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Chen Q, Malki S, Xu X, Bennett B, Lackford BL, Kirsanov O, Geyer CB, Hu G. Cnot3 is required for male germ cell development and spermatogonial stem cell maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562256. [PMID: 37873304 PMCID: PMC10592795 DOI: 10.1101/2023.10.13.562256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The foundation of spermatogenesis and lifelong fertility is provided by spermatogonial stem cells (SSCs). SSCs divide asymmetrically to either replenish their numbers (self-renewal) or produce undifferentiated progenitors that proliferate before committing to differentiation. However, regulatory mechanisms governing SSC maintenance are poorly understood. Here, we show that the CCR4-NOT mRNA deadenylase complex subunit CNOT3 plays a critical role in maintaining spermatogonial populations in mice. Cnot3 is highly expressed in undifferentiated spermatogonia, and its deletion in spermatogonia resulted in germ cell loss and infertility. Single cell analyses revealed that Cnot3 deletion led to the de-repression of transcripts encoding factors involved in spermatogonial differentiation, including those in the glutathione redox pathway that are critical for SSC maintenance. Together, our study reveals that CNOT3 - likely via the CCR4-NOT complex - actively degrades transcripts encoding differentiation factors to sustain the spermatogonial pool and ensure the progression of spermatogenesis, highlighting the importance of CCR4-NOT-mediated post-transcriptional gene regulation during male germ cell development.
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Affiliation(s)
- Qing Chen
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
- Present address: Clinical Microbiome Unit (CMU), Laboratory of Host Immunity and Microbiome (LHIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Safia Malki
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Xiaojiang Xu
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
- Present address: Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Brian Bennett
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Brad L. Lackford
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Oleksandr Kirsanov
- Department of Anatomy & Cell Biology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Christopher B. Geyer
- Department of Anatomy & Cell Biology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute East Carolina University, Greenville, NC, USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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Jueterbock A, Duarte B, Coyer J, Olsen JL, Kopp MEL, Smolina I, Arnaud-Haond S, Hu ZM, Hoarau G. Adaptation of Temperate Seagrass to Arctic Light Relies on Seasonal Acclimatization of Carbon Capture and Metabolism. FRONTIERS IN PLANT SCIENCE 2021; 12:745855. [PMID: 34925400 PMCID: PMC8675887 DOI: 10.3389/fpls.2021.745855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/29/2021] [Indexed: 06/14/2023]
Abstract
Due to rising global surface temperatures, Arctic habitats are becoming thermally suitable for temperate species. Whether a temperate species can immigrate into an ice-free Arctic depends on its ability to tolerate extreme seasonal fluctuations in daylength. Thus, understanding adaptations to polar light conditions can improve the realism of models predicting poleward range expansions in response to climate change. Plant adaptations to polar light have rarely been studied and remain unknown in seagrasses. If these ecosystem engineers can migrate polewards, seagrasses will enrich biodiversity, and carbon capture potential in shallow coastal regions of the Arctic. Eelgrass (Zostera marina) is the most widely distributed seagrass in the northern hemisphere. As the only seagrass species growing as far north as 70°N, it is the most likely candidate to first immigrate into an ice-free Arctic. Here, we describe seasonal (and diurnal) changes in photosynthetic characteristics, and in genome-wide gene expression patterns under strong annual fluctuations of daylength. We compared PAM measurements and RNA-seq data between two populations at the longest and shortest day of the year: (1) a Mediterranean population exposed to moderate annual fluctuations of 10-14 h daylength and (2) an Arctic population exposed to high annual fluctuations of 0-24 h daylength. Most of the gene expression specificities of the Arctic population were found in functions of the organelles (chloroplast and mitochondrion). In winter, Arctic eelgrass conserves energy by repressing respiration and reducing photosynthetic energy fluxes. Although light-reactions, and genes involved in carbon capture and carbon storage were upregulated in summer, enzymes involved in CO2 fixation and chlorophyll-synthesis were upregulated in winter, suggesting that winter metabolism relies not only on stored energy resources but also on active use of dim light conditions. Eelgrass is unable to use excessive amounts of light during summer and demonstrates a significant reduction in photosynthetic performance under long daylengths, possibly to prevent photoinhibition constrains. Our study identified key mechanisms that allow eelgrass to survive under Arctic light conditions and paves the way for experimental research to predict whether and up to which latitude eelgrass can potentially migrate polewards in response to climate change.
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Affiliation(s)
- Alexander Jueterbock
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Bernardo Duarte
- Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon, Lisbon, Portugal
- Departamento de Biologia Vegetal da Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - James Coyer
- Shoals Marine Laboratory, University of New Hampshire, Durham, NH, United States
| | - Jeanine L. Olsen
- Ecological Genetics-Genomics Group, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Irina Smolina
- Marine Molecular Ecology Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Sophie Arnaud-Haond
- UMR MARBEC Marine Biodiversity Exploitation and Conservation, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Zi-Min Hu
- Ocean School, Yantai University, Yantai, China
| | - Galice Hoarau
- Marine Molecular Ecology Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Schörnig M, Ju X, Fast L, Ebert S, Weigert A, Kanton S, Schaffer T, Nadif Kasri N, Treutlein B, Peter BM, Hevers W, Taverna E. Comparison of induced neurons reveals slower structural and functional maturation in humans than in apes. eLife 2021; 10:59323. [PMID: 33470930 PMCID: PMC7870144 DOI: 10.7554/elife.59323] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
We generated induced excitatory neurons (iNeurons, iNs) from chimpanzee, bonobo, and human stem cells by expressing the transcription factor neurogenin-2 (NGN2). Single-cell RNA sequencing showed that genes involved in dendrite and synapse development are expressed earlier during iNs maturation in the chimpanzee and bonobo than the human cells. In accordance, during the first 2 weeks of differentiation, chimpanzee and bonobo iNs showed repetitive action potentials and more spontaneous excitatory activity than human iNs, and extended neurites of higher total length. However, the axons of human iNs were slightly longer at 5 weeks of differentiation. The timing of the establishment of neuronal polarity did not differ between the species. Chimpanzee, bonobo, and human neurites eventually reached the same level of structural complexity. Thus, human iNs develop slower than chimpanzee and bonobo iNs, and this difference in timing likely depends on functions downstream of NGN2.
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Affiliation(s)
- Maria Schörnig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Xiangchun Ju
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luise Fast
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sebastian Ebert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne Weigert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sabina Kanton
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Theresa Schaffer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nael Nadif Kasri
- Department of Human Genetics and Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Radboudumc, Nijmegen, Netherlands
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Wulf Hevers
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Taverna
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Sun D, Wang J, Han Y, Dong X, Ge J, Zheng R, Shi X, Wang B, Li Z, Ren P, Sun L, Yan Y, Zhang P, Zhang F, Li T, Wang C. TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. Nucleic Acids Res 2021; 49:D1420-D1430. [PMID: 33179754 PMCID: PMC7778907 DOI: 10.1093/nar/gkaa1020] [Citation(s) in RCA: 522] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/04/2020] [Accepted: 10/16/2020] [Indexed: 02/05/2023] Open
Abstract
Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade shows remarkable efficacy in a variety of cancer types. However, only a minority of patients respond to treatment due to the stochastic heterogeneity of tumor microenvironment (TME). Recent advances in single-cell RNA-seq technologies enabled comprehensive characterization of the immune system heterogeneity in tumors but posed computational challenges on integrating and utilizing the massive published datasets to inform immunotherapy. Here, we present Tumor Immune Single Cell Hub (TISCH, http://tisch.comp-genomics.org), a large-scale curated database that integrates single-cell transcriptomic profiles of nearly 2 million cells from 76 high-quality tumor datasets across 27 cancer types. All the data were uniformly processed with a standardized workflow, including quality control, batch effect removal, clustering, cell-type annotation, malignant cell classification, differential expression analysis and functional enrichment analysis. TISCH provides interactive gene expression visualization across multiple datasets at the single-cell level or cluster level, allowing systematic comparison between different cell-types, patients, tissue origins, treatment and response groups, and even different cancer-types. In summary, TISCH provides a user-friendly interface for systematically visualizing, searching and downloading gene expression atlas in the TME from multiple cancer types, enabling fast, flexible and comprehensive exploration of the TME.
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Affiliation(s)
- Dongqing Sun
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Jin Wang
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Ya Han
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Xin Dong
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Jun Ge
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Rongbin Zheng
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Xiaoying Shi
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Binbin Wang
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Ziyi Li
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Pengfei Ren
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
| | - Liangdong Sun
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Yilv Yan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Fan Zhang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science, Tongji University, Shanghai 200433, China
| | - Taiwen Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chenfei Wang
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200060, China
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Transcriptional activity and strain-specific history of mouse pseudogenes. Nat Commun 2020; 11:3695. [PMID: 32728065 PMCID: PMC7392758 DOI: 10.1038/s41467-020-17157-w] [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: 08/02/2018] [Accepted: 06/08/2020] [Indexed: 01/07/2023] Open
Abstract
Pseudogenes are ideal markers of genome remodelling. In turn, the mouse is an ideal platform for studying them, particularly with the recent availability of strain-sequencing and transcriptional data. Here, combining both manual curation and automatic pipelines, we present a genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains (available via the mouse.pseudogene.org resource). We also annotate 165 unitary pseudogenes in mouse, and 303, in human. The overall pseudogene repertoire in mouse is similar to that in human in terms of size, biotype distribution, and family composition (e.g. with GAPDH and ribosomal proteins being the largest families). Notable differences arise in the pseudogene age distribution, with multiple retro-transpositional bursts in mouse evolutionary history and only one in human. Furthermore, in each strain about a fifth of all pseudogenes are unique, reflecting strain-specific evolution. Finally, we find that ~15% of the mouse pseudogenes are transcribed, and that highly transcribed parent genes tend to give rise to many processed pseudogenes.
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Bushel PR, Paules RS, Auerbach SS. A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. Front Genet 2018; 9:485. [PMID: 30420870 PMCID: PMC6217592 DOI: 10.3389/fgene.2018.00485] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/28/2018] [Indexed: 11/13/2022] Open
Abstract
The TempO-SeqTM platform allows for targeted transcriptomic analysis and is currently used by many groups to perform high-throughput gene expression analysis. Herein we performed a comparison of gene expression characteristics measured using 45 purified RNA samples from the livers of rats exposed to chemicals that fall into one of five modes of action (MOAs). These samples have been previously evaluated using AffymetrixTM rat genome 230 2.0 microarrays and Illumina® whole transcriptome RNA-Seq. Comparison of these data with TempO-Seq analysis using the rat S1500+ beta gene set identified clear differences in the platforms related to signal to noise, root mean squared error, and/or sources of variability. Microarray and TempO-Seq captured the most variability in terms of MOA and chemical treatment whereas RNA-Seq had higher noise and larger differences between samples within a MOA. However, analysis of the data by hierarchical clustering, gene subnetwork connectivity and biological process representation of MOA-varying genes revealed that the samples clearly grouped by treatment as opposed to gene expression platform. Overall these findings demonstrate that the results from the TempO-Seq platform are consistent with findings on other more established approaches for measuring the genome-wide transcriptome.
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Affiliation(s)
- Pierre R Bushel
- Biostatistics and Computational Biology Branch, NIEHS, Research Triangle Park, Durham, NC, United States
| | - Richard S Paules
- Biomolecular Screening Branch, National Toxicology Program, NIEHS, Research Triangle Park, Durham, NC, United States
| | - Scott S Auerbach
- Biomolecular Screening Branch, National Toxicology Program, NIEHS, Research Triangle Park, Durham, NC, United States
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