1
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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. ENVIRONMENTAL EPIGENETICS 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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2
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Ayers KL, Eggers S, Rollo BN, Smith KR, Davidson NM, Siddall NA, Zhao L, Bowles J, Weiss K, Zanni G, Burglen L, Ben-Shachar S, Rosensaft J, Raas-Rothschild A, Jørgensen A, Schittenhelm RB, Huang C, Robevska G, van den Bergen J, Casagranda F, Cyza J, Pachernegg S, Wright DK, Bahlo M, Oshlack A, O'Brien TJ, Kwan P, Koopman P, Hime GR, Girard N, Hoffmann C, Shilon Y, Zung A, Bertini E, Milh M, Ben Rhouma B, Belguith N, Bashamboo A, McElreavey K, Banne E, Weintrob N, BenZeev B, Sinclair AH. Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects. Nat Commun 2023; 14:3403. [PMID: 37296101 PMCID: PMC10256788 DOI: 10.1038/s41467-023-39040-0] [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: 04/03/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Squamous cell carcinoma antigen recognized by T cells 3 (SART3) is an RNA-binding protein with numerous biological functions including recycling small nuclear RNAs to the spliceosome. Here, we identify recessive variants in SART3 in nine individuals presenting with intellectual disability, global developmental delay and a subset of brain anomalies, together with gonadal dysgenesis in 46,XY individuals. Knockdown of the Drosophila orthologue of SART3 reveals a conserved role in testicular and neuronal development. Human induced pluripotent stem cells carrying patient variants in SART3 show disruption to multiple signalling pathways, upregulation of spliceosome components and demonstrate aberrant gonadal and neuronal differentiation in vitro. Collectively, these findings suggest that bi-allelic SART3 variants underlie a spliceosomopathy which we tentatively propose be termed INDYGON syndrome (Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY GONadal dysgenesis). Our findings will enable additional diagnoses and improved outcomes for individuals born with this condition.
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Affiliation(s)
- Katie L Ayers
- The Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Stefanie Eggers
- The Victorian Clinical Genetics Services, Melbourne, Australia
| | - Ben N Rollo
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Katherine R Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Nadia M Davidson
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- School of BioSciences, Faculty of Science, University of Melbourne, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Nicole A Siddall
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Liang Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Institute of Technology, Haifa, Israel
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Et Laboratoire de Neurogénétique Moléculaire, Département de Génétique et Embryologie Médicale, APHP. Sorbonne Université, Hôpital Trousseau, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Shay Ben-Shachar
- Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jenny Rosensaft
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Annick Raas-Rothschild
- Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anne Jørgensen
- Department of Growth and Reproduction, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | | | | | - Franca Casagranda
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Justyna Cyza
- The Murdoch Children's Research Institute, Melbourne, Australia
| | - Svenja Pachernegg
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - David K Wright
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Melanie Bahlo
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, Melbourne, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Terrence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gary R Hime
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Nadine Girard
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Chen Hoffmann
- Radiology Department, Sheba medical Centre, Tel Aviv, Israel
| | - Yuval Shilon
- Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Amnon Zung
- Pediatrics Department, Kaplan Medical Center, Rehovot, 76100, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School, Jerusalem, Israel
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mathieu Milh
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Bochra Ben Rhouma
- Higher Institute of Nursing Sciences of Gabes, University of Gabes, Gabes, Tunisia
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Neila Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Anu Bashamboo
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Kenneth McElreavey
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Ehud Banne
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
- The Rina Mor Genetic Institute, Wolfson Medical Center, Holon, 58100, Israel
| | - Naomi Weintrob
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Endocrinology Unit, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
| | | | - Andrew H Sinclair
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
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Özbek M, Beyaz F, Ergün E, Ergün L, Karaca H, Cabir A, Alesawi YAK. Identification of some calcium binding proteins and neural cell markers in rat testis and epididymis during postnatal development. Andrologia 2022; 54:e14633. [DOI: 10.1111/and.14633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Mehmet Özbek
- Department of Histology and Embryology, Faculty of Veterinary Medicine Mehmet Akif Ersoy University Burdur Turkey
| | - Feyzullah Beyaz
- Department of Histology and Embryology, Faculty of Veterinary Medicine Erciyes University Kayseri Turkey
| | - Emel Ergün
- Department of Histology and Embryology, Faculty of Veterinary Medicine Ankara University Ankara Turkey
| | - Levent Ergün
- Department of Histology and Embryology, Faculty of Veterinary Medicine Ankara University Ankara Turkey
| | - Harun Karaca
- Department of Histology and Embryology, Faculty of Veterinary Medicine Mehmet Akif Ersoy University Burdur Turkey
| | - Ahmet Cabir
- Department of Histology and Embryology, Faculty of Veterinary Medicine Erciyes University Kayseri Turkey
| | - Yahy Abood Kareem Alesawi
- Department of Histology and Embryology, Faculty of Veterinary Medicine Ankara University Ankara Turkey
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4
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Pham T, Patel A, Muquith M, Zimmern V, Goodspeed K. Abnormal Genetic Testing in Males With Concomitant Neurodevelopmental Disabilities and Genital Malformation. Pediatr Neurol 2022; 134:72-77. [PMID: 35841714 DOI: 10.1016/j.pediatrneurol.2022.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) affect 1:6 children in the United States and are often linked to genetic disorders. Because many genes are enriched in brain and testicular tissue, genital malformations identified early may be a predictor of genetic disorders in children with NDDs. However, few studies have evaluated the specific effects of genital malformations. This study assesses the association between genital malformations and abnormal genetic testing among male patients with NDD. METHODS A retrospective chart review was performed of 447 male patients seen at Children's Health Dallas (2009 to 2019) with concomitant genital malformations and NDDs. We assessed the strength of factors associated with obtaining a genetic test and having abnormal results. RESULTS We identified 447 patients with concomitant genital malformations and NDD. Fifty-six percent (251 of 447) received genetic testing, of which 68.5% (172 of 251) had abnormal results. Patients with mixed genitourinary malformations, global developmental delay (GDD), intellectual delay, or autism spectrum disorder were more likely to have a genetic test. Patients with bilateral testicular involvement, GDD, severe language delay, wheelchair dependence, or abnormal magnetic resonance imaging findings were more likely to have abnormal results. CONCLUSION The diagnostic yield of 68.5% in our cohort of male patients with genital malformations was higher than previous reports of 5% to 35% in NDD populations. More severe phenotypic features may be associated with increased yield. Identification of genital malformations during infancy may guide clinical surveillance, and copresentations with NDDs may support genetic testing.
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Affiliation(s)
- Tri Pham
- University of Texas Southwestern Medical School, Dallas, Texas
| | - Akshat Patel
- University of Texas Southwestern Medical School, Dallas, Texas
| | | | - Vincent Zimmern
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kimberly Goodspeed
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas.
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Zhang X, Zhang Q, Shan Y, Xiao J, Cheng J, Ye F, Sai Y. Transcriptomic investigation of the effects of TDCPP on PC12 and GC2 cells with experimental validation. Gene X 2022; 822:146349. [PMID: 35182677 DOI: 10.1016/j.gene.2022.146349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 11/25/2022] Open
Abstract
TDCPP is a flame retardant which has nervous and reproductive toxicity. Although there is a close association between nervous and reproductive system, the exact toxic mechanism of TDCPP in these systems is still seldom, especially in a genome scale. In this study, we explored the transcriptomic landscape of TDCPP in PC12 and GC2 cells using RNAseq method. A total of 465 co-differential expressed genes were found. These genes were mainly enriched in extra-cellular matrix, cell adhesion, cell cycle arrest, oxidoreductase activity GO terms, and PI3K/AKT, focal adhesion, ECM-receptor interaction KEGG pathways. Hub genes (ANXA1, COL27A1, GAS6, GNB4 and THBS1) were extracted using STRING and confirmed by qPCR experiment. Vimentin, HSPA5 and Caspase3 were proved to be responsible to TDCPP in GC2 and PC12 cells. Knockdown assay in PC12 cells showed that these hub genes could also affect the protein expression of vimentin, HSPA5 and Caspase3. In summary, TDCPP might exert its toxic effect through disturbing focal adhesion, ECM-receptor interaction and PI3K/Akt pathways. One of the mechanisms could be influence on the cytoskeleton (vimentin), ER stress (HSPA5) and apoptosis (Caspase3). The sequence data in this study might be a useful resource for future TDCPP related researches.
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Affiliation(s)
- Xi Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Qifu Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yaohui Shan
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jingsong Xiao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jin Cheng
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Feng Ye
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yan Sai
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China.
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6
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Tommasi S, Kitapci TH, Blumenfeld H, Besaratinia A. Secondhand smoke affects reproductive functions by altering the mouse testis transcriptome, and leads to select intron retention in Pde1a. ENVIRONMENT INTERNATIONAL 2022; 161:107086. [PMID: 35063792 PMCID: PMC8891074 DOI: 10.1016/j.envint.2022.107086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Human exposure to secondhand smoke (SHS) is known to result in adverse effects in multiple organ systems. However, the impact of SHS on the male reproductive system, particularly on the regulation of genes and molecular pathways that govern sperm production, maturation, and functions remains largely understudied. OBJECTIVE We investigated the effects of SHS on the testis transcriptome in a validated mouse model. METHODS Adult male mice were exposed to SHS (5 h/day, 5 days/week for 4 months) as compared to controls (clean air-exposed). RNA-seq analysis was performed on the testis of SHS-exposed mice and controls. Variant discovery and plink association analyses were also conducted to detect exposure-related transcript variants in SHS-treated mice. RESULTS Exposure of mice to SHS resulted in the aberrant expression of 131 testicular genes. Whilst approximately two thirds of the differentially expressed genes were protein-coding, the remaining (30.5%) comprised noncoding elements, mostly lncRNAs (19.1%). Variant discovery analysis identified a homozygous frameshift variant that is statistically significantly associated with SHS exposure (P = 7.744e-06) and is generated by retention of a short intron within Pde1a, a key regulator of spermatogenesis. Notably, this SHS-associated intron variant harbors an evolutionarily conserved, premature termination codon (PTC) that disrupts the open reading frame of Pde1a, presumably leading to its degradation via nonsense-mediated decay. DISCUSSION SHS alters the expression of genes involved in molecular pathways that are crucial for normal testis development and function. Preferential targeting of lncRNAs in the testis of SHS-exposed mice is especially significant considering their crucial role in the spatial and temporal modulation of spermatogenesis. Equally important is our discovery of a novel homozygous frameshift variant that is exclusively and significantly associated with SHS-exposure and is likely to represent a safeguard mechanism to regulate transcription of Pde1a and preserve normal testis function during harmful exposure to environmental agents.
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Affiliation(s)
- Stella Tommasi
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA.
| | - Tevfik H Kitapci
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
| | - Hannah Blumenfeld
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
| | - Ahmad Besaratinia
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
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7
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Du K, Pippel M, Kneitz S, Feron R, da Cruz I, Winkler S, Wilde B, Avila Luna EG, Myers E, Guiguen Y, Macias Garcia C, Schartl M. Genome biology of the Darkedged Splitfin, Girardinichthys multiradiatus, and the evolution of sex chromosomes and placentation. Genome Res 2022; 32:583-594. [PMID: 35082141 PMCID: PMC8896457 DOI: 10.1101/gr.275826.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/10/2022] [Indexed: 11/24/2022]
Abstract
Viviparity evolved independently about 150 times in vertebrates and more than 20 times in fish. Several lineages added to the protection of the embryo inside the body of the mother, the provisioning of nutrients, and physiological exchange. This often led to the evolution of a placenta. Among fish, one of the most complex systems serving the function of the placenta is the embryonal trophotaenia/ovarian luminal epithelium of the goodeid fishes. For a better understanding of this feature and others of this group of fishes, high-quality genomic resources are essential. We have sequenced the genome of the darkedged splitfin, Girardinichthys multiradiatus. The assembly is chromosome level and includes the X and Y Chromosomes. A large male-specific region on the Y was identified covering 80% of Chromosome 20, allowing some first inferences on the recent origin and a candidate male sex determining gene. Genome-wide transcriptomics uncovered sex-specific differences in brain gene expression with an enrichment for neurosteroidogenesis and testis genes in males. The expression signatures of the splitfin embryonal and maternal placenta showed overlap with homologous tissues including human placenta, the ovarian follicle epithelium of matrotrophic poeciliid fish species and the brood pouch epithelium of the seahorse. Our comparative analyses on the evolution of embryonal and maternal placenta indicate that the evolutionary novelty of maternal provisioning development repeatedly made use of genes that already had the same function in other tissues. In this way, preexisting modules are assembled and repurposed to provide the molecular changes for this novel trait.
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Affiliation(s)
| | - Martin Pippel
- Max-Planck Institute of Molecular Cell Biology and Genetics
| | | | - Romain Feron
- University of Lausanne, Swiss Institute of Bioinformatics, INRAE, LPGP
| | | | - Sylke Winkler
- Max-Planck Institute of Molecular Cell Biology and Genetics
| | | | - Edgar G Avila Luna
- Instituto de Ecologia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito exterior s/n anexo al Jardín Botánico
| | - Eugene Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics
| | | | - Constantino Macias Garcia
- Instituto de Ecologia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito exterior s/n anexo al Jardín Botánico
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Implications of testicular ACE2 and the renin-angiotensin system for SARS-CoV-2 on testis function. Nat Rev Urol 2022; 19:116-127. [PMID: 34837081 PMCID: PMC8622117 DOI: 10.1038/s41585-021-00542-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/16/2022]
Abstract
Although many studies have focused on SARS-CoV-2 infection in the lungs, comparatively little is known about the potential effects of the virus on male fertility. SARS-CoV-2 infection of target cells requires the presence of furin, angiotensin-converting enzyme 2 (ACE2) receptors, and transmembrane protease serine 2 (TMPRSS2). Thus, cells in the body that express these proteins might be highly susceptible to viral entry and downstream effects. Currently, reports regarding the expression of the viral entry proteins in the testes are conflicting; however, other members of the SARS-CoV family of viruses - such as SARS-CoV - have been suspected to cause testicular dysfunction and/or orchitis. SARS-CoV-2, which displays many similarities to SARS-CoV, could potentially cause similar adverse effects. Commonalities between SARS family members, taken in combination with sparse reports of testicular discomfort and altered hormone levels in patients with SARS-CoV-2, might indicate possible testicular dysfunction. Thus, SARS-CoV-2 infection has the potential for effects on testis somatic and germline cells and experimental approaches might be required to help identify potential short-term and long-term effects of SARS-CoV-2 on male fertility.
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9
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Su X, Li W, Lv L, Li X, Yang J, Luo XJ, Liu J. Transcriptome-Wide Association Study Provides Insights Into the Genetic Component of Gene Expression in Anxiety. Front Genet 2021; 12:740134. [PMID: 34650599 PMCID: PMC8505959 DOI: 10.3389/fgene.2021.740134] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/15/2021] [Indexed: 01/10/2023] Open
Abstract
Anxiety disorders are common mental disorders that often result in disability. Recently, large-scale genome-wide association studies (GWASs) have identified several novel risk variants and loci for anxiety disorders (or anxiety traits). Nevertheless, how the reported risk variants confer risk of anxiety remains unknown. To identify genes whose cis-regulated expression levels are associated with risk of anxiety traits, we conducted a transcriptome-wide association study (TWAS) by integrating genome-wide associations from a large-scale GWAS (N = 175,163) (which evaluated anxiety traits based on Generalized Anxiety Disorder 2-item scale (GAD-2) score) and brain expression quantitative trait loci (eQTL) data (from the PsychENCODE and GTEx). We identified 19 and 17 transcriptome-wide significant (TWS) genes in the PsychENCODE and GTEx, respectively. Intriguingly, 10 genes showed significant associations with anxiety in both datasets, strongly suggesting that genetic risk variants may confer risk of anxiety traits by regulating the expression of these genes. Top TWS genes included RNF123, KANSL1-AS1, GLYCTK, CRHR1, DND1P1, MAPT and ARHGAP27. Of note, 25 TWS genes were not implicated in the original GWAS. Our TWAS identified 26 risk genes whose cis-regulated expression were significantly associated with anxiety, providing important insights into the genetic component of gene expression in anxiety disorders/traits and new clues for future drug development.
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Affiliation(s)
- Xi Su
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, China
| | - Wenqiang Li
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, China
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, China
| | - Xiaoyan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jinfeng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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10
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Matos B, Publicover SJ, Castro LFC, Esteves PJ, Fardilha M. Brain and testis: more alike than previously thought? Open Biol 2021; 11:200322. [PMID: 34062096 PMCID: PMC8169208 DOI: 10.1098/rsob.200322] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several strands of evidence indicate the presence of marked similarities between human brain and testis. Understanding these similarities and their implications has become a topic of interest among the scientific community. Indeed, an association of intelligence with some semen quality parameters has been reported and a relation between dysfunctions of the human brain and testis has also been evident. Numerous common molecular features are evident when these tissues are compared, which is reflected in the huge number of common proteins. At the functional level, human neurons and sperm share a number of characteristics, including the importance of the exocytotic process and the presence of similar receptors and signalling pathways. The common proteins are mainly involved in exocytosis, tissue development and neuron/brain-associated biological processes. With this analysis, we conclude that human brain and testis share several biochemical characteristics which, in addition to their involvement in the speciation process, could, at least in part, be responsible for the expression of a huge number of common proteins. Nonetheless, this is an underexplored topic, and the connection between these tissues needs to be clarified, which could help to understand the dysfunctions affecting brain and testis, as well as to develop improved therapeutic strategies.
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Affiliation(s)
- Bárbara Matos
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Stephen J Publicover
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Luis Filipe C Castro
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal.,CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrico de Vairão, University of Porto, 4485-661 Vairão, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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11
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Goszczynski DE, Halstead MM, Islas-Trejo AD, Zhou H, Ross PJ. Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage. Genome Res 2021; 31:732-744. [PMID: 33722934 PMCID: PMC8015843 DOI: 10.1101/gr.267336.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/01/2021] [Indexed: 01/04/2023]
Abstract
Characterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was released; however, the functional annotation of the bovine genome lacks precise transcription start sites and contains a low number of transcripts in comparison to human and mouse. By using the RAMPAGE approach, this study identified transcription start sites at high resolution in a large collection of bovine tissues. We found several known and novel transcription start sites attributed to promoters of protein-coding and lncRNA genes that were validated through experimental and in silico evidence. With these findings, the annotation of transcription start sites in cattle reached a level comparable to the mouse and human genome annotations. In addition, we identified and characterized transcription start sites for antisense transcripts derived from bidirectional promoters, potential lncRNAs, mRNAs, and pre-miRNAs. We also analyzed the quantitative aspects of RAMPAGE to produce a promoter activity atlas, reaching highly reproducible results comparable to traditional RNA-seq. Coexpression networks revealed considerable use of tissue-specific promoters, especially between brain and testicle, which expressed several genes in common from alternate loci. Furthermore, regions surrounding coexpressed modules were enriched in binding factor motifs representative of each tissue. The comprehensive annotation of promoters in such a large collection of tissues will substantially contribute to our understanding of gene expression in cattle and other mammalian species, shortening the gap between genotypes and phenotypes.
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Affiliation(s)
- Daniel E Goszczynski
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Michelle M Halstead
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Alma D Islas-Trejo
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Pablo J Ross
- Department of Animal Science, University of California, Davis, California 95616, USA
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12
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Kulkarni A, Lopez DH, Extavour CG. Shared Cell Biological Functions May Underlie Pleiotropy of Molecular Interactions in the Germ Lines and Nervous Systems of Animals. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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13
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Breschi A, Muñoz-Aguirre M, Wucher V, Davis CA, Garrido-Martín D, Djebali S, Gillis J, Pervouchine DD, Vlasova A, Dobin A, Zaleski C, Drenkow J, Danyko C, Scavelli A, Reverter F, Snyder MP, Gingeras TR, Guigó R. A limited set of transcriptional programs define major cell types. Genome Res 2020; 30:1047-1059. [PMID: 32759341 PMCID: PMC7397875 DOI: 10.1101/gr.263186.120] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components of many tissues and organs. Based on gene expression, these cell types redefine the basic histological types by which tissues have been traditionally classified. We identified genes whose expression is specific to these cell types, and from these genes, we estimated the contribution of the major cell types to the composition of human tissues. We found this cellular composition to be a characteristic signature of tissues and to reflect tissue morphological heterogeneity and histology. We identified changes in cellular composition in different tissues associated with age and sex, and found that departures from the normal cellular composition correlate with histological phenotypes associated with disease.
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Affiliation(s)
- Alessandra Breschi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E-08003 Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Catalonia, Spain
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E-08003 Barcelona, Catalonia, Spain
- Universitat Politècnica de Catalunya. Departament d'Estadística i Investigació Operativa, 08034 Barcelona, Catalonia, Spain
| | - Valentin Wucher
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E-08003 Barcelona, Catalonia, Spain
| | - Carrie A Davis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11742, USA
| | - Diego Garrido-Martín
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E-08003 Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Catalonia, Spain
| | - Sarah Djebali
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E-08003 Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Catalonia, Spain
- Institut National de Recherche en Santé Digestive (IRSD), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), École Nationale Vétérinaire de Toulouse (ENVT), Université Paul Sabatier (UPS), 31024 Toulouse, France
| | - Jesse Gillis
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Dmitri D Pervouchine
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E-08003 Barcelona, Catalonia, Spain
- Skolkovo Institute for Science and Technology, Moscow, Russia 143025
| | - Anna Vlasova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11742, USA
| | - Chris Zaleski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11742, USA
| | - Jorg Drenkow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11742, USA
| | - Cassidy Danyko
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11742, USA
| | | | - Ferran Reverter
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E-08003 Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Catalonia, Spain
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Thomas R Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11742, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, E-08003 Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Catalonia, Spain
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14
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Devlin DJ, Agrawal Zaneveld S, Nozawa K, Han X, Moye AR, Liang Q, Harnish JM, Matzuk MM, Chen R. Knockout of mouse receptor accessory protein 6 leads to sperm function and morphology defects†. Biol Reprod 2020; 102:1234-1247. [PMID: 32101290 DOI: 10.1093/biolre/ioaa024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/31/2019] [Accepted: 05/26/2020] [Indexed: 02/07/2023] Open
Abstract
Receptor accessory protein 6 (REEP6) is a member of the REEP/Ypt-interacting protein family that we recently identified as essential for normal endoplasmic reticulum homeostasis and protein trafficking in the retina of mice and humans. Interestingly, in addition to the loss of REEP6 in our knockout (KO) mouse model recapitulating the retinal degeneration of humans with REEP6 mutations causing retinitis pigmentosa (RP), we also found that male mice are sterile. Herein, we characterize the infertility caused by loss of Reep6. Expression of both Reep6 mRNA transcripts is present in the testis; however, isoform 1 becomes overexpressed during spermiogenesis. In vitro fertilization assays reveal that Reep6 KO spermatozoa are able to bind the zona pellucida but are only able to fertilize oocytes lacking the zona pellucida. Although spermatogenesis appears normal in KO mice, cauda epididymal spermatozoa have severe motility defects and variable morphological abnormalities, including bent or absent tails. Immunofluorescent staining reveals that REEP6 expression first appears in stage IV tubules within step 15 spermatids, and REEP6 localizes to the connecting piece, midpiece, and annulus of mature spermatozoa. These data reveal an important role for REEP6 in sperm motility and morphology and is the first reported function for a REEP protein in reproductive processes. Additionally, this work identifies a new gene potentially responsible for human infertility and has implications for patients with RP harboring mutations in REEP6.
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Affiliation(s)
- Darius J Devlin
- Interdepartmental Program in Translational Biology & Molecular Medicine, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Smriti Agrawal Zaneveld
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kaori Nozawa
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA
| | - Xiao Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Reproductive Medical Center, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Abigail R Moye
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Qingnan Liang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jacob Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Martin M Matzuk
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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15
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González CR, González B. Exploring the Stress Impact in the Paternal Germ Cells Epigenome: Can Catecholamines Induce Epigenetic Reprogramming? Front Endocrinol (Lausanne) 2020; 11:630948. [PMID: 33679612 PMCID: PMC7933579 DOI: 10.3389/fendo.2020.630948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/30/2020] [Indexed: 12/30/2022] Open
Abstract
Spermatogenesis is characterized by unique epigenetic programs that enable chromatin remodeling and transcriptional regulation for proper meiotic divisions and germ cells maturation. Paternal lifestyle stressors such as diet, drug abuse, or psychological trauma can directly impact the germ cell epigenome and transmit phenotypes to the next generation, pointing to the importance of epigenetic regulation during spermatogenesis. It is established that environmental perturbations can affect the development and behavior of the offspring through epigenetic inheritance, including changes in small non-coding RNAs, DNA methylation, and histones post-translational modifications. But how male germ cells react to lifestyle stressors and encode them in the paternal epigenome is still a research gap. Most lifestyle stressors activate catecholamine circuits leading to both acute and long-term changes in neural functions, and epigenetic mechanisms show strong links to both long-term and rapid, dynamic gene expression regulation during stress. Importantly, the testis shares a molecular and transcriptional signature with the brain tissue, including a rich expression of catecholaminergic elements in germ cells that seem to respond to stressors with similar epigenetic and transcriptional profiles. In this minireview, we put on stage the action of catecholamines as possible mediators between paternal stress responses and epigenetic marks alterations during spermatogenesis. Understanding the epigenetic regulation in spermatogenesis will contribute to unravel the coding mechanisms in the transmission of the biological impacts of stress between generations.
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Affiliation(s)
- Candela R. González
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | - Betina González
- Instituto de Investigaciones Farmacológicas (Universidad de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- *Correspondence: Betina González,
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16
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Jung M, Wells D, Rusch J, Ahmad S, Marchini J, Myers SR, Conrad DF. Unified single-cell analysis of testis gene regulation and pathology in five mouse strains. eLife 2019; 8:e43966. [PMID: 31237565 PMCID: PMC6615865 DOI: 10.7554/elife.43966] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
To fully exploit the potential of single-cell functional genomics in the study of development and disease, robust methods are needed to simplify the analysis of data across samples, time-points and individuals. Here we introduce a model-based factor analysis method, SDA, to analyze a novel 57,600 cell dataset from the testes of wild-type mice and mice with gonadal defects due to disruption of the genes Mlh3, Hormad1, Cul4a or Cnp. By jointly analyzing mutant and wild-type cells we decomposed our data into 46 components that identify novel meiotic gene-regulatory programs, mutant-specific pathological processes, and technical effects, and provide a framework for imputation. We identify, de novo, DNA sequence motifs associated with individual components that define temporally varying modes of gene expression control. Analysis of SDA components also led us to identify a rare population of macrophages within the seminiferous tubules of Mlh3-/- and Hormad1-/- mice, an area typically associated with immune privilege.
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Affiliation(s)
- Min Jung
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Daniel Wells
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Jannette Rusch
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Suhaira Ahmad
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Jonathan Marchini
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Simon R Myers
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Donald F Conrad
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
- Division of Genetics, Oregon National Primate Research CenterOregon Health & Science UniversityPortlandUnited States
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17
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Ramaiah M, Tan K, Plank TDM, Song HW, Chousal JN, Jones S, Shum EY, Sheridan SD, Peterson KJ, Gromoll J, Haggarty SJ, Cook-Andersen H, Wilkinson MF. A microRNA cluster in the Fragile-X region expressed during spermatogenesis targets FMR1. EMBO Rep 2019; 20:e46566. [PMID: 30573526 PMCID: PMC6362356 DOI: 10.15252/embr.201846566] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 01/08/2023] Open
Abstract
Testis-expressed X-linked genes typically evolve rapidly. Here, we report on a testis-expressed X-linked microRNA (miRNA) cluster that despite rapid alterations in sequence has retained its position in the Fragile-X region of the X chromosome in placental mammals. Surprisingly, the miRNAs encoded by this cluster (Fx-mir) have a predilection for targeting the immediately adjacent gene, Fmr1, an unexpected finding given that miRNAs usually act in trans, not in cis Robust repression of Fmr1 is conferred by combinations of Fx-mir miRNAs induced in Sertoli cells (SCs) during postnatal development when they terminate proliferation. Physiological significance is suggested by the finding that FMRP, the protein product of Fmr1, is downregulated when Fx-mir miRNAs are induced, and that FMRP loss causes SC hyperproliferation and spermatogenic defects. Fx-mir miRNAs not only regulate the expression of FMRP, but also regulate the expression of eIF4E and CYFIP1, which together with FMRP form a translational regulatory complex. Our results support a model in which Fx-mir family members act cooperatively to regulate the translation of batteries of mRNAs in a developmentally regulated manner in SCs.
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Affiliation(s)
- Madhuvanthi Ramaiah
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Terra-Dawn M Plank
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Hye-Won Song
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer N Chousal
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Samantha Jones
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Eleen Y Shum
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Steven D Sheridan
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Boston, MA, USA
- Departments of Neurology and Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Jörg Gromoll
- Center for Reproductive Medicine and Andrology, University of Münster, Münster, Germany
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Boston, MA, USA
- Departments of Neurology and Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
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18
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Dianatpour A, Ghafouri-Fard S. Long Non Coding RNA Expression Intersecting Cancer and Spermatogenesis: A Systematic Review. Asian Pac J Cancer Prev 2017; 18:2601-2610. [PMID: 29072050 PMCID: PMC5747377 DOI: 10.22034/apjcp.2017.18.10.2601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background: Numerous similarities have been noted between gametogenic and tumorigenic programs in features
such as global hypomethylation, immune evasion, immortalization, meiosis induction, and migration. In addition, aberrant
expression of testis specific genes has been detected in various cancers which has led to categorization of these genes
as “cancer-testis genes”. Most of the examples identified in this category are protein encoding. However, recent studies
have revealed that non-coding RNAs, including long non coding RNAs (lncRNAs), may have essential regulatory
roles in telomere biology, chromatin dynamics, modulation of gene expression and genome structural organization.
All of these functions are implicated in both gametogenic and tumorigenic programs. Methods: In the present study,
we conducted a computerized search of the MEDLINE/PUBMED and Embase databases with the key words lncRNA,
gametogenesis, testis and cancer. Results: We found a number of lncRNAs with essential roles and notable expression
in both gametogenic and cancer tissues. Conclusions: Comparison between cancer tissues and gametogenic tissues
has shown that numerous lncRNAs are expressed in both, playing similar roles in processes modulated by signaling
pathways such as Wnt/β-catenin and PI3K/AKT/mTOR. Evaluation of expression patterns and functions of these
genes should pave the way to discovery of biomarkers for early detection, prognostic assessment and evaluation of
therapeutic responses in cancers.
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Affiliation(s)
- Ali Dianatpour
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical sciences, Tehran, Iran.
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19
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Doldur-Balli F, Ozel MN, Gulsuner S, Tekinay AB, Ozcelik T, Konu O, Adams MM. Characterization of a novel zebrafish (Danio rerio) gene, wdr81, associated with cerebellar ataxia, mental retardation and dysequilibrium syndrome (CAMRQ). BMC Neurosci 2015; 16:96. [PMID: 27390838 PMCID: PMC4690267 DOI: 10.1186/s12868-015-0229-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 12/03/2015] [Indexed: 11/16/2022] Open
Abstract
Background WDR81 (WD repeat-containing protein 81) is associated with cerebellar ataxia, mental retardation and disequilibrium syndrome (CAMRQ2, [MIM 610185]). Human and mouse studies suggest that it might be a gene of importance during neurodevelopment. This study aimed at fully characterizing the structure of the wdr81 transcript, detecting the possible transcript variants and revealing its expression profile in zebrafish, a powerful model organism for studying development and disease. Results As expected in human and mouse orthologous proteins, zebrafish wdr81 is predicted to possess a BEACH (Beige and Chediak-Higashi) domain, a major facilitator superfamily domain and WD40-repeats, which indicates a conserved function in these species. We observed that zebrafish wdr81 encodes one open reading frame while the transcript has one 5′ untranslated region (UTR) and the prediction of the 3′ UTR was mainly confirmed along with a detected insertion site in the embryo and adult brain. This insertion site was also found in testis, heart, liver, eye, tail and muscle, however, there was no amplicon in kidney, intestine and gills, which might be the result of possible alternative polyadenylation processes among tissues. The 5 and 18 hpf were critical timepoints of development regarding wdr81 expression. Furthermore, the signal of the RNA probe was stronger in the eye and brain at 18 and 48 hpf, then decreased at 72 hpf. Finally, expression of wdr81 was detected in the adult brain and eye tissues, including but not restricted to photoreceptors of the retina, presumptive Purkinje cells and some neurogenic brains regions. Conclusions Taken together these data emphasize the importance of this gene during neurodevelopment and a possible role for neuronal proliferation. Our data provide a basis for further studies to fully understand the function of wdr81. Electronic supplementary material The online version of this article (doi:10.1186/s12868-015-0229-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fusun Doldur-Balli
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Mehmet Neset Ozel
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Suleyman Gulsuner
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Ayse B Tekinay
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey.,Interdisciplinary Program in Neuroscience, Bilkent University, Ankara, Turkey
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey.,Interdisciplinary Program in Neuroscience, Bilkent University, Ankara, Turkey
| | - Ozlen Konu
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,Interdisciplinary Program in Neuroscience, Bilkent University, Ankara, Turkey.,Molecular Biology and Genetics Department Zebrafish Facility, Bilkent University, Ankara, Turkey
| | - Michelle M Adams
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, Turkey. .,Interdisciplinary Program in Neuroscience, Bilkent University, Ankara, Turkey. .,Molecular Biology and Genetics Department Zebrafish Facility, Bilkent University, Ankara, Turkey. .,Psychology Department, Bilkent University, Ankara, Turkey.
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20
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Hadziselimovic F, Hadziselimovic NO, Demougin P, Oakeley EJ. Decreased expression of genes associated with memory and x-linked mental retardation in boys with non-syndromic cryptorchidism and high infertility risk. Mol Syndromol 2014; 5:76-80. [PMID: 24715854 DOI: 10.1159/000357931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2013] [Indexed: 02/05/2023] Open
Abstract
An elevated odds ratio for low IQ has been found for cryptorchid boys. Furthermore, poor school performance has been observed in cryptorchid boys with impaired mini-puberty. Gene expression analysis, qPCR and immunohistology were performed on testicular biopsies from 7 boys who underwent orchiopexy and had testicular histology typical of a high risk of infertility (HIR). The results were compared with 12 biopsies from cryptorchid boys with a low risk for developing infertility. The following genes associated with mental retardation were identically expressed: GDI1, OPHN1, PAK3, ARHGEF6, IL1RAPL, ACSL4, MECP2, RPS6KA3, ARX, and ATRX. However, boys in the HIR group had low or no expression of EGR4, FMR2 (AFF2) and VCX3A. In conclusion, impaired expression of genes known to encode proteins involved in signaling pathways that regulate cytoskeletal organization, synaptic vesicle transport and the establishment of connections between neuronal cells may contribute to reduced intellectual and cognitive functioning in infertile cryptorchid males.
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Affiliation(s)
- F Hadziselimovic
- Institute of Andrology, Liestal, University of Basel, Basel, Switzerland
| | - N O Hadziselimovic
- Institute of Andrology, Liestal, University of Basel, Basel, Switzerland ; Division of Molecular Neuroscience, Department of Psychology, University of Basel, Basel, Switzerland
| | - P Demougin
- Department of Molecular Biology, Biozentrum, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - E J Oakeley
- Department of Molecular Biology, Novartis Institutes for Biomedical Research, Basel, Switzerland
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Abstract
First discovered in maize by Barbara McClintock in the 1940s, transposable elements (TEs) are DNA sequences that in some cases have the ability to move along chromosomes or "transpose" in the genome. This revolutionary finding was initially met with resistance by the scientific community and viewed by some as heretical. A large body of knowledge has accumulated over the last 60 years on the biology of TEs. Indeed, it is now known that TEs can generate genomic instability and reconfigure gene expression networks both in the germline and somatic cells. This review highlights recent findings on the role of TEs in health and diseases of the CNS, which were presented at the 2013 Society for Neuroscience meeting. The work of the speakers in this symposium shows that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings on TE expression and function in the CNS have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in shaping individual behavior and contribute to vulnerability to disease.
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Chatterjee N, Rollins J, Mahowald AP, Bazinet C. Neurotransmitter Transporter-Like: a male germline-specific SLC6 transporter required for Drosophila spermiogenesis. PLoS One 2011; 6:e16275. [PMID: 21298005 PMCID: PMC3029318 DOI: 10.1371/journal.pone.0016275] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 12/13/2010] [Indexed: 02/03/2023] Open
Abstract
The SLC6 class of membrane transporters, known primarily as neurotransmitter transporters, is increasingly appreciated for its roles in nutritional uptake of amino acids and other developmentally specific functions. A Drosophila SLC6 gene, Neurotransmitter transporter-like (Ntl), is expressed only in the male germline. Mobilization of a transposon inserted near the 3' end of the Ntl coding region yields male-sterile mutants defining a single complementation group. Germline transformation with Ntl cDNAs under control of male germline-specific control elements restores Ntl/Ntl homozygotes to normal fertility, indicating that Ntl is required only in the germ cells. In mutant males, sperm morphogenesis appears normal, with elongated, individualized and coiled spermiogenic cysts accumulating at the base of the testes. However, no sperm are transferred to the seminal vesicle. The level of polyglycylation of Ntl mutant sperm tubulin appears to be significantly lower than that of wild type controls. Glycine transporters are the most closely related SLC6 transporters to Ntl, suggesting that Ntl functions as a glycine transporter in developing sperm, where augmentation of the cytosolic pool of glycine may be required for the polyglycylation of the massive amounts of tubulin in the fly's giant sperm. The male-sterile phenotype of Ntl mutants may provide a powerful genetic system for studying the function of an SLC6 transporter family in a model organism.
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Affiliation(s)
- Nabanita Chatterjee
- Department of Biological Sciences, St. John's University, Jamaica, New York, United States of America
| | - Janet Rollins
- Department of Biological Sciences, St. John's University, Jamaica, New York, United States of America
| | - Anthony P. Mahowald
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Christopher Bazinet
- Department of Biological Sciences, St. John's University, Jamaica, New York, United States of America
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23
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Kim CW, Tak HM, Kim GT, Mun YJ, Jeon BT, Kim HJ, Roh GS, Han J, Kang D. H2O2-induced up-regulation of CatSper3 in mouse brain. Mol Reprod Dev 2010; 77:650. [PMID: 20586097 DOI: 10.1002/mrd.21216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Abstract
Patterns and risks of human disease have evolved. In this article, I review evidence regarding the importance of recent adaptive evolution, positive selection, and genomic conflicts in shaping the genetic and phenotypic architectures of polygenic human diseases. Strong recent selection in human populations can create and maintain genetically based disease risk primarily through three processes: increased scope for dysregulation from recent human adaptations, divergent optima generated by intraspecific genomic conflicts, and transient or stable deleterious by-products of positive selection caused by antagonistic pleiotropy, ultimately due to trade-offs at the levels of molecular genetics, development, and physiology. Human disease due to these processes appears to be concentrated in three sets of phenotypes: cognition and emotion, reproductive traits, and life-history traits related to long life-span. Diverse, convergent lines of evidence suggest that a small set of tissues whose pleiotropic patterns of gene function and expression are under especially strong selection-brain, placenta, testis, prostate, breast, and ovary-has mediated a considerable proportion of disease risk in modern humans.
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Affiliation(s)
- Bernard J Crespi
- Department of Biosciences, Simon Fraser University, Burnaby, B. C., Canada V5A 1S6.
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Lindenmeyer MT, Eichinger F, Sen K, Anders HJ, Edenhofer I, Mattinzoli D, Kretzler M, Rastaldi MP, Cohen CD. Systematic analysis of a novel human renal glomerulus-enriched gene expression dataset. PLoS One 2010; 5:e11545. [PMID: 20634963 PMCID: PMC2902524 DOI: 10.1371/journal.pone.0011545] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 06/16/2010] [Indexed: 02/04/2023] Open
Abstract
Glomerular diseases account for the majority of cases with chronic renal failure. Several genes have been identified with key relevance for glomerular function. Quite a few of these genes show a specific or preferential mRNA expression in the renal glomerulus. To identify additional candidate genes involved in glomerular function in humans we generated a human renal glomerulus-enriched gene expression dataset (REGGED) by comparing gene expression profiles from human glomeruli and tubulointerstitium obtained from six transplant living donors using Affymetrix HG-U133A arrays. This analysis resulted in 677 genes with prominent overrepresentation in the glomerulus. Genes with 'a priori' known prominent glomerular expression served for validation and were all found in the novel dataset (e.g. CDKN1, DAG1, DDN, EHD3, MYH9, NES, NPHS1, NPHS2, PDPN, PLA2R1, PLCE1, PODXL, PTPRO, SYNPO, TCF21, TJP1, WT1). The mRNA expression of several novel glomerulus-enriched genes in REGGED was validated by qRT-PCR. Gene ontology and pathway analysis identified biological processes previously not reported to be of relevance in glomeruli of healthy human adult kidneys including among others axon guidance. This finding was further validated by assessing the expression of the axon guidance molecules neuritin (NRN1) and roundabout receptor ROBO1 and -2. In diabetic nephropathy, a prevalent glomerulopathy, differential regulation of glomerular ROBO2 mRNA was found.In summary, novel transcripts with predominant expression in the human glomerulus could be identified using a comparative strategy on microdissected nephrons. A systematic analysis of this glomerulus-specific gene expression dataset allows the detection of target molecules and biological processes involved in glomerular biology and renal disease.
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Affiliation(s)
- Maja T. Lindenmeyer
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
- Institute of Physiology with Zurich Center of Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Felix Eichinger
- Department of Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kontheari Sen
- Institute of Physiology with Zurich Center of Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | | | - Ilka Edenhofer
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Deborah Mattinzoli
- Renal Research Laboratory, Fondazione IRCCS Policlinico & Fondazione D'Amico per la Ricerca sulle Malattie Renali, Milan, Italy
| | - Matthias Kretzler
- Department of Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Maria P. Rastaldi
- Renal Research Laboratory, Fondazione IRCCS Policlinico & Fondazione D'Amico per la Ricerca sulle Malattie Renali, Milan, Italy
| | - Clemens D. Cohen
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
- Institute of Physiology with Zurich Center of Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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Lin L, Shen S, Jiang P, Sato S, Davidson BL, Xing Y. Evolution of alternative splicing in primate brain transcriptomes. Hum Mol Genet 2010; 19:2958-73. [PMID: 20460271 DOI: 10.1093/hmg/ddq201] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing is a predominant form of gene regulation in higher eukaryotes. The evolution of alternative splicing provides an important mechanism for the acquisition of novel gene functions. In this work, we carried out a genome-wide phylogenetic survey of lineage-specific splicing patterns in the primate brain, via high-density exon junction array profiling of brain transcriptomes of humans, chimpanzees and rhesus macaques. We identified 509 genes showing splicing differences among these species. RT-PCR analysis of 40 exons confirmed the predicted splicing evolution of 33 exons. Of these 33 exons, outgroup analysis using rhesus macaques confirmed 13 exons with human-specific increase or decrease in transcript inclusion levels after humans diverged from chimpanzees. Some of the human-specific brain splicing patterns disrupt domains critical for protein-protein interactions, and some modulate translational efficiency of their host genes. Strikingly, for exons showing splicing differences across species, we observed a significant increase in the rate of silent substitutions within exons, coupled with accelerated sequence divergence in flanking introns. This indicates that evolution of cis-regulatory signals is a major contributor to the emergence of human-specific splicing patterns. In one gene (MAGOH), using minigene reporter assays, we demonstrated that the combination of two human-specific cis-sequence changes created its human-specific splicing pattern. Together, our data reveal widespread human-specific changes of alternative splicing in the brain and suggest an important role of splicing in the evolution of neuronal gene regulation and functions.
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Affiliation(s)
- Lan Lin
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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Crespi B, Summers K, Dorus S. Evolutionary genomics of human intellectual disability. Evol Appl 2010; 3:52-63. [PMID: 25567903 PMCID: PMC3352458 DOI: 10.1111/j.1752-4571.2009.00098.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 07/28/2009] [Indexed: 01/28/2023] Open
Abstract
Previous studies have postulated that X-linked and autosomal genes underlying human intellectual disability may have also mediated the evolution of human cognition. We have conducted the first comprehensive assessment of the extent and patterns of positive Darwinian selection on intellectual disability genes in humans. We report three main findings. First, as noted in some previous reports, intellectual disability genes with primary functions in the central nervous system exhibit a significant concentration to the X chromosome. Second, there was no evidence for a higher incidence of recent positive selection on X-linked than autosomal intellectual disability genes, nor was there a higher incidence of selection on such genes overall, compared to sets of control genes. However, the X-linked intellectual disability genes inferred to be subject to recent positive selection were concentrated in the Rho GTP-ase pathway, a key signaling pathway in neural development and function. Third, among all intellectual disability genes, there was evidence for a higher incidence of recent positive selection on genes involved in DNA repair, but not for genes involved in other functions. These results provide evidence that alterations to genes in the Rho GTP-ase and DNA-repair pathways may play especially-important roles in the evolution of human cognition and vulnerability to genetically-based intellectual disability.
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Affiliation(s)
- Bernard Crespi
- Department of Biosciences, Simon Fraser UniversityBurnaby, BC, Canada
| | - Kyle Summers
- Department of Biology, East Carolina UniversityGreenville, NC, USA
| | - Steve Dorus
- Department of Biology and Biochemistry, University of BathBath, UK
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Orban L, Sreenivasan R, Olsson PE. Long and winding roads: testis differentiation in zebrafish. Mol Cell Endocrinol 2009; 312:35-41. [PMID: 19422878 DOI: 10.1016/j.mce.2009.04.014] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 03/31/2009] [Accepted: 04/25/2009] [Indexed: 02/02/2023]
Abstract
Zebrafish sex determination, gonad differentiation and reproduction are far from being fully understood. Although the mode of sex determination is still being disputed, most experimental data point towards the lack of sex chromosomes and a multigenic sex determination system. Secondary effects from the environment and/or (xeno)hormones may influence the process, resulting in biased sex ratios. The exact time point of sex determination is unknown. Gonad differentiation involves a compulsory 'juvenile ovary' stage with subsequent transformation of the gonad into a testis in males. As the latter is a late event, there is a delay between sex determination and testis differentiation in zebrafish, in contrast to mammals. Information on the expression of several candidate genes thought to be involved in these processes has been supplemented with data from large-scale gonadal transcriptomic studies. New approaches and methodologies provide hope that answers to a number of important questions will be deciphered in the future.
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Affiliation(s)
- Laszlo Orban
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, Singapore.
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29
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Sreenivasan R, Cai M, Bartfai R, Wang X, Christoffels A, Orban L. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. PLoS One 2008; 3:e1791. [PMID: 18335061 PMCID: PMC2262149 DOI: 10.1371/journal.pone.0001791] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 02/07/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs. METHODOLOGY/PRINCIPAL FINDINGS We have identified 116638 gonad-derived zebrafish expressed sequence tags (ESTs), 21% of which were isolated in our lab. Following in silico normalization, we constructed a gonad-derived microarray comprising 6370 unique, full-length cDNAs from differentiating and adult gonads. Labeled targets from adult gonad, brain, kidney and 'rest-of-body' from both sexes were hybridized onto the microarray. Our analyses revealed 1366, 881 and 656 differentially expressed transcripts (34.7% novel) that showed highest expression in ovary, testis and both gonads respectively. Hierarchical clustering showed correlation of the two gonadal transcriptomes and their similarities to those of the brains. In addition, we have identified 276 genes showing sexually dimorphic expression both between the brains and between the gonads. By in situ hybridization, we showed that the gonadal transcripts with the strongest array signal intensities were germline-expressed. We found that five members of the GTP-binding septin gene family, from which only one member (septin 4) has previously been implicated in reproduction in mice, were all strongly expressed in the gonads. CONCLUSIONS/SIGNIFICANCE We have generated a gonad-derived zebrafish cDNA microarray and demonstrated its usefulness in identifying genes with sexually dimorphic co-expression in both the gonads and the brains. We have also provided the first evidence of large-scale differential gene expression between female and male brains of a teleost. Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations. Since several genes have been shown to play similar roles in gonadogenesis in zebrafish and other vertebrates, our array may even provide information on genetic disorders affecting gonadal phenotypes and fertility in mammals.
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Affiliation(s)
- Rajini Sreenivasan
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Minnie Cai
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Richard Bartfai
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Xingang Wang
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Alan Christoffels
- Computational Biology, Temasek Life Sciences Laboratory, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Laszlo Orban
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * To whom correspondence should be addressed. E-mail:
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30
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Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jørgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Stærfeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshøj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol 2007; 8:R45. [PMID: 17407547 PMCID: PMC1895994 DOI: 10.1186/gb-2007-8-4-r45] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 01/18/2007] [Accepted: 04/02/2007] [Indexed: 12/05/2022] Open
Abstract
A resource consisting of one million porcine ESTs is described, providing an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies. Background Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from public databases. The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages. Results Using the Distiller package, the ESTs were assembled to roughly 48,000 contigs and 73,000 singletons, of which approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues with the greatest number of different expressed genes, whereas tissues with more specialized function, such as developing liver, have fewer expressed genes. There are at least 65 high confidence housekeeping gene candidates and 876 cDNA library-specific gene candidates. We identified differential expression of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories. Conclusion This EST collection, the largest to date in pig, represents an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.
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Affiliation(s)
- Jan Gorodkin
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Susanna Cirera
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Jakob Hedegaard
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Michael J Gilchrist
- The Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, CB2 1QN, UK
| | - Frank Panitz
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Claus Jørgensen
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Karsten Scheibye-Knudsen
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Troels Arvin
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Steen Lumholdt
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Milena Sawera
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Trine Green
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Bente J Nielsen
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Jakob H Havgaard
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Carina Rosenkilde
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Jun Wang
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
- Institute of Human Genetics, University of Aarhus, Nordre Ringgade 1, DK-8000 Aarhus C, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campus Vej 55, DK-5230 Odense M, Denmark
| | - Heng Li
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
- Institute of Human Genetics, University of Aarhus, Nordre Ringgade 1, DK-8000 Aarhus C, Denmark
| | - Ruiqiang Li
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campus Vej 55, DK-5230 Odense M, Denmark
| | - Bin Liu
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Songnian Hu
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Wei Dong
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Wei Li
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Jun Yu
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Jian Wang
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Hans-Henrik Stærfeldt
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, DK-2800 Lyngby, Denmark
| | - Rasmus Wernersson
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, DK-2800 Lyngby, Denmark
| | - Lone B Madsen
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Bo Thomsen
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Henrik Hornshøj
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Zhan Bujie
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Xuegang Wang
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Xuefei Wang
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Lars Bolund
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
- Institute of Human Genetics, University of Aarhus, Nordre Ringgade 1, DK-8000 Aarhus C, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, DK-2800 Lyngby, Denmark
| | - Huanming Yang
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Christian Bendixen
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Merete Fredholm
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
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Cáceres M, Suwyn C, Maddox M, Thomas JW, Preuss TM. Increased cortical expression of two synaptogenic thrombospondins in human brain evolution. ACTA ACUST UNITED AC 2006; 17:2312-21. [PMID: 17182969 DOI: 10.1093/cercor/bhl140] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Thrombospondins are extracellular-matrix glycoproteins implicated in the control of synaptogenesis and neurite growth. Previous microarray studies suggested that one gene of this family, thrombospondin 4 (THBS4), was upregulated during human brain evolution. Using independent techniques to examine thrombospondin expression patterns in adult brain samples, we report approximately 6-fold and approximately 2-fold greater expression of THBS4 and THBS2 messenger RNA (mRNA), respectively, in human cerebral cortex compared with chimpanzees and macaques, with corresponding differences in protein levels. In humans and chimpanzees, thrombospondin expression differences were observed in the forebrain (cortex and caudate), whereas the cerebellum and most nonbrain tissues exhibited similar levels of the 2 mRNAs. Histological examination revealed THBS4 mRNA and protein expression in numerous pyramidal and glial cells in the 3 species but humans also exhibited very prominent immunostaining of the synapse-rich cortical neuropil. In humans, additionally, THBS4 antibodies labeled beta-amyloid containing plaques in Alzheimer's cases and some control cases. This is the first detailed characterization of gene-expression changes in human evolution that involve specific brain regions, including portions of cerebral cortex. Increased expression of thrombospondins in human brain evolution could result in changes in synaptic organization and plasticity, and contribute to the distinctive cognitive abilities of humans, as well as to our unique vulnerability to neurodegenerative disease.
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Affiliation(s)
- Mario Cáceres
- Division of Neuroscience and Center for Behavioral Neuroscience, Yerkes National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA 30329, USA
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