101
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Post-transcriptional regulation in planarian stem cells. Semin Cell Dev Biol 2018; 87:69-78. [PMID: 29870807 DOI: 10.1016/j.semcdb.2018.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 12/17/2022]
Abstract
Planarians are known for their immense regenerative abilities. A pluripotent stem cell population provides the cellular source for this process, as well as for the homeostatic cell turnover of the animals. These stem cells, known as neoblasts, present striking similarities at the morphological and molecular level to germ cells, but however, give rise to somatic tissue. Many RNA binding proteins known to be important for germ cell biology are also required for neoblast function, highlighting the importance of post-transcriptional regulation for stem cell control. Many of its aspects, including alternative splicing, alternative polyadenylation, translational control and mRNA deadenylation, as well as small RNAs such as microRNAs and piRNA are critical for stem cells. Their inhibition often abrogates both regeneration and cell turnover, resulting in lethality. Some of aspects of post-transcriptional regulation are conserved from planarian to mammalian stem cells.
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102
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Causes and evolutionary consequences of primordial germ-cell specification mode in metazoans. Proc Natl Acad Sci U S A 2018; 114:5784-5791. [PMID: 28584112 DOI: 10.1073/pnas.1610600114] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In animals, primordial germ cells (PGCs) give rise to the germ lines, the cell lineages that produce sperm and eggs. PGCs form in embryogenesis, typically by one of two modes: a likely ancestral mode wherein germ cells are induced during embryogenesis by cell-cell signaling (induction) or a derived mechanism whereby germ cells are specified by using germ plasm-that is, maternally specified germ-line determinants (inheritance). The causes of the shift to germ plasm for PGC specification in some animal clades remain largely unknown, but its repeated convergent evolution raises the question of whether it may result from or confer an innate selective advantage. It has been hypothesized that the acquisition of germ plasm confers enhanced evolvability, resulting from the release of selective constraint on somatic gene networks in embryogenesis, thus leading to acceleration of an organism's protein-sequence evolution, particularly for genes expressed at early developmental stages, and resulting in high speciation rates in germ plasm-containing lineages (denoted herein as the "PGC-specification hypothesis"). Although that hypothesis, if supported, could have major implications for animal evolution, our recent large-scale coding-sequence analyses from vertebrates and invertebrates provided important examples of genera that do not support the hypothesis of liberated constraint under germ plasm. Here, we consider reasons why germ plasm might be neither a direct target of selection nor causally linked to accelerated animal evolution. We explore alternate scenarios that could explain the repeated evolution of germ plasm and propose potential consequences of the inheritance and induction modes to animal evolutionary biology.
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103
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Control of Pem protein level by localized maternal factors for transcriptional regulation in the germline of the ascidian, Halocynthia roretzi. PLoS One 2018; 13:e0196500. [PMID: 29709000 PMCID: PMC5927453 DOI: 10.1371/journal.pone.0196500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/13/2018] [Indexed: 12/04/2022] Open
Abstract
Localized maternal mRNAs play important roles in embryogenesis, e.g. the establishment of embryonic axes and the developmental cell fate specification, in various animal species. In ascidians, a group of maternal mRNAs, called postplasmic/PEM RNAs, is localized to a subcellular structure, called the Centrosome-Attracting Body (CAB), which contains the ascidian germ plasm, and is inherited by the germline cells during embryogenesis. Posterior end mark (Pem), a postplasmic/PEM RNAs member, represses somatic gene expression in the germline during cleavage stages by inhibition of RNA polymerase II activity. However, the functions of other postplasmic/ PEM RNAs members in germline formation are largely unknown. In this study, we analyzed the functions of two postplasmic/PEM RNAs, Popk-1 and Zf-1, in transcriptional regulation in the germline cells. We show that Popk-1 contributes to transcriptional quiescence by controlling the size of the CAB and amount of Pem protein translated at the CAB. Our studies also indicated that zygotic expression of a germline gene starts around the onset of gastrulation and that the decrease of Pem protein is necessary and sufficient for the zygotic germline gene expression. Finally, further studies showed that the decrease of the Pem protein level is facilitated by Zf-1. Taken together, we propose that postplasmic/PEM RNAs such as Popk-1 and Zf-1 control the protein level of the transcriptional repressor Pem and regulate its transcriptional state in the ascidian germline.
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104
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Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs. G3-GENES GENOMES GENETICS 2018; 8:531-550. [PMID: 29208647 PMCID: PMC5919742 DOI: 10.1534/g3.117.300253] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Germ-soma differentiation is a hallmark of complex multicellular organisms, yet its origins are not well understood. Volvox carteri is a simple multicellular green alga that has recently evolved a simple germ-soma dichotomy with only two cell-types: large germ cells called gonidia and small terminally differentiated somatic cells. Here, we provide a comprehensive characterization of the gonidial and somatic transcriptomes of V. carteri to uncover fundamental differences between the molecular and metabolic programming of these cell-types. We found extensive transcriptome differentiation between cell-types, with somatic cells expressing a more specialized program overrepresented in younger, lineage-specific genes, and gonidial cells expressing a more generalist program overrepresented in more ancient genes that shared striking overlap with stem cell-specific genes from animals and land plants. Directed analyses of different pathways revealed a strong dichotomy between cell-types with gonidial cells expressing growth-related genes and somatic cells expressing an altruistic metabolic program geared toward the assembly of flagella, which support organismal motility, and the conversion of storage carbon to sugars, which act as donors for production of extracellular matrix (ECM) glycoproteins whose secretion enables massive organismal expansion. V. carteri orthologs of diurnally controlled genes from C. reinhardtii, a single-celled relative, were analyzed for cell-type distribution and found to be strongly partitioned, with expression of dark-phase genes overrepresented in somatic cells and light-phase genes overrepresented in gonidial cells- a result that is consistent with cell-type programs in V. carteri arising by cooption of temporal regulons in a unicellular ancestor. Together, our findings reveal fundamental molecular, metabolic, and evolutionary mechanisms that underlie the origins of germ-soma differentiation in V. carteri and provide a template for understanding the acquisition of germ-soma differentiation in other multicellular lineages.
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105
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Nakajima K. Be my baby: patterning toward plant germ cells. CURRENT OPINION IN PLANT BIOLOGY 2018; 41:110-115. [PMID: 29223127 DOI: 10.1016/j.pbi.2017.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 05/28/2023]
Abstract
In flowering plants, germ cells are formed via tightly coordinated patterning processes that facilitate specification of spore mother cells and meiosis during sporogenesis, as well as functional differentiation of germ cells in gametogenesis. Studies using the conventional Arabidopsis system and the newly emerged bryophyte system have revealed novel interactions between regulatory factors that restrict the number of spore mother cells, and evolutionarily conserved factors that promote germ cell differentiation. This short review summarizes recent advances in our understanding of the cellular events that lead to the formation of germ cells in plants, and highlights questions that remain to be addressed in the field.
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Affiliation(s)
- Keiji Nakajima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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106
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West SM, Mecenas D, Gutwein M, Aristizábal-Corrales D, Piano F, Gunsalus KC. Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline. Genome Biol 2018; 19:8. [PMID: 29368663 PMCID: PMC5784609 DOI: 10.1186/s13059-017-1369-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 12/03/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The 3' untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types. Using LITE-Seq, a new quantitative method to capture transcript 3' ends expressed in vivo, we have characterized sex- and cell type-specific transcriptome-wide changes in gene expression and 3'UTR diversity in Caenorhabditis elegans germline cells undergoing proliferation and differentiation. RESULTS We show that nearly half of germline transcripts are alternatively polyadenylated, that differential regulation of endogenous 3'UTR variants is common, and that alternative isoforms direct distinct spatiotemporal protein expression patterns in vivo. Dynamic expression profiling also reveals temporal regulation of X-linked gene expression, selective stabilization of transcripts, and strong evidence for a novel developmental program that promotes nucleolar dissolution in oocytes. We show that the RNA-binding protein NCL-1/Brat is a posttranscriptional regulator of numerous ribosome-related transcripts that acts through specific U-rich binding motifs to down-regulate mRNAs encoding ribosomal protein subunits, rRNA processing factors, and tRNA synthetases. CONCLUSIONS These results highlight the pervasive nature and functional potential of patterned gene and isoform expression during early animal development.
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Affiliation(s)
- Sean M West
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Desirea Mecenas
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Michelle Gutwein
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - David Aristizábal-Corrales
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Fabio Piano
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
| | - Kristin C Gunsalus
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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107
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The Vertebrate Protein Dead End Maintains Primordial Germ Cell Fate by Inhibiting Somatic Differentiation. Dev Cell 2017; 43:704-715.e5. [DOI: 10.1016/j.devcel.2017.11.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/14/2017] [Accepted: 11/20/2017] [Indexed: 12/14/2022]
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108
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Fields C, Levin M. Multiscale memory and bioelectric error correction in the cytoplasm-cytoskeleton-membrane system. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10. [DOI: 10.1002/wsbm.1410] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/19/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Chris Fields
- 21 Rue des Lavandiéres, 11160 Caunes Minervois; France
| | - Michael Levin
- Allen Discovery Center at Tufts University; Medford MA USA
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109
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Abstract
PURPOSE OF REVIEW This review summarizes the unmet need of headache burden and management in resource-limited settings. It provides a general overview of the nuances and peculiarities of headache disorders in resource-limited settings. The review delivers perspectives and explanations for the emerging burden of both primary and secondary headache disorders. Important discussion on demographic and epidemiologic transition pertinent to low-resource settings is included. A critical analysis of headache disorders is made within the context of growing burden non-communicable disorders in low-resource countries. Challenges are examined and prospective feasible solutions tailored to existing resources are provided to address headache disorders in resource-limited settings. RECENT FINDINGS Many low-resource countries are entering into the third epidemiological transition featuring increasing burden of non-communicable disorders of which headache disorders contribute a significant proportion. Exponential population growth involving youthful demographic and massive rural-urban migration is taking place in low-resource countries. Youthful demographic is the natural cohort for primary headache such as migraine. Socioeconomic mobility and lifestyle changes are leading to higher levels of physical inactivity and obesity, both of which are related to headache. Life expectancy is rising in some resource-restricted countries; this increases prevalence of secondary headache attributed to neurovascular causes. Many low-resource countries are still burdened with tropical infectious causes of secondary headache. Health care facilities are primarily designed to respond to infectious epidemic and not to chronic burden such as headache. Many low-resource-restricted settings are plagued by poor and corrupt governance, ill-equipped regimes with malfunctioning health policies, war, and poverty. Many low-resource settings do not have access to generic headache medications such as triptans. Headache training and expertise is low. Healthy lifestyle changes emphasizing on improving regular exercise can be inexpensive method to reducing primary headache burden and its comorbidities (e.g. obesity). Addressing the increasing burden of headache disorders in resource-limited settings is important to avert accrued disability which in turn lowers productivity and socioeconomic performance in a young booming population.
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Affiliation(s)
- Yohannes W Woldeamanuel
- Stanford Headache and Facial Pain Program, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Advanced Clinic and Research Center, Addis Abäba, Ethiopia.
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110
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DeHaan H, McCambridge A, Armstrong B, Cruse C, Solanki D, Trinidad JC, Arkov AL, Gao M. An in vivo proteomic analysis of the Me31B interactome in Drosophila germ granules. FEBS Lett 2017; 591:3536-3547. [PMID: 28945271 DOI: 10.1002/1873-3468.12854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/07/2017] [Accepted: 09/15/2017] [Indexed: 12/11/2022]
Abstract
Drosophila Me31B is a conserved protein of germ granules, ribonucleoprotein complexes essential for germ cell development. Me31B post-transcriptionally regulates mRNAs by interacting with other germ granule proteins. However, a Me31B interactome is lacking. Here, we use an in vivo proteomics approach to show that the Me31B interactome contains polypeptides from four functional groups: RNA regulatory proteins, glycolytic enzymes, cytoskeleton/motor proteins, and germ plasm components. We further show that Me31B likely colocalizes with the germ plasm components Tudor (Tud), Vasa, and Aubergine in the nuage and germ plasm and provide evidence that Me31B may directly bind to Tud in a symmetrically dimethylated arginine-dependent manner. Our study supports the role of Me31B in RNA regulation and suggests its novel roles in germ granule assembly and function.
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Affiliation(s)
- Hunter DeHaan
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | | | - Carlie Cruse
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Dhruv Solanki
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | - Alexey L Arkov
- Department of Biological Sciences, Murray State University, Murray, KY, USA
| | - Ming Gao
- Biology Department, Indiana University Northwest, Gary, IN, USA
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111
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Translational Control in the Latency of Apicomplexan Parasites. Trends Parasitol 2017; 33:947-960. [PMID: 28942109 DOI: 10.1016/j.pt.2017.08.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 01/07/2023]
Abstract
Apicomplexan parasites Toxoplasma gondii and Plasmodium spp. use latent stages to persist in the host, facilitate transmission, and thwart treatment of infected patients. Therefore, it is important to understand the processes driving parasite differentiation to and from quiescent stages. Here, we discuss how a family of protein kinases that phosphorylate the eukaryotic initiation factor-2 (eIF2) function in translational control and drive differentiation. This translational control culminates in reprogramming of the transcriptome to facilitate parasite transition towards latency. We also discuss how eIF2 phosphorylation contributes to the maintenance of latency and provides a crucial role in the timing of reactivation of latent parasites towards proliferative stages.
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112
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Aguero T, Jin Z, Chorghade S, Kalsotra A, King ML, Yang J. Maternal Dead-end 1 promotes translation of nanos1 by binding the eIF3 complex. Development 2017; 144:3755-3765. [PMID: 28870987 DOI: 10.1242/dev.152611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/22/2017] [Indexed: 12/30/2022]
Abstract
In the developing embryo, primordial germ cells (PGCs) represent the exclusive progenitors of the gametes, and their loss results in adult infertility. During early development, PGCs are exposed to numerous signals that specify somatic cell fates. To prevent somatic differentiation, PGCs must transiently silence their genome, an early developmental process that requires Nanos activity. However, it is unclear how Nanos translation is regulated in developing embryos. We report here that translation of nanos1 after fertilization requires Dead-end 1 (Dnd1), a vertebrate-specific germline RNA-binding protein. We provide evidence that Dnd1 protein, expression of which is low in oocytes, but increases dramatically after fertilization, directly interacts with, and relieves the inhibitory function of eukaryotic initiation factor 3f, a repressive component in the 43S preinitiation complex. This work uncovers a novel translational regulatory mechanism that is fundamentally important for germline development.
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Affiliation(s)
- Tristan Aguero
- Department of Cell Biology, University of Miami, Miami, FL 33136, USA
| | - Zhigang Jin
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
| | - Sandip Chorghade
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mary Lou King
- Department of Cell Biology, University of Miami, Miami, FL 33136, USA
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
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113
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Arur S. Signaling-Mediated Regulation of Meiotic Prophase I and Transition During Oogenesis. Results Probl Cell Differ 2017; 59:101-123. [PMID: 28247047 DOI: 10.1007/978-3-319-44820-6_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Generation of healthy oocytes requires coordinated regulation of multiple cellular events and signaling pathways. Oocytes undergo a unique developmental growth and differentiation pattern interspersed with long periods of arrest. Oocytes from almost all species arrest in prophase I of oogenesis that allows for long period of growth and differentiation essential for normal oocyte development. Depending on species, oocytes that transit from prophase I to meiosis I also arrest at meiosis I for fairly long periods of time and then undergo a second arrest at meiosis II that is completed upon fertilization. While there are species-specific differences in C. elegans, D. melanogaster, and mammalian oocytes in stages of prophase I, meiosis I, or meiosis II arrest, in all cases cell signaling pathways coordinate the developmental events controlling oocyte growth and differentiation to regulate these crucial phases of transition. In particular, the ERK MAP kinase signaling pathway, cyclic AMP second messengers, and the cell cycle regulators CDK1/cyclin B are key signaling pathways that seem evolutionarily conserved in their control of oocyte growth and meiotic maturation across species. Here, I identify the common themes and differences in the regulation of key meiotic events during oocyte growth and maturation.
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Affiliation(s)
- Swathi Arur
- Department of Genetics, UT M.D. Anderson Cancer Center, Houston, TX, USA.
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114
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Cell Fate Maintenance and Reprogramming During the Oocyte-to-Embryo Transition. Results Probl Cell Differ 2017; 59:269-286. [PMID: 28247053 DOI: 10.1007/978-3-319-44820-6_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
This chapter reviews our current understanding of the mechanisms that regulate reprogramming during the oocyte-to-embryo transition (OET). There are two major events reshaping the transcriptome during OET. One is the clearance of maternal transcripts in the early embryo, extensively reviewed by others. The other event, which is the focus of this chapter, is the embryonic (or zygotic) genome activation (EGA). The mechanisms controlling EGA can be broadly divided into transcriptional and posttranscriptional. The former includes the regulation of the basal transcription machinery, the regulation by specific transcription factors and chromatin modifications. The latter is performed mostly via specific RNA-binding proteins (RBPs). Different animal models have been used to decipher the regulation of EGA. These models are often biased for the specific type of regulation, which is why we discuss the models ranging from invertebrates to mammals. Whether these biases stem from incomplete understanding of EGA in these models, or reflect evolutionarily distinct solutions to EGA regulation, is a key unresolved problem in developmental biology. As the mechanisms controlling developmental reprogramming can, and in some cases have been shown to, function in differentiated cells subjected to induced reprogramming, our understanding of EGA regulation may have implications for the efficiency of induced reprogramming and, thus, for regenerative medicine.
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115
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Lev I, Seroussi U, Gingold H, Bril R, Anava S, Rechavi O. MET-2-Dependent H3K9 Methylation Suppresses Transgenerational Small RNA Inheritance. Curr Biol 2017; 27:1138-1147. [DOI: 10.1016/j.cub.2017.03.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 02/13/2017] [Accepted: 03/06/2017] [Indexed: 10/19/2022]
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116
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Toombs JA, Sytnikova YA, Chirn GW, Ang I, Lau NC, Blower MD. Xenopus Piwi proteins interact with a broad proportion of the oocyte transcriptome. RNA (NEW YORK, N.Y.) 2017; 23:504-520. [PMID: 28031481 PMCID: PMC5340914 DOI: 10.1261/rna.058859.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
Piwi proteins utilize small RNAs (piRNAs) to recognize target transcripts such as transposable elements (TE). However, extensive piRNA sequence diversity also suggests that Piwi/piRNA complexes interact with many transcripts beyond TEs. To determine Piwi target RNAs, we used ribonucleoprotein-immunoprecipitation (RIP) and cross-linking and immunoprecipitation (CLIP) to identify thousands of transcripts associated with the Piwi proteins XIWI and XILI (Piwi-protein-associated transcripts, PATs) from early stage oocytes of X. laevis and X. tropicalis Most PATs associate with both XIWI and XILI and include transcripts of developmentally important proteins in oogenesis and embryogenesis. Only a minor fraction of PATs in both frog species displayed near perfect matches to piRNAs. Since predicting imperfect pairing between all piRNAs and target RNAs remains intractable, we instead determined that PAT read counts correlate well with the lengths and expression levels of transcripts, features that have also been observed for oocyte mRNAs associated with Drosophila Piwi proteins. We used an in vitro assay with exogenous RNA to confirm that XIWI associates with RNAs in a length- and concentration-dependent manner. In this assay, noncoding transcripts with many perfectly matched antisense piRNAs were unstable, whereas coding transcripts with matching piRNAs were stable, consistent with emerging evidence that Piwi proteins both promote the turnover of TEs and other RNAs, and may also regulate mRNA localization and translation. Our study suggests that Piwi proteins play multiple roles in germ cells and establishes a tractable vertebrate system to study the role of Piwi proteins in transcript regulation.
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Affiliation(s)
- James A Toombs
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yuliya A Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Gung-Wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Ignatius Ang
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Nelson C Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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117
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Germ Granules Prevent Accumulation of Somatic Transcripts in the Adult Caenorhabditis elegans Germline. Genetics 2017; 206:163-178. [PMID: 28258184 DOI: 10.1534/genetics.116.198549] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/01/2017] [Indexed: 11/18/2022] Open
Abstract
The germ cells of multicellular organisms protect their developmental potential through specialized mechanisms. A shared feature of germ cells from worms to humans is the presence of nonmembrane-bound, ribonucleoprotein organelles called germ granules. Depletion of germ granules in Caenorhabditis elegans (i.e., P granules) leads to sterility and, in some germlines, expression of the neuronal transgene unc-119::gfp and the muscle myosin MYO-3 Thus, P granules are hypothesized to maintain germ cell totipotency by preventing somatic development, although the mechanism by which P granules carry out this function is unknown. In this study, we performed transcriptome and single molecule RNA-FISH analyses of dissected P granule-depleted gonads at different developmental stages. Our results demonstrate that P granules are necessary for adult germ cells to downregulate spermatogenesis RNAs and to prevent the accumulation of numerous soma-specific RNAs. P granule-depleted gonads that express the unc-119::gfp transgene also express many other genes involved in neuronal development and concomitantly lose expression of germ cell fate markers. Finally, we show that removal of either of two critical P-granule components, PGL-1 or GLH-1, is sufficient to cause germ cells to express UNC-119::GFP and MYO-3 and to display RNA accumulation defects similar to those observed after depletion of P granules. Our data identify P granules as critical modulators of the germline transcriptome and guardians of germ cell fate.
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118
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Feng L, Shi Z, Chen X. Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis. PLoS Genet 2017; 13:e1006571. [PMID: 28196077 PMCID: PMC5308785 DOI: 10.1371/journal.pgen.1006571] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/04/2017] [Indexed: 12/31/2022] Open
Abstract
Stem cells reside in a particular microenvironment known as a niche. The interaction between extrinsic cues originating from the niche and intrinsic factors in stem cells determines their identity and activity. Maintenance of stem cell identity and stem cell self-renewal are known to be controlled by chromatin factors. Herein, we use the Drosophila adult testis which has two adult stem cell lineages, the germline stem cell (GSC) lineage and the cyst stem cell (CySC) lineage, to study how chromatin factors regulate stem cell differentiation. We find that the chromatin factor Enhancer of Polycomb [E(Pc)] acts in the CySC lineage to negatively control transcription of genes associated with multiple signaling pathways, including JAK-STAT and EGF, to promote cellular differentiation in the CySC lineage. E(Pc) also has a non-cell-autonomous role in regulating GSC lineage differentiation. When E(Pc) is specifically inactivated in the CySC lineage, defects occur in both germ cell differentiation and maintenance of germline identity. Furthermore, compromising Tip60 histone acetyltransferase activity in the CySC lineage recapitulates loss-of-function phenotypes of E(Pc), suggesting that Tip60 and E(Pc) act together, consistent with published biochemical data. In summary, our results demonstrate that E(Pc) plays a central role in coordinating differentiation between the two adult stem cell lineages in Drosophila testes. Tissue maintenance and repair rely on adult stem cells, which can divide to generate new stem cells as well as cells committed for becoming specific cell types. Stem cell activity needs to be tightly controlled because insufficient or unlimited stem cell division may lead to tissue degeneration or tumorigenesis. This control depends not only on stem cells themselves, but also on the microenvironment where stem cells reside. The chromatin structure of stem cells is crucial to determine their activities. The signaling pathways connecting stem cells with their microenvironment is also important. Here we ask how chromatin factors interact with signaling pathways in determining stem cell activity. We use Drosophila adult testis as a model system, in which two types of stem cells co-exist and interact: germline stem cells and somatic stem cells. We find that a chromatin regulator called Enhancer of Polycomb [E(Pc)] acts in somatic cells to promote germ cell differentiation and maintain germ cell fate. This regulation is mediated by several signaling pathways, such as EGF and JAK-STAT pathways. E(Pc) also works with another chromatin regulator, the histone acetyltransferase Tip60, in somatic cells. Insufficient activity of the E(Pc) homolog in human leads to cancers. Our studies of E(Pc) may help understanding its roles as a tumor suppressor.
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Affiliation(s)
- Lijuan Feng
- Department of Biology, The Johns Hopkins University, Baltimore, MD, United States of America
| | - Zhen Shi
- Department of Biology, The Johns Hopkins University, Baltimore, MD, United States of America
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD, United States of America
- * E-mail:
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119
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Andralojc KM, Campbell AC, Kelly AL, Terrey M, Tanner PC, Gans IM, Senter-Zapata MJ, Khokhar ES, Updike DL. ELLI-1, a novel germline protein, modulates RNAi activity and P-granule accumulation in Caenorhabditis elegans. PLoS Genet 2017; 13:e1006611. [PMID: 28182654 PMCID: PMC5325599 DOI: 10.1371/journal.pgen.1006611] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 02/24/2017] [Accepted: 01/31/2017] [Indexed: 12/13/2022] Open
Abstract
Germ cells contain non-membrane bound cytoplasmic organelles that help maintain germline integrity. In C. elegans they are called P granules; without them, the germline undergoes partial masculinization and aberrant differentiation. One key P-granule component is the Argonaute CSR-1, a small-RNA binding protein that antagonizes accumulation of sperm-specific transcripts in developing oocytes and fine-tunes expression of proteins critical to early embryogenesis. Loss of CSR-1 complex components results in a very specific, enlarged P-granule phenotype. In a forward screen to identify mutants with abnormal P granules, ten alleles were recovered with a csr-1 P-granule phenotype, eight of which contain mutations in known components of the CSR-1 complex (csr-1, ego-1, ekl-1, and drh-3). The remaining two alleles are in a novel gene now called elli-1 (enlarged germline granules). ELLI-1 is first expressed in primordial germ cells during mid-embryogenesis, and continues to be expressed in the adult germline. While ELLI-1 forms cytoplasmic aggregates, they occasionally dock, but do not co-localize with P granules. Instead, the majority of ELLI-1 aggregates accumulate in the shared germline cytoplasm. In elli-1 mutants, several genes that promote RNAi and P-granule accumulation are upregulated, and embryonic lethality, sterility, and RNAi resistance in a hypomorphic drh-3 allele is enhanced, suggesting that ELLI-1 functions with CSR-1 to modulate RNAi activity, P-granule accumulation, and post-transcriptional expression in the germline.
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Affiliation(s)
- Karolina M. Andralojc
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Anne C. Campbell
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Ashley L. Kelly
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Markus Terrey
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Paige C. Tanner
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Ian M. Gans
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | | | - Eraj S. Khokhar
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Dustin L. Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
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120
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Zheng J, Gao M, Huynh N, Tindell SJ, Vo HDL, McDonald WH, Arkov AL. In vivo mapping of a dynamic ribonucleoprotein granule interactome in early Drosophila embryos. FEBS Open Bio 2016; 6:1248-1256. [PMID: 28203524 PMCID: PMC5302063 DOI: 10.1002/2211-5463.12144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/21/2016] [Accepted: 10/03/2016] [Indexed: 12/22/2022] Open
Abstract
Macromolecular complexes and organelles play crucial roles within cells, but their native architectures are often unknown. Here, we use an evolutionarily conserved germline organelle, the germ granule, as a paradigm. In Drosophila embryos, we map one of its interactomes using a novel in vivo crosslinking approach that employs two interacting granule proteins and determines their common neighbor molecules. We identified an in vivo granule assembly of Tudor, Aubergine, motor and metabolic proteins, and RNA helicases, and provide evidence for direct interactions within this assembly using purified components. Our study indicates that germ granules contain efficient biochemical reactors involved in post‐transcriptional gene regulation.
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Affiliation(s)
- Jimiao Zheng
- Department of Biological Sciences Murray State University USA
| | - Ming Gao
- Biology Department Indiana University Northwest Gary IN USA
| | - Nhan Huynh
- Department of Biological Sciences Murray State University USA; Present address: University of Alberta Edmonton AB Canada
| | | | - Hieu D L Vo
- Department of Biological Sciences Murray State University USA
| | - W Hayes McDonald
- Department of Biochemistry Mass Spectrometry Research Center Vanderbilt University School of Medicine Nashville TN USA
| | - Alexey L Arkov
- Department of Biological Sciences Murray State University USA
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121
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Abstract
The germ track is the cellular path by which genes are transmitted to future generations whereas somatic cells die with their body and do not leave direct descendants. Transposable elements (TEs) evolve to be silent in somatic cells but active in the germ track. Thus, the performance of most bodily functions by a sequestered soma reduces organismal costs of TEs. Flexible forms of gene regulation are permissible in the soma because of the self-imposed silence of TEs, but strict licensing of transcription and translation is maintained in the germ track to control proliferation of TEs. Delayed zygotic genome activation (ZGA) and maternally inherited germ granules are adaptations that enhance germ-track security. Mammalian embryos exhibit very early ZGA associated with extensive mobilization of retroelements. This window of vulnerability to retrotransposition in early embryos is an indirect consequence of evolutionary conflicts within the mammalian genome over postzygotic maternal provisioning.
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Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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122
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Ellis RE. "The persistence of memory"-Hermaphroditism in nematodes. Mol Reprod Dev 2016; 84:144-157. [PMID: 27291983 DOI: 10.1002/mrd.22668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/01/2016] [Indexed: 12/13/2022]
Abstract
Self-fertility has evolved many times in nematodes. This transition often produces an androdioecious species, with XX hermaphrodites and XO males. Although these hermaphrodites resemble females in most respects, early germ cells differentiate as sperm, and late ones as oocytes. The sperm then receive an activation signal, populate the spermathecae, and are stored for later use in self-fertilization. These traits are controlled by complex modifications to the sex-determination and sperm activation pathways, which have arisen independently during the evolution of each hermaphroditic species. This transformation in reproductive strategy then promotes other major changes in the development, evolution, and population structure of these animals. Mol. Reprod. Dev. 84: 144-157, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ronald E Ellis
- Department of Molecular Biology, Rowan University SOM, Stratford, New Jersey
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123
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Abstract
The Symposium on the Comparative Biology of Tissue Repair, Regeneration and Aging, held 26 June to 28 June 2015 at the MDI Biological Laboratory in Salisbury Cove, Maine, brought together a diverse group of biologists with a common interest in understanding why regenerative capacity varies among animal species, why it is progressively lost in senescence, and how answers obtained from studies that address those questions might be applied in regenerative medicine.
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124
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Abstract
DNA does not make phenotypes on its own. In this volume entitled "Genes and Phenotypic Evolution," the present review draws the attention on the process of phenotype construction-including development of multicellular organisms-and the multiple interactions and feedbacks between DNA, organism, and environment at various levels and timescales in the evolutionary process. First, during the construction of an individual's phenotype, DNA is recruited as a template for building blocks within the cellular context and may in addition be involved in dynamical feedback loops that depend on the environmental and organismal context. Second, in the production of phenotypic variation among individuals, stochastic, environmental, genetic, and parental sources of variation act jointly. While in controlled laboratory settings, various genetic and environmental factors can be tested one at a time or in various combinations, they cannot be separated in natural populations because the environment is not controlled and the genotype can rarely be replicated. Third, along generations, genotype and environment each have specific properties concerning the origin of their variation, the hereditary transmission of this variation, and the evolutionary feedbacks. Natural selection acts as a feedback from phenotype and environment to genotype. This review integrates recent results and concrete examples that illustrate these three points. Although some themes are shared with recent calls and claims to a new conceptual framework in evolutionary biology, the viewpoint presented here only means to add flesh to the standard evolutionary synthesis.
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Affiliation(s)
- M-A Félix
- Institut de Biologie Ecole Normale Supérieure, CNRS, Paris, France.
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Langenbacher AD, De Tomaso AW. Temporally and spatially dynamic germ cell niches in Botryllus schlosseri revealed by expression of a TGF-beta family ligand and vasa. EvoDevo 2016; 7:9. [PMID: 27073614 PMCID: PMC4828856 DOI: 10.1186/s13227-016-0047-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/30/2016] [Indexed: 02/04/2023] Open
Abstract
Background Germ cells are specified during early development and are responsible for generating gametes in the adult. After germ cells are specified, they typically migrate to a particular niche in the organism where they reside for the remainder of its lifetime. For some model organisms, the specification and migration of germ cells have been extensively studied, but how these events occur in animals that reproduce both sexually and asexually is not well understood. Results We have identified a novel TGF-β family member in Botryllus schlosseri, tgfβ-f, and found that it is expressed by follicle cell progenitors and the differentiated follicle and support cells surrounding the maturing gametes. Using the expression of tgfβ-f and the germ cell marker vasa, we have found that nearly all germ cells in Botryllus are associated with tgfβ-f-expressing follicle progenitors in clusters consisting solely of those two cell types. These clusters were mostly small, consisting of ten or fewer cells, and generally contained between a 2:1 and 1:1 ratio of follicle progenitors to germ cells. Clusters of germ and follicle progenitor cells were primarily localized to niches in the primary and secondary buds, but could also be found in other locations including the vasculature. We analyzed the location of germ cell clusters throughout the asexual life cycle of Botryllus and found that at the stage when germ cells are first detected in the secondary bud niche, a dramatic change in the size and location of germ/follicle cell clusters also occurred. Conclusions Our findings suggest that germ/follicle cell clusters have predictable migratory patterns during the weekly asexual developmental cycle in Botryllus. An increased number of small clusters and the presence of clusters in the vasculature coinciding with the appearance of clusters in the secondary bud suggest that fragmentation of clusters and the migration of smaller clusters through the vasculature may be an important aspect of Botryllus reproductive biology, ensuring the transmission of the germline to subsequent asexual generations. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0047-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam D Langenbacher
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9610 USA ; Department of MCD Biology, UCLA, Los Angeles, CA 90095 USA
| | - Anthony W De Tomaso
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9610 USA
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Abstract
The evolution of multicellular animals has been attributed to many kinds of selective advantage; here I suggest that the evolution of somatic cells to feed and protect the germline was central to the appearance of animals. This would have been driven by selection for extreme anisogamy--the evolution of sperm and egg. Evidence is adduced from the germline stem cells of simple animals (defining germline as any cell that normally produces the next generation via the sexual process) and from the control circuitry ubiquitous in animal germlines. With the soma and its elaboration came animal development, as we understand it.
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Affiliation(s)
- Hugh R Woodland
- School of Life Sciences, University of Warwick, Coventry, United Kingdom.
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127
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Abstract
Primordial germ cells are usually made early in the development of an organism. These are the mother of all stem cells that are necessary for propagation of the species, yet use highly diverse mechanisms between organisms. How they are specified, and when and where they form, are central to developmental biology. Using diverse organisms to study this development is illuminating for understanding the mechanics these cells use in this essential function and for identifying the breadth of evolutionary changes that have occurred between species. This essay emphasizes how echinoderms may contribute to the patchwork quilt of our understanding of germ line formation during embryogenesis.
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Affiliation(s)
- Gary M Wessel
- Department of Molecular and Cellular Biology, Brown University, Providence, Rhode Island, USA.
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A Forward Genetic Screen for Suppressors of Somatic P Granules in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2015; 5:2209-15. [PMID: 26100681 PMCID: PMC4593002 DOI: 10.1534/g3.115.019257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In Caenorhabditis elegans, germline expression programs are actively repressed in somatic tissue by components of the synMuv (synthetic multi-vulva) B chromatin remodeling complex, which include homologs of tumor suppressors Retinoblastoma (Rb/LIN-35) and Malignant Brain Tumor (MBT/LIN-61). However, the full scope of pathways that suppress germline expression in the soma is unknown. To address this, we performed a mutagenesis and screened for somatic expression of GFP-tagged PGL-1, a core P-granule nucleating protein. Eight alleles were isolated from 4000 haploid genomes. Five of these alleles exhibit a synMuv phenotype, whereas the remaining three were identified as hypomorphic alleles of known synMuv B genes, lin-13 and dpl-1. These findings suggest that most suppressors of germline programs in the soma of C. elegans are either required for viability or function through synMuv B chromatin regulation.
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