogenous BAG-1, were thus lit up selectively by DTOA-based fluorescence in situ hybridization (DTOA FISH). We believe the DTOA conjugation chemistry shown in this study could be generally applied to investigate the spatial distribution of nascent transcription dynamics in cellular processes.
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Affiliation(s)
- Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Luo He
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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Xie Z, Song P, Zhong Y, Guo J, Gui L, Li M. Medaka gcnf is a component of chromatoid body during spermiogenesis. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2020.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J. Structure and dynamics of the quaternary hunchback mRNA translation repression complex. Nucleic Acids Res 2021; 49:8866-8885. [PMID: 34329466 PMCID: PMC8421216 DOI: 10.1093/nar/gkab635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 01/02/2023] Open
Abstract
A key regulatory process during Drosophila development is the localized suppression of the hunchback mRNA translation at the posterior, which gives rise to a hunchback gradient governing the formation of the anterior-posterior body axis. This suppression is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for proper Drosophila development. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins during RNA suppression remains a long-standing open question. Here, we characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos with hunchback mRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternary hunchback mRNA suppression complex comprising the RNA binding domains is flexible with unoccupied nucleotides functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, the presence of the Pum-HD/Nanos-ZnF complex has no effect on the equilibrium RNA binding affinity of the Brat RNA binding domain. This is in accordance with previous studies, which showed that Brat can suppress mRNA independently and is distributed uniformly throughout the embryo.
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Affiliation(s)
- Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Sophie L Winter
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jaelle Foot
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Kathryn Perez
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Miloš T Ivanović
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Inga Loedige
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Frank Gabel
- Institut Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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14
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Pillay S, Takahashi H, Carninci P, Kanhere A. Antisense RNAs during early vertebrate development are divided in groups with distinct features. Genome Res 2021; 31:995-1010. [PMID: 33795334 PMCID: PMC8168585 DOI: 10.1101/gr.262964.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/29/2021] [Indexed: 01/15/2023]
Abstract
Long noncoding RNAs or lncRNAs are a class of non-protein-coding RNAs that are >200 nt in length. Almost 50% of lncRNAs during zebrafish development are transcribed in an antisense direction to a protein-coding gene. However, the role of these natural antisense transcripts (NATs) during development remains enigmatic. To understand NATs in early vertebrate development, we took a computational biology approach and analyzed existing as well as novel data sets. Our analysis indicates that zebrafish NATs can be divided into two major classes based on their coexpression patterns with respect to the overlapping protein-coding genes. Group 1 NATs have characteristics similar to maternally deposited RNAs in that their levels decrease as development progresses. Group 1 NAT levels are negatively correlated with that of overlapping sense-strand protein-coding genes. Conversely, Group 2 NATs are coexpressed with overlapping protein-coding genes. In contrast to Group 1, which is enriched in genes involved in developmental pathways, Group 2 protein-coding genes are enriched in housekeeping functions. Group 1 NATs also show larger overlap and higher complementarity with the sense-strand mRNAs compared to other NATs. In addition, our transcriptomics data, quantifying RNA levels from cytoplasmic and nuclear compartments, indicates that Group 1 NATs are more abundant in the cytosol. Based on their expression pattern, cytosolic nature, and their higher complementarity to the overlapping developmental mRNAs, we speculate that Group 1 NATs function post-transcriptionally to silence spurious expression of developmental genes.
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Affiliation(s)
- Sanjana Pillay
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York 10029, USA
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Fondazione Human Technopole, 20157 Milan, Italy
| | - Aditi Kanhere
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3GE, United Kingdom
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15
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Sankaranarayanan M, Weil TT. Granule regulation by phase separation during Drosophila oogenesis. Emerg Top Life Sci 2020; 4:343-352. [PMID: 32573699 PMCID: PMC7733668 DOI: 10.1042/etls20190155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
Drosophila eggs are highly polarised cells that use RNA-protein complexes to regulate storage and translational control of maternal RNAs. Ribonucleoprotein granules are a class of biological condensates that form predominantly by intracellular phase separation. Despite extensive in vitro studies testing the physical principles regulating condensates, how phase separation translates to biological function remains largely unanswered. In this perspective, we discuss granules in Drosophila oogenesis as a model system for investigating the physiological role of phase separation. We review key maternal granules and their properties while highlighting ribonucleoprotein phase separation behaviours observed during development. Finally, we discuss how concepts and models from liquid-liquid phase separation could be used to test mechanisms underlying granule assembly, regulation and function in Drosophila oogenesis.
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Affiliation(s)
- M Sankaranarayanan
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, U.K
| | - Timothy T Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, U.K
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16
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Zhang L, Chen L, Chen J, Shen W, Meng A. Mini-III RNase-based dual-color system for in vivo mRNA tracking. Development 2020; 147:dev.190728. [PMID: 33093152 PMCID: PMC7725608 DOI: 10.1242/dev.190728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/15/2020] [Indexed: 11/25/2022]
Abstract
Mini-III RNase (mR3), a member of RNase III endonuclease family, can bind to and cleave double-stranded RNAs (dsRNAs). Inactive mR3 protein without the α5β-α6 loop loses the dsRNA cleavage activity, but retains dsRNA binding activity. Here, we establish an inactive mR3-based non-engineered mR3/dsRNA system for RNA tracking in zebrafish embryos. In vitro binding experiments show that inactive Staphylococcus epidermidis mR3 (dSmR3) protein possesses the highest binding affinity with dsRNAs among mR3s from other related species, and its binding property is retained in zebrafish embryos. Combined with a fluorescein-labeled antisense RNA probe recognizing the target mRNAs, dSmR3 tagged with a nuclear localization sequence and a fluorescent protein could allow visualization of the dynamics of endogenous target mRNAs. The dSmR3/antisense probe dual-color system provides a new approach for tracking non-engineered RNAs in real-time, which will help understand how endogenous RNAs dynamically move during embryonic development. Summary: A fluorescent antisense probe and the inactive form of Staphylococcus epidermidis Mini-III RNase with a fluorescent tag may be used together to visualize endogenous mRNAs in zebrafish embryos.
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Affiliation(s)
- Lin Zhang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Luxi Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jing Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
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17
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Petibon C, Malik Ghulam M, Catala M, Abou Elela S. Regulation of ribosomal protein genes: An ordered anarchy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1632. [PMID: 33038057 PMCID: PMC8047918 DOI: 10.1002/wrna.1632] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Ribosomal protein genes are among the most highly expressed genes in most cell types. Their products are generally essential for ribosome synthesis, which is the cornerstone for cell growth and proliferation. Many cellular resources are dedicated to producing ribosomal proteins and thus this process needs to be regulated in ways that carefully balance the supply of nascent ribosomal proteins with the demand for new ribosomes. Ribosomal protein genes have classically been viewed as a uniform interconnected regulon regulated in eukaryotic cells by target of rapamycin and protein kinase A pathway in response to changes in growth conditions and/or cellular status. However, recent literature depicts a more complex picture in which the amount of ribosomal proteins produced varies between genes in response to two overlapping regulatory circuits. The first includes the classical general ribosome‐producing program and the second is a gene‐specific feature responsible for fine‐tuning the amount of ribosomal proteins produced from each individual ribosomal gene. Unlike the general pathway that is mainly controlled at the level of transcription and translation, this specific regulation of ribosomal protein genes is largely achieved through changes in pre‐mRNA splicing efficiency and mRNA stability. By combining general and specific regulation, the cell can coordinate ribosome production, while allowing functional specialization and diversity. Here we review the many ways ribosomal protein genes are regulated, with special focus on the emerging role of posttranscriptional regulatory events in fine‐tuning the expression of ribosomal protein genes and its role in controlling the potential variation in ribosome functions. This article is categorized under:Translation > Ribosome Biogenesis Translation > Ribosome Structure/Function Translation > Translation Regulation
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Affiliation(s)
- Cyrielle Petibon
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mustafa Malik Ghulam
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mathieu Catala
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
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18
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Abstract
RNA movements and localization pervade biology, from embryonic development to disease. To identify RNAs at specific locations, we developed a strategy in which a uridine-adding enzyme is anchored to subcellular sites, where it directly marks RNAs with 3' terminal uridines. This localized RNA recording approach yields a record of RNA locations, and is validated through identification of RNAs localized selectively to the endoplasmic reticulum (ER) or mitochondria. We identify a broad dual localization pattern conserved from yeast to human cells, in which the same battery of mRNAs encounter both ER and mitochondria in both species, and include an mRNA encoding a key stress sensor. Subunits of many multiprotein complexes localize to both the ER and mitochondria, suggesting coordinated assembly. Noncoding RNAs in the course of RNA surveillance and processing encounter both organelles. By providing a record of RNA locations over time, the approach complements those that capture snapshots of instantaneous positions.
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19
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Savulescu AF, Jacobs C, Negishi Y, Davignon L, Mhlanga MM. Pinpointing Cell Identity in Time and Space. Front Mol Biosci 2020; 7:209. [PMID: 32923457 PMCID: PMC7456825 DOI: 10.3389/fmolb.2020.00209] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/30/2020] [Indexed: 01/15/2023] Open
Abstract
Mammalian cells display a broad spectrum of phenotypes, morphologies, and functional niches within biological systems. Our understanding of mechanisms at the individual cellular level, and how cells function in concert to form tissues, organs and systems, has been greatly facilitated by centuries of extensive work to classify and characterize cell types. Classic histological approaches are now complemented with advanced single-cell sequencing and spatial transcriptomics for cell identity studies. Emerging data suggests that additional levels of information should be considered, including the subcellular spatial distribution of molecules such as RNA and protein, when classifying cells. In this Perspective piece we describe the importance of integrating cell transcriptional state with tissue and subcellular spatial and temporal information for thorough characterization of cell type and state. We refer to recent studies making use of single cell RNA-seq and/or image-based cell characterization, which highlight a need for such in-depth characterization of cell populations. We also describe the advances required in experimental, imaging and analytical methods to address these questions. This Perspective concludes by framing this argument in the context of projects such as the Human Cell Atlas, and related fields of cancer research and developmental biology.
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Affiliation(s)
- Anca F. Savulescu
- Division of Chemical, Systems & Synthetic Biology, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Caron Jacobs
- Division of Chemical, Systems & Synthetic Biology, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Yutaka Negishi
- Division of Chemical, Systems & Synthetic Biology, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laurianne Davignon
- Division of Chemical, Systems & Synthetic Biology, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Musa M. Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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20
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Hybrid larval lethality of Drosophila is caused by parent-of-origin expression: an insight from imaginal discs morphogenesis of Lhr pausing rescue hybrids of D. melanogaster and D. simulans. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00327-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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21
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Flora P, Wong-Deyrup SW, Martin ET, Palumbo RJ, Nasrallah M, Oligney A, Blatt P, Patel D, Fuchs G, Rangan P. Sequential Regulation of Maternal mRNAs through a Conserved cis-Acting Element in Their 3' UTRs. Cell Rep 2019; 25:3828-3843.e9. [PMID: 30590052 PMCID: PMC6328254 DOI: 10.1016/j.celrep.2018.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/28/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022] Open
Abstract
Maternal mRNAs synthesized during oogenesis initiate the development of future generations. Some maternal mRNAs are either somatic or germline determinants and must be translationally repressed until embryogenesis. However, the translational repressors themselves are temporally regulated. We used polar granule component (pgc), a Drosophila maternal mRNA, to ask how maternal transcripts are repressed while the regulatory landscape is shifting. pgc, a germline determinant, is translationally regulated throughout oogenesis. We find that different conserved RNA-binding proteins bind a 10-nt sequence in the 3′ UTR of pgc mRNA to continuously repress translation at different stages of oogenesis. Pumilio binds to this sequence in undifferentiated and early-differentiating oocytes to block Pgc translation. After differentiation, Bruno levels increase, allowing Bruno to bind the same sequence and take over translational repression of pgc mRNA. We have identified a class of maternal mRNAs that are regulated similarly, including zelda, the activator of the zygotic genome. Flora et al. show that pgc, a germline determinant, is translationally regulated throughout oogenesis. Different conserved RBPs bind a 10-nt sequence in the 3′ UTR to continuously repress translation throughout oogenesis. This mode of regulation applies to a class of maternal mRNAs, including zelda, the activator of the zygotic genome.
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Affiliation(s)
- Pooja Flora
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Siu Wah Wong-Deyrup
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Elliot Todd Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Ryan J Palumbo
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Mohamad Nasrallah
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Andrew Oligney
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Dhruv Patel
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Gabriele Fuchs
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA.
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22
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Abstract
3' untranslated regions (3' UTRs) of messenger RNAs (mRNAs) are best known to regulate mRNA-based processes, such as mRNA localization, mRNA stability, and translation. In addition, 3' UTRs can establish 3' UTR-mediated protein-protein interactions (PPIs), and thus can transmit genetic information encoded in 3' UTRs to proteins. This function has been shown to regulate diverse protein features, including protein complex formation or posttranslational modifications, but is also expected to alter protein conformations. Therefore, 3' UTR-mediated information transfer can regulate protein features that are not encoded in the amino acid sequence. This review summarizes both 3' UTR functions-the regulation of mRNA and protein-based processes-and highlights how each 3' UTR function was discovered with a focus on experimental approaches used and the concepts that were learned. This review also discusses novel approaches to study 3' UTR functions in the future by taking advantage of recent advances in technology.
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Affiliation(s)
- Christine Mayr
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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23
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Tetreau G, Dhinaut J, Gourbal B, Moret Y. Trans-generational Immune Priming in Invertebrates: Current Knowledge and Future Prospects. Front Immunol 2019; 10:1938. [PMID: 31475001 PMCID: PMC6703094 DOI: 10.3389/fimmu.2019.01938] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/30/2019] [Indexed: 01/15/2023] Open
Abstract
Trans-generational immune priming (TGIP) refers to the transfer of the parental immunological experience to its progeny. This may result in offspring protection from repeated encounters with pathogens that persist across generations. Although extensively studied in vertebrates for over a century, this phenomenon has only been identified 20 years ago in invertebrates. Since then, invertebrate TGIP has been the focus of an increasing interest, with half of studies published during the last few years. TGIP has now been tested in several invertebrate systems using various experimental approaches and measures to study it at both functional and evolutionary levels. However, drawing an overall picture of TGIP from available studies still appears to be a difficult task. Here, we provide a comprehensive review of TGIP in invertebrates with the objective of confronting all the data generated to date to highlight the main features and mechanisms identified in the context of its ecology and evolution. To this purpose, we describe all the articles reporting experimental investigation of TGIP in invertebrates and propose a critical analysis of the experimental procedures performed to study this phenomenon. We then investigate the outcome of TGIP in the offspring and its ecological and evolutionary relevance before reviewing the potential molecular mechanisms identified to date. In the light of this review, we build hypothetical scenarios of the mechanisms through which TGIP might be achieved and propose guidelines for future investigations.
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Affiliation(s)
- Guillaume Tetreau
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Julien Dhinaut
- UMR CNRS 6282 BioGéoSciences, Équipe Écologie Évolutive, Université Bourgogne-Franche Comté, Dijon, France
| | - Benjamin Gourbal
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Yannick Moret
- UMR CNRS 6282 BioGéoSciences, Équipe Écologie Évolutive, Université Bourgogne-Franche Comté, Dijon, France
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24
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Bioinformatics Approaches to Gain Insights into cis-Regulatory Motifs Involved in mRNA Localization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:165-194. [PMID: 31811635 DOI: 10.1007/978-3-030-31434-7_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Messenger RNA (mRNA) is a fundamental intermediate in the expression of proteins. As an integral part of this important process, protein production can be localized by the targeting of mRNA to a specific subcellular compartment. The subcellular destination of mRNA is suggested to be governed by a region of its primary sequence or secondary structure, which consequently dictates the recruitment of trans-acting factors, such as RNA-binding proteins or regulatory RNAs, to form a messenger ribonucleoprotein particle. This molecular ensemble is requisite for precise and spatiotemporal control of gene expression. In the context of RNA localization, the description of the binding preferences of an RNA-binding protein defines a motif, and one, or more, instance of a given motif is defined as a localization element (zip code). In this chapter, we first discuss the cis-regulatory motifs previously identified as mRNA localization elements. We then describe motif representation in terms of entropy and information content and offer an overview of motif databases and search algorithms. Finally, we provide an outline of the motif topology of asymmetrically localized mRNA molecules.
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25
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Hamm DC, Harrison MM. Regulatory principles governing the maternal-to-zygotic transition: insights from Drosophila melanogaster. Open Biol 2018; 8:180183. [PMID: 30977698 PMCID: PMC6303782 DOI: 10.1098/rsob.180183] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022] Open
Abstract
The onset of metazoan development requires that two terminally differentiated germ cells, a sperm and an oocyte, become reprogrammed to the totipotent embryo, which can subsequently give rise to all the cell types of the adult organism. In nearly all animals, maternal gene products regulate the initial events of embryogenesis while the zygotic genome remains transcriptionally silent. Developmental control is then passed from mother to zygote through a process known as the maternal-to-zygotic transition (MZT). The MZT comprises an intimately connected set of molecular events that mediate degradation of maternally deposited mRNAs and transcriptional activation of the zygotic genome. This essential developmental transition is conserved among metazoans but is perhaps best understood in the fruit fly, Drosophila melanogaster. In this article, we will review our understanding of the events that drive the MZT in Drosophila embryos and highlight parallel mechanisms driving this transition in other animals.
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Affiliation(s)
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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26
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Chen YC, Chang YW, Huang YS. Dysregulated Translation in Neurodevelopmental Disorders: An Overview of Autism-Risk Genes Involved in Translation. Dev Neurobiol 2018; 79:60-74. [PMID: 30430754 DOI: 10.1002/dneu.22653] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/17/2018] [Accepted: 10/25/2018] [Indexed: 01/08/2023]
Abstract
Regulated local translation-whereby specific mRNAs are transported and localized in subcellular domains where they are translated in response to regional signals-allows for remote control of gene expression to concentrate proteins in subcellular compartments. Neurons are highly polarized cells with unique features favoring local control for axonal pathfinding and synaptic plasticity, which are key processes involved in constructing functional circuits in the developing brain. Neurodevelopmental disorders are caused by genetic or environmental factors that disturb the nervous system's development during prenatal and early childhood periods. The growing list of genetic mutations that affect mRNA translation raises the question of whether aberrant translatomes in individuals with neurodevelopmental disorders share common molecular features underlying their stereotypical phenotypes and, vice versa, cause a certain degree of phenotypic heterogeneity. Here, we briefly give an overview of the role of local translation during neuronal development. We take the autism-risk gene list and discuss the molecules that (perhaps) are involved in mRNA transport and translation. Both exaggerated and suppressed translation caused by mutations in those genes have been identified or suggested. Finally, we discuss some proof-of-principle regimens for use in autism mouse models to correct dysregulated translation.
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Affiliation(s)
- Yan-Chu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Wei Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
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27
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hnRNPDL extensively regulates transcription and alternative splicing. Gene 2018; 687:125-134. [PMID: 30447347 DOI: 10.1016/j.gene.2018.11.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 08/30/2018] [Accepted: 11/08/2018] [Indexed: 01/31/2023]
Abstract
RNA binding proteins (RBPs) are key players of genome regulation. Here we report the transcriptome study of HnRNP D-Like protein, which belongs to the hnRNP family. We used RNA-seq to analyze the global transcript level and alternative splicing on hnRNPDL shRNA-treated cells and control. Sh-hnRNPDL extensively increased in the expression of genes involved in female pregnancy, cell apoptosis, cell proliferation and cell migration. HnRNPDL regulated alternative splicing of hundreds of genes enriched in transcription regulation and signaling pathways including NOD-like receptor signaling, Notch signaling, and TNF signaling. This study provides the first transcriptome-wide analysis of hnRNPDL regulation of gene expression, which adds to the understanding of critical hnRNPDL functions.
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28
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A simple computer vision pipeline reveals the effects of isolation on social interaction dynamics in Drosophila. PLoS Comput Biol 2018; 14:e1006410. [PMID: 30161262 PMCID: PMC6135522 DOI: 10.1371/journal.pcbi.1006410] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 09/12/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
Isolation profoundly influences social behavior in all animals. In humans, isolation has serious effects on health. Drosophila melanogaster is a powerful model to study small-scale, temporally-transient social behavior. However, longer-term analysis of large groups of flies is hampered by the lack of effective and reliable tools. We built a new imaging arena and improved the existing tracking algorithm to reliably follow a large number of flies simultaneously. Next, based on the automatic classification of touch and graph-based social network analysis, we designed an algorithm to quantify changes in the social network in response to prior social isolation. We observed that isolation significantly and swiftly enhanced individual and local social network parameters depicting near-neighbor relationships. We explored the genome-wide molecular correlates of these behavioral changes and found that whereas behavior changed throughout the six days of isolation, gene expression alterations occurred largely on day one. These changes occurred mostly in metabolic genes, and we verified the metabolic changes by showing an increase of lipid content in isolated flies. In summary, we describe a highly reliable tracking and analysis pipeline for large groups of flies that we use to unravel the behavioral, molecular and physiological impact of isolation on social network dynamics in Drosophila. Social isolation severely affects the behavior and physiology of social animals, including humans. The fruit fly is a powerful model for studying the mechanisms of development, health and disease and is also used to study social behaviors such as mating and aggression. However, these studies are limited to examining few individuals for shorts amounts of time, due to the lack of effective computational tools for the analysis of large groups over prolonged time. To overcome this hurdle, we built a new behavioral arena and developed new software that accurately tracks many flies simultaneously over long time periods. The arena is cheap and easy to build and the software works with low resolution videos. Using these improved tools, we studied social isolation in groups of male flies. We found that isolation caused flies to form stronger interactions with neighboring flies in their social network. These behavioral changes were preceded by transient changes in the expression of metabolism genes and eventually resulted in isolated flies accumulating fat, as has been previously observed in studies in mice and humans. Our study opens the door for the use of fruit flies in future studies of social isolation.
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29
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Robert HS, Park C, Gutièrrez CL, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. NATURE PLANTS 2018; 4:548-553. [PMID: 30013211 PMCID: PMC6076996 DOI: 10.1038/s41477-018-0204-z] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/15/2018] [Indexed: 05/18/2023]
Abstract
The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5-7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8-10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development.
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Affiliation(s)
- Hélène S Robert
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
| | - Chulmin Park
- BIOSS Centre for Biological Signaling Studies, Faculty of Biology, Albert-Ludwigs-Universitaet Freiburg, Freiburg, Germany
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Carla Loreto Gutièrrez
- BIOSS Centre for Biological Signaling Studies, Faculty of Biology, Albert-Ludwigs-Universitaet Freiburg, Freiburg, Germany
| | - Barbara Wójcikowska
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University and Institute of Experimental Botany CAS, Olomouc, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University and Institute of Experimental Botany CAS, Olomouc, Czech Republic
| | - Junyi Chen
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Regensburg, Germany
| | - Wim Grunewald
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Regensburg, Germany
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.
| | - Thomas Laux
- BIOSS Centre for Biological Signaling Studies, Faculty of Biology, Albert-Ludwigs-Universitaet Freiburg, Freiburg, Germany.
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30
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Vega‐Trejo R, Kruuk LEB, Jennions MD, Head ML. What happens to offspring when parents are inbred, old or had a poor start in life? Evidence for sex‐specific parental effects. J Evol Biol 2018; 31:1138-1151. [DOI: 10.1111/jeb.13292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 04/30/2018] [Accepted: 05/14/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Regina Vega‐Trejo
- Division of Ecology & Evolution, Research School of Biology The Australian National University, Acton Canberra ACT Australia
| | - Loeske E. B. Kruuk
- Division of Ecology & Evolution, Research School of Biology The Australian National University, Acton Canberra ACT Australia
| | - Michael D. Jennions
- Division of Ecology & Evolution, Research School of Biology The Australian National University, Acton Canberra ACT Australia
| | - Megan L. Head
- Division of Ecology & Evolution, Research School of Biology The Australian National University, Acton Canberra ACT Australia
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31
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Otto GM, Brar GA. Seq-ing answers: uncovering the unexpected in global gene regulation. Curr Genet 2018; 64:1183-1188. [PMID: 29675618 PMCID: PMC6223828 DOI: 10.1007/s00294-018-0839-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 11/26/2022]
Abstract
The development of techniques for measuring gene expression globally has greatly expanded our understanding of gene regulatory mechanisms in depth and scale. We can now quantify every intermediate and transition in the canonical pathway of gene expression—from DNA to mRNA to protein—genome-wide. Employing such measurements in parallel can produce rich datasets, but extracting the most information requires careful experimental design and analysis. Here, we argue for the value of genome-wide studies that measure multiple outputs of gene expression over many timepoints during the course of a natural developmental process. We discuss our findings from a highly parallel gene expression dataset of meiotic differentiation, and those of others, to illustrate how leveraging these features can provide new and surprising insight into fundamental mechanisms of gene regulation.
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Affiliation(s)
- George Maxwell Otto
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, 94720, USA.
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32
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Jansova D, Tetkova A, Koncicka M, Kubelka M, Susor A. Localization of RNA and translation in the mammalian oocyte and embryo. PLoS One 2018. [PMID: 29529035 PMCID: PMC5846722 DOI: 10.1371/journal.pone.0192544] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The tight correlation between mRNA distribution and subsequent protein localization and function indicate a major role for mRNA localization within the cell. RNA localization, followed by local translation, presents a mechanism for spatial and temporal gene expression regulation utilized by various cell types. However, little is known about mRNA localization and translation in the mammalian oocyte and early embryo. Importantly, fully-grown oocyte becomes transcriptionally inactive and only utilizes transcripts previously synthesized and stored during earlier development. We discovered an abundant RNA population in the oocyte and early embryo nucleus together with RNA binding proteins. We also characterized specific ribosomal proteins, which contribute to translation in the oocyte and embryo. By applying selected markers to mouse and human oocytes, we found that there might be a similar mechanism of RNA metabolism in both species. In conclusion, we visualized the localization of RNAs and translation machinery in the oocyte, that could shed light on this terra incognita of these unique cell types in mouse and human.
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Affiliation(s)
- Denisa Jansova
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
- * E-mail: (DJ); (AS)
| | - Anna Tetkova
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Marketa Koncicka
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Michal Kubelka
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
| | - Andrej Susor
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
- * E-mail: (DJ); (AS)
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33
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Lefebvre FA, Lécuyer É. Flying the RNA Nest: Drosophila Reveals Novel Insights into the Transcriptome Dynamics of Early Development. J Dev Biol 2018; 6:jdb6010005. [PMID: 29615554 PMCID: PMC5875563 DOI: 10.3390/jdb6010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/01/2018] [Accepted: 03/05/2018] [Indexed: 01/02/2023] Open
Abstract
Early development is punctuated by a series of pervasive and fast paced transitions. These events reshape a differentiated oocyte into a totipotent embryo and allow it to gradually mount a genetic program of its own, thereby framing a new organism. Specifically, developmental transitions that ensure the maternal to embryonic control of developmental events entail a deep remodeling of transcriptional and transcriptomic landscapes. Drosophila provides an elegant and genetically tractable system to investigate these conserved changes at a dazzling developmental pace. Here, we review recent studies applying emerging technologies such as ribosome profiling, in situ Hi-C chromatin probing and live embryo RNA imaging to investigate the transcriptional dynamics at play during Drosophila embryogenesis. In light of this new literature, we revisit the main models of zygotic genome activation (ZGA). We also review the contributions played by zygotic transcription in shaping embryogenesis and explore emerging concepts of processes such as transcriptional bursting and transcriptional memory.
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Affiliation(s)
- Fabio Alexis Lefebvre
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Éric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada.
- Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada.
- IRCM, RNA Biology Laboratory, 110 Avenue des Pins, Ouest, Montréal, QC H2W 1R7, Canada.
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34
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Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL. High-throughput identification of RNA nuclear enrichment sequences. EMBO J 2018; 37:embj.201798452. [PMID: 29335281 PMCID: PMC5852646 DOI: 10.15252/embj.201798452] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 11/21/2022] Open
Abstract
In the post‐genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever‐growing catalogs require high‐throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse. Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA‐based functionality. We applied MPRNA to identify RNA‐based nuclear localization domains harbored in lncRNAs. We examined a pool of 11,969 oligos densely tiling 38 human lncRNAs that were fused to a cytosolic transcript. After cell fractionation and barcode sequencing, we identified 109 unique RNA regions that significantly enriched this cytosolic transcript in the nucleus including a cytosine‐rich motif. These nuclear enrichment sequences are highly conserved and over‐represented in global nuclear fractionation sequencing. Importantly, many of these regions were independently validated by single‐molecule RNA fluorescence in situ hybridization. Overall, we demonstrate the utility of MPRNA for future investigation of RNA‐based functionalities.
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Affiliation(s)
- Chinmay J Shukla
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Alexandra L McCorkindale
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Keegan D Korthauer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - David M Shechner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rafael A Irizarry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
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35
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Li X, Seidel CW, Szerszen LT, Lange JJ, Workman JL, Abmayr SM. Enzymatic modules of the SAGA chromatin-modifying complex play distinct roles in Drosophila gene expression and development. Genes Dev 2017; 31:1588-1600. [PMID: 28887412 PMCID: PMC5630023 DOI: 10.1101/gad.300988.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/11/2017] [Indexed: 01/03/2023]
Abstract
In this study, Li et al. demonstrate that the two enzymatic modules of the Drosophila Spt–Ada–Gcn5–acetyltransferase (SAGA) chromatin-modifying complex are differently required in oogenesis. Their findings demonstrate that loss of the histone acetyltransferase (HAT) activity blocks oogenesis, while loss of H2B deubiquitinase (DUB) activity does not, suggesting that the DUB module has functions within SAGA as well as independent functions. The Spt–Ada–Gcn5–acetyltransferase (SAGA) chromatin-modifying complex is a transcriptional coactivator that contains four different modules of subunits. The intact SAGA complex has been well characterized for its function in transcription regulation and development. However, little is known about the roles of individual modules within SAGA and whether they have any SAGA-independent functions. Here we demonstrate that the two enzymatic modules of Drosophila SAGA are differently required in oogenesis. Loss of the histone acetyltransferase (HAT) activity blocks oogenesis, while loss of the H2B deubiquitinase (DUB) activity does not. However, the DUB module regulates a subset of genes in early embryogenesis, and loss of the DUB subunits causes defects in embryogenesis. ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) analysis revealed that both the DUB and HAT modules bind most SAGA target genes even though many of these targets do not require the DUB module for expression. Furthermore, we found that the DUB module can bind to chromatin and regulate transcription independently of the HAT module. Our results suggest that the DUB module has functions within SAGA and independent functions.
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Affiliation(s)
- Xuanying Li
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | | | - Leanne T Szerszen
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Susan M Abmayr
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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36
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Jeske M, Müller CW, Ephrussi A. The LOTUS domain is a conserved DEAD-box RNA helicase regulator essential for the recruitment of Vasa to the germ plasm and nuage. Genes Dev 2017; 31:939-952. [PMID: 28536148 PMCID: PMC5458760 DOI: 10.1101/gad.297051.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/08/2017] [Indexed: 12/15/2022]
Abstract
DEAD-box RNA helicases play important roles in a wide range of metabolic processes. Regulatory proteins can stimulate or block the activity of DEAD-box helicases. Here, we show that LOTUS (Limkain, Oskar, and Tudor containing proteins 5 and 7) domains present in the germline proteins Oskar, TDRD5 (Tudor domain-containing 5), and TDRD7 bind and stimulate the germline-specific DEAD-box RNA helicase Vasa. Our crystal structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of Vasa reveals that the LOTUS domain occupies a surface on a DEAD-box helicase not implicated previously in the regulation of the enzyme's activity. We show that, in vivo, the localization of Drosophila Vasa to the nuage and germ plasm depends on its interaction with LOTUS domain proteins. The binding and stimulation of Vasa DEAD-box helicases by LOTUS domains are widely conserved.
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Affiliation(s)
- Mandy Jeske
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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37
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Kadosh D. Control of Candida albicans morphology and pathogenicity by post-transcriptional mechanisms. Cell Mol Life Sci 2016; 73:4265-4278. [PMID: 27312239 PMCID: PMC5582595 DOI: 10.1007/s00018-016-2294-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/23/2016] [Accepted: 06/10/2016] [Indexed: 02/01/2023]
Abstract
Candida albicans is a major human fungal pathogen responsible for both systemic and mucosal infections in a wide variety of immunocompromised individuals. Because the ability of C. albicans to undergo a reversible morphological transition from yeast to filaments is important for virulence, significant research efforts have focused on mechanisms that control this transition. While transcriptional and post-translational mechanisms have been well-studied, considerably less is known about the role of post-transcriptional mechanisms. However, in recent years several discoveries have begun to shed light on this important, but understudied, area. Here, I will review a variety of post-transcriptional mechanisms that have recently been shown to control C. albicans morphology, virulence and/or virulence-related processes, including those involving alternative transcript localization, mRNA stability and translation. I will also discuss the role that these mechanisms play in other pathogens as well as the potential they may hold to serve as targets for new antifungal strategies. Ultimately, gaining a better understanding of C. albicans post-transcriptional mechanisms will significantly improve our knowledge of how morphogenesis and virulence are controlled in fungal pathogens and open new avenues for the development of novel and more effective antifungals.
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Affiliation(s)
- David Kadosh
- Department of Microbiology and Immunology, University of Texas Health Science, Center at San Antonio, 7703 Floyd Curl Drive, MC: 7758, San Antonio, TX, 78229, USA.
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38
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c-Fos Repression by Piwi Regulates Drosophila Ovarian Germline Formation and Tissue Morphogenesis. PLoS Genet 2016; 12:e1006281. [PMID: 27622269 PMCID: PMC5021354 DOI: 10.1371/journal.pgen.1006281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/04/2016] [Indexed: 11/19/2022] Open
Abstract
Drosophila melanogaster Piwi functions within the germline stem cells (GSCs) and the somatic niche to regulate GSC self-renewal and differentiation. How Piwi influences GSCs is largely unknown. We uncovered a genetic interaction between Piwi and c-Fos in the somatic niche that influences GSCs. c-Fos is a proto-oncogene that influences many cell and developmental processes. In wild-type ovarian cells, c-Fos is post-transcriptionally repressed by Piwi, which destabilized the c-Fos mRNA by promoting the processing of its 3' untranslated region (UTR) into Piwi-interacting RNAs (piRNAs). The c-Fos 3' UTR was sufficient to trigger Piwi-dependent destabilization of a GFP reporter. Piwi represses c-Fos in the somatic niche to regulate GSC maintenance and differentiation and in the somatic follicle cells to affect somatic cell disorganization, tissue dysmorphogenesis, oocyte maturation arrest, and infertility.
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39
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Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J 2016; 35:2087-2103. [PMID: 27436874 DOI: 10.15252/embj.201694699] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/16/2016] [Indexed: 12/26/2022] Open
Abstract
Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal-to-zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by post-transcriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs, this pathway does not fully explain mRNA clearance. We investigated how codon identity and translation affect mRNA stability during development and homeostasis. We show that the codon triplet contains translation-dependent regulatory information that influences transcript decay. Codon composition shapes maternal mRNA clearance during the maternal-to-zygotic transition in zebrafish, Xenopus, mouse, and Drosophila, and gene expression during homeostasis across human tissues. Some synonymous codons show consistent stabilizing or destabilizing effects, suggesting that amino acid composition influences mRNA stability. Codon composition affects both polyadenylation status and translation efficiency. Thus, the ribosome interprets two codes within the mRNA: the genetic code which specifies the amino acid sequence and a conserved "codon optimality code" that shapes mRNA stability and translation efficiency across vertebrates.
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Affiliation(s)
- Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Florencia Del Viso
- Departments of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Timothy G Johnstone
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Yidan Qin
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Mustafa K Khokha
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Departments of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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40
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Garbiec A, Kubrakiewicz J, Mazurkiewicz-Kania M, Simiczyjew B, Jędrzejowska I. Asymmetry in structure of the eggshell in Osmylus fulvicephalus (Neuroptera: Osmylidae): an exceptional case of breaking symmetry during neuropteran oogenesis. PROTOPLASMA 2016; 253:1033-1042. [PMID: 26224214 PMCID: PMC4947476 DOI: 10.1007/s00709-015-0860-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/15/2015] [Indexed: 06/06/2023]
Abstract
Ovaries of neuropterans are of meroistic-polytrophic type. The ovarian tubes, the ovarioles, are divided into two major parts: a germarium, comprised of newly formed germ cell clusters; and a vitellarium, housing linearly arranged ovarian follicles. Each ovarian follicle consists of the germ cell cluster diversified into different number of nurse cells, and the oocyte enclosed by follicular epithelium. In Osmylus fulvicephalus, a representative of Neuroptera, during consecutive stages of oogenesis, the follicular cells undergo a multistep process of diversification which leads to the appearance of several follicular cell subpopulations i.e., the main-body follicular cells, the stretched cells, the anterior centripetal cells, and posterior centripetal cells. The anterior centripetal cells occupy the anterior pole of the oocyte and in advanced oogenesis due to hypertrophy that transform into anterior fold cells. Initially, the anterior fold cells form a symmetric fold, but in advanced oogenesis, quite different from other neuropterans studied so far, they undergo uneven hypertrophic growth which results in breaking symmetry of the anterior fold that becomes shifted to the ventral side of the oocyte. Since the anterior fold cells participate in the production of the specialized chorion structure, the micropyle, asymmetric structure of the anterior fold, is reflected both in its asymmetric position and in the asymmetric construction of the micropyle. As a consequence of breaking symmetry of the anterior fold, Osmylus eggshell gains dorso-ventral polarity, which is unusual for neuropterans.
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Affiliation(s)
- Arnold Garbiec
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wrocław, Sienkiewicza 21, 50-335, Wrocław, Poland.
| | - Janusz Kubrakiewicz
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wrocław, Sienkiewicza 21, 50-335, Wrocław, Poland
| | - Marta Mazurkiewicz-Kania
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wrocław, Sienkiewicza 21, 50-335, Wrocław, Poland
| | - Bożena Simiczyjew
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wrocław, Sienkiewicza 21, 50-335, Wrocław, Poland
| | - Izabela Jędrzejowska
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wrocław, Sienkiewicza 21, 50-335, Wrocław, Poland
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Yuan K, Seller CA, Shermoen AW, O'Farrell PH. Timing the Drosophila Mid-Blastula Transition: A Cell Cycle-Centered View. Trends Genet 2016; 32:496-507. [PMID: 27339317 DOI: 10.1016/j.tig.2016.05.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/19/2016] [Accepted: 05/23/2016] [Indexed: 11/18/2022]
Abstract
At the mid-blastula transition (MBT), externally developing embryos refocus from increasing cell number to elaboration of the body plan. Studies in Drosophila reveal a sequence of changes in regulators of Cyclin:Cdk1 that increasingly restricts the activity of this cell cycle kinase to slow cell cycles during early embryogenesis. By reviewing these events, we provide an outline of the mechanisms slowing the cell cycle at and around the time of MBT. The perspectives developed should provide a guiding paradigm for the study of other MBT changes as the embryo transits from maternal control to a regulatory program centered on the expression of zygotic genes.
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Affiliation(s)
- Kai Yuan
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Charles A Seller
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Antony W Shermoen
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Patrick H O'Farrell
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA 94158, USA.
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Wang M, Yu Y, Liang C, Lu A, Zhang G. Recent Advances in Developing Small Molecules Targeting Nucleic Acid. Int J Mol Sci 2016; 17:ijms17060779. [PMID: 27248995 PMCID: PMC4926330 DOI: 10.3390/ijms17060779] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/01/2016] [Accepted: 05/09/2016] [Indexed: 12/19/2022] Open
Abstract
Nucleic acids participate in a large number of biological processes. However, current approaches for small molecules targeting protein are incompatible with nucleic acids. On the other hand, the lack of crystallization of nucleic acid is the limiting factor for nucleic acid drug design. Because of the improvements in crystallization in recent years, a great many structures of nucleic acids have been reported, providing basic information for nucleic acid drug discovery. This review focuses on the discovery and development of small molecules targeting nucleic acids.
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Affiliation(s)
- Maolin Wang
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Yuanyuan Yu
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Chao Liang
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Aiping Lu
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Ge Zhang
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
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43
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Zheng Z, Li H, Zhang Q, Yang L, Qi H. Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos. Reproduction 2016; 151:351-67. [DOI: 10.1530/rep-15-0301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/13/2016] [Indexed: 12/30/2022]
Abstract
Cell lineage determination during early embryogenesis has profound effects on adult animal development. Pre-patterning of embryos, such as that of Drosophila and Caenorhabditis elegans, is driven by asymmetrically localized maternal or zygotic factors, including mRNA species and RNA binding proteins. However, it is not clear how mammalian early embryogenesis is regulated and what the early cell fate determinants are. Here we show that, in mouse, mitochondrial ribosomal RNAs (mtrRNAs) are differentially distributed between 2-cell sister blastomeres. This distribution pattern is not related to the overall quantity or activity of mitochondria which appears equal between 2-cell sister blastomeres. Like in lower species, 16S mtrRNA is found to localize in the cytoplasm outside of mitochondria in mouse 2-cell embryos. Alterations of 16S mtrRNA levels in one of the 2-cell sister blastomere via microinjection of either sense or anti-sense RNAs drive its progeny into different cell lineages in blastocyst. These results indicate that mtrRNAs are differentially distributed among embryonic cells at the beginning of embryogenesis in mouse and they are functionally involved in the regulation of cell lineage allocations in blastocyst, suggesting an underlying molecular mechanism that regulates pre-implantation embryogenesis in mouse.
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Multiple Roles for Egalitarian in Polarization of the Drosophila Egg Chamber. Genetics 2016; 203:415-32. [PMID: 27017624 DOI: 10.1534/genetics.115.184622] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/20/2016] [Indexed: 01/08/2023] Open
Abstract
The Drosophila egg chamber provides a useful model for examining mechanisms by which cell fates are specified and maintained in the context of a complex tissue. The egg chamber is also an excellent model for understanding the mechanism by which cytoskeletal filaments are organized and the critical interplay between cytoskeletal organization, polarity establishment, and cell fate specification. Previous work has shown that Egalitarian (Egl) is required for specification and maintenance of oocyte fate. Mutants in egl either completely fail to specify an oocyte, or if specified, the oocyte eventually reverts back to nurse cell fate. Due to this very early role for Egl in egg chamber maturation, it is unclear whether later stages of egg chamber development also require Egl function. In this report, we have depleted Egl at specific stages of egg chamber development. We demonstrate that in early-stage egg chambers, Egl has an additional role in organization of oocyte microtubules. In the absence of Egl function, oocyte microtubules completely fail to reorganize. As such, the localization of microtubule motors and their cargo is disrupted. In addition, Egl also appears to function in regulating the translation of critical polarity determining messenger RNAs (mRNAs). Finally, we demonstrate that in midstage egg chambers, Egl does not appear to be required for microtubule organization, but rather for the correct spatial localization of oskar, bicoid, and gurken mRNAs.
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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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46
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Khan AY, Suresh Kumar G. Spectroscopic studies on the binding interaction of phenothiazinium dyes, azure A and azure B to double stranded RNA polynucleotides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 152:417-425. [PMID: 26241827 DOI: 10.1016/j.saa.2015.07.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 07/08/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
This manuscript presents spectroscopic characterization of the interaction of two phenothiazinium dyes, azure A and azure B with double stranded (ds) ribonucleic acids, poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C). Absorbance and fluorescence studies revealed that these dyes bind to the RNAs with binding affinities of the order 10(6)M(-1) to poly(A).poly(U), and 10(5)M(-1) to poly(C).poly(G) and poly(I).poly(C), respectively. Fluorescence quenching and viscosity data gave conclusive evidence for the intercalation of the dyes to these RNA duplexes. Circular dichroism results suggested that the conformation of the RNAs was perturbed on interaction and the dyes acquired strong induced optical activity on binding. Azure B bound to all the three RNAs stronger than azure A and the binding affinity varied as poly(A).poly(U)>poly(C).poly(G)>poly(I).poly(C) for both dyes.
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Affiliation(s)
- Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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Abstract
For many decades, the major function of mRNA was thought to be to provide protein-coding information embedded in the genome. The advent of high-throughput sequencing has led to the discovery of pervasive transcription of eukaryotic genomes and opened the world of RNA-mediated gene regulation. Many regulatory RNAs have been found to be incapable of protein coding and are hence termed as non-coding RNAs (ncRNAs). However, studies in recent years have shown that several previously annotated non-coding RNAs have the potential to encode proteins, and conversely, some coding RNAs have regulatory functions independent of the protein they encode. Such bi-functional RNAs, with both protein coding and non-coding functions, which we term as 'cncRNAs', have emerged as new players in cellular systems. Here, we describe the functions of some cncRNAs identified from bacteria to humans. Because the functions of many RNAs across genomes remains unclear, we propose that RNAs be classified as coding, non-coding or both only after careful analysis of their functions.
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Affiliation(s)
- Pooja Kumari
- Division of Biomedical Cell Biology, Warwick Medical School, The University of Warwick, Gibbet Hill Road, Coventry CV47AJ, United Kingdom
| | - Karuna Sampath
- Division of Biomedical Cell Biology, Warwick Medical School, The University of Warwick, Gibbet Hill Road, Coventry CV47AJ, United Kingdom.
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48
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Copf T. Importance of gene dosage in controlling dendritic arbor formation during development. Eur J Neurosci 2015; 42:2234-49. [PMID: 26108333 DOI: 10.1111/ejn.13002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/05/2015] [Accepted: 06/18/2015] [Indexed: 12/11/2022]
Abstract
Proper dendrite morphology is crucial for normal nervous system functioning. While a number of genes have been implicated in dendrite morphogenesis in both invertebrates and mammals, it remains unclear how developing dendrites respond to changes in gene dosage and what type of patterns their responses may follow. To understand this, I review here evidence from the recent literature, focusing on the genetic studies performed in the Drosophila larval dendritic arborization class IV neuron, an excellent cell type to understand dendrite morphogenesis. I summarize how class IV arbors change morphology in response to developmental fluctuations in the expression levels of 47 genes, studied by means of genetic manipulations such as loss-of-function and gain-of-function, and for which sufficient information is available. I find that arbors can respond to changing gene dosage in several distinct ways, each characterized by a singular dose-response curve. Interestingly, in 72% of cases arbors are sensitive, and thus adjust their morphology, in response to both decreases and increases in the expression of a given gene, indicating that dendrite morphogenesis is a process particularly sensitive to gene dosage. By summarizing the parallels between Drosophila and mammals, I show that many Drosophila dendrite morphogenesis genes have orthologs in mammals, and that some of these are associated with mammalian dendrite outgrowth and human neurodevelopmental disorders. One notable disease-related molecule is kinase Dyrk1A, thought to be a causative factor in Down syndrome. Both increases and decreases in Dyrk1A gene dosage lead to impaired dendrite morphogenesis, which may contribute to Down syndrome pathoetiology.
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Affiliation(s)
- Tijana Copf
- Institute of Molecular Biology and Biotechnology, Nikolaou Plastira 100, PO Box 1385, Heraklion, GR-70013, Crete, Greece
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49
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Siebert M, Böhme MA, Driller JH, Babikir H, Mampell MM, Rey U, Ramesh N, Matkovic T, Holton N, Reddy-Alla S, Göttfert F, Kamin D, Quentin C, Klinedinst S, Andlauer TF, Hell SW, Collins CA, Wahl MC, Loll B, Sigrist SJ. A high affinity RIM-binding protein/Aplip1 interaction prevents the formation of ectopic axonal active zones. eLife 2015; 4. [PMID: 26274777 PMCID: PMC4536467 DOI: 10.7554/elife.06935] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 07/24/2015] [Indexed: 12/17/2022] Open
Abstract
Synaptic vesicles (SVs) fuse at active zones (AZs) covered by a protein scaffold, at Drosophila synapses comprised of ELKS family member Bruchpilot (BRP) and RIM-binding protein (RBP). We here demonstrate axonal co-transport of BRP and RBP using intravital live imaging, with both proteins co-accumulating in axonal aggregates of several transport mutants. RBP, via its C-terminal Src-homology 3 (SH3) domains, binds Aplip1/JIP1, a transport adaptor involved in kinesin-dependent SV transport. We show in atomic detail that RBP C-terminal SH3 domains bind a proline-rich (PxxP) motif of Aplip1/JIP1 with submicromolar affinity. Pointmutating this PxxP motif provoked formation of ectopic AZ-like structures at axonal membranes. Direct interactions between AZ proteins and transport adaptors seem to provide complex avidity and shield synaptic interaction surfaces of pre-assembled scaffold protein transport complexes, thus, favouring physiological synaptic AZ assembly over premature assembly at axonal membranes. DOI:http://dx.doi.org/10.7554/eLife.06935.001 To pass on information, the neurons that make up the nervous system connect at structures known as synapses. Chemical messengers called neurotransmitters are released from one neuron, and travel across the synapse to trigger a response in the neighbouring cell. The formation of new synapses plays an important role in learning and memory, but many aspects of this process are not well understood. In a specific region of the synapse called the active zone, a scaffold of proteins helps to release the neurotransmitters. These proteins are made in the cell body of the neuron, and are then transported to the end of the long, thin axons that protrude from the cell body. This presents a challenge for the cell, because the components of the active zone scaffold must be correctly targeted to the synapse at the end of the axon, ensuring the active zone scaffold assembles only at its proper location. Siebert, Böhme et al. studied how some of the proteins that are found in the active zone scaffold of the fruit fly Drosophila are transported along axons. Labelling the proteins with fluorescent markers allowed their movement to be examined under a microscope in living Drosophila larvae. The results showed that two of the proteins—known as BRP and RBP—are transported along the axons together. Further investigation revealed that a transport adaptor protein called Aplip1, which binds to RBP, is required for this movement. Siebert, Böhme et al. established the structure of the part of RBP where this interaction occurs, and found that mutating this region causes premature active zone scaffold assembly in the axonal part of the neuron. The interaction between RBP and Aplip1 is very strong, and this helps to prevent the scaffold assembling before it has reached the correct part of the neuron. Exactly how the transport adaptor and active zone protein are separated once they reach their final destination (the synapse) remains to be discovered. DOI:http://dx.doi.org/10.7554/eLife.06935.002
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Affiliation(s)
- Matthias Siebert
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Mathias A Böhme
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Jan H Driller
- Institute of Chemistry and Biochemisty/Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Husam Babikir
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Malou M Mampell
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Ulises Rey
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Niraja Ramesh
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Tanja Matkovic
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Nicole Holton
- Institute of Chemistry and Biochemisty/Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Suneel Reddy-Alla
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Fabian Göttfert
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Kamin
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christine Quentin
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Susan Klinedinst
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Till Fm Andlauer
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Stefan W Hell
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Catherine A Collins
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Markus C Wahl
- Institute of Chemistry and Biochemisty/Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Bernhard Loll
- Institute of Chemistry and Biochemisty/Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Stephan J Sigrist
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
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50
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Zhang Y, Wang P, Shao W, Zhu JK, Dong J. The BASL polarity protein controls a MAPK signaling feedback loop in asymmetric cell division. Dev Cell 2015; 33:136-49. [PMID: 25843888 PMCID: PMC4406870 DOI: 10.1016/j.devcel.2015.02.022] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/16/2015] [Accepted: 02/25/2015] [Indexed: 11/24/2022]
Abstract
Cell polarization is linked to fate determination during asymmetric division of plant stem cells, but the underlying molecular mechanisms remain unknown. In Arabidopsis, BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL) is polarized to control stomatal asymmetric division. A mitogen-activated protein kinase (MAPK) cascade determines terminal stomatal fate by promoting the degradation of the lineage determinant SPEECHLESS (SPCH). Here, we demonstrate that a positive-feedback loop between BASL and the MAPK pathway constitutes a polarity module at the cortex. Cortical localization of BASL requires phosphorylation mediated by MPK3/6. Phosphorylated BASL functions as a scaffold and recruits the MAPKKK YODA and MPK3/6 to spatially concentrate signaling at the cortex. Activated MPK3/6 reinforces the feedback loop by phosphorylating BASL and inhibits stomatal fate by phosphorylating SPCH. Polarization of the BASL-MAPK signaling feedback module represents a mechanism connecting cell polarity to fate differentiation during asymmetric stem cell division in plants.
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Affiliation(s)
- Ying Zhang
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Pengcheng Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Wanchen Shao
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, Piscataway, NJ 08901, USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Juan Dong
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, Piscataway, NJ 08901, USA.
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