1
|
Abou Abdallah F, Abdel Massih C, Attieh C, Chebly A. The impact of mosaic loss of the Y chromosome (mLOY) in men of advanced age. Biogerontology 2024; 25:943-955. [PMID: 39223433 DOI: 10.1007/s10522-024-10133-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
The Y chromosome has long been considered to be a "genetic wasteland" harboring only few genes essentially involved in male sex development and spermatogenesis. However, the discovery of mosaic loss of the Y chromosome (mLOY) in older men has led to revisiting of the potential impact of the Y chromosome on health and the pathophysiological processes of multiple diseases such as cancer, Alzheimer's disease and cardiovascular disease. Hence, developing more sensitive techniques for the detection of mLOY has become an emergent concern. In this article, we present a comprehensive review of the literature regarding mLOY. Additionally, we discuss the emerging discoveries concerning mLOY as well as the underlying mechanisms promoting disease in men of advanced age.
Collapse
Affiliation(s)
| | | | - Charbel Attieh
- Center Jacques Loiselet for Medical Genetics and Genomics (CGGM), Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Alain Chebly
- Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon.
- Center Jacques Loiselet for Medical Genetics and Genomics (CGGM), Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon.
| |
Collapse
|
2
|
Liu P, Yu S, Zheng W, Zhang Q, Qiao J, Li Z, Deng Z, Zhang H. Identification and functional verification of Y-chromosome-specific gene typo-gyf in Bactrocera dorsalis. INSECT SCIENCE 2024; 31:1270-1284. [PMID: 38189161 DOI: 10.1111/1744-7917.13311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 01/09/2024]
Abstract
Genes on the Y chromosome play important roles in male sex determination and development. The identification of Y-chromosome-specific genes not only provides a theoretical basis for the study of male reproductive development, but also offers genetic control targets for agricultural pests. However, Y-chromosome genes are rarely characterized due to their high repeatability and high heterochromatinization, especially in the oriental fruit fly. In this study, 1 011 Y-chromosome-specific candidate sequences were screened from 2 to 4 h Bactrocera dorsalis embryo datasets with the chromosome quotient method, 6 of which were identified as Y-chromosome-specific sequences by polymerase chain reaction, including typo-gyf, a 19 126-bp DNA sequence containing a 575-amino acid open reading frame. Testicular deformation and a significant reduction in sperm number were observed after typo-gyf knockdown with RNA interference in embryos. After typo-gyf knockout with clustered regularly interspaced palindromic repeats (CRISPR) / CRISPR-associated protein 9 in the embryonic stage, the sex ratio of the emergent adults was unbalanced, with far more females than males. A genotype analysis of these females with the Y-chromosome gene MoY revealed no sex reversal. Typo-gyf knockout led to the death of XY individuals in the embryonic stage. We conclude that typo-gyf is an essential gene for male survival, and is also involved in testicular development and spermatogenesis. The identification of typo-gyf and its functional verification provide insight into the roles of Y-chromosome genes in male development.
Collapse
Affiliation(s)
- Peipei Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuning Yu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenping Zheng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiuyuan Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiao Qiao
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziniu Li
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhurong Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongyu Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
3
|
Claerhout S, Noppe H, Cohn B, Borry P. Opt-in or out? Public perspectives on forensic DNA kinship investigations within the Dutch-speaking community. Heliyon 2024; 10:e30074. [PMID: 38720757 PMCID: PMC11076844 DOI: 10.1016/j.heliyon.2024.e30074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Forensic DNA kinship investigation involves analyzing genetic relationships between individuals to offer new leads for solving (cold) cases. Familial DNA matching has become a valuable asset in criminal case investigations, especially when traditional DNA methods hit dead ends. However, concerns surrounding ethical and privacy implications raised questions about its implementation and acceptance among the general public. The present study investigated the public perspectives regarding forensic DNA kinship investigations among 1710 Dutch-speaking Belgians using an online cross-sectional survey. The questionnaire consisted of three categories, including personal information, DNA knowledge, and their opinion on several familial DNA searching and investigative genetic genealogy related questions. The participants' average DNA knowledge score was 71 %, indicating a relatively high level of understanding of DNA-related concepts. Remarkably, the study revealed that 92 % of the participants expressed willingness to cooperate as a volunteer in a forensic DNA kinship investigation, irrespective of their scientific background or educational level. Key factors influencing participation included assurance of painless sampling and robust privacy safeguards. Participants lacking familiarity with DNA hesitated more towards participating in forensic DNA analysis, referring to "the fear of the unknown". Despite ethical and privacy concerns, the highly positive attitude towards forensic DNA analysis reflects a level of empathy and willingness to contribute to the pursuit of justice. Nearly all participants (95 %) agreed to use online DNA databases for resolving violent crimes with forensic genetic genealogy, but half emphasized the need for prior informed consent, referring to the current "opt-in" system. The results underscore the need for stringent regulations and ethical oversight to ensure the responsible use of genetic data while striking a balance between public safety and the protection of individuals' privacy rights. These findings add to the growing body of evidence regarding the potential benefits of forensic DNA kinship matching as a tool in criminal investigations, suggesting its potential future utilization and legalization.
Collapse
Affiliation(s)
- Sofie Claerhout
- Laboratory for Forensic Genetics, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
- Interdisciplinary Research Facility, KU Leuven Kulak, Kortrijk, Belgium
- Centre for Sociological Research, KU Leuven, Leuven, Belgium
| | - Hanna Noppe
- Biomedical Forensic Sciences, KU Leuven, Leuven, Belgium
| | - Betty Cohn
- Institute of Public Health Genetics, University of Washington, Seattle, USA
| | - Pascal Borry
- Center of Biomedical Ethics and Law, Department of Public Health, KU Leuven, Leuven, Belgium
| |
Collapse
|
4
|
Bhattacharya S, Sadhukhan D, Saraswathy R. Role of sex in immune response and epigenetic mechanisms. Epigenetics Chromatin 2024; 17:1. [PMID: 38247002 PMCID: PMC10802034 DOI: 10.1186/s13072-024-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
The functioning of the human immune system is highly dependent on the sex of the individual, which comes by virtue of sex chromosomes and hormonal differences. Epigenetic mechanisms such as X chromosome inactivation, mosaicism, skewing, and dimorphism in X chromosome genes and Y chromosome regulatory genes create a sex-based variance in the immune response between males and females. This leads to differential susceptibility in immune-related disorders like infections, autoimmunity, and malignancies. Various naturally available immunomodulators are also available which target immune pathways containing X chromosome genes.
Collapse
Affiliation(s)
- Sombodhi Bhattacharya
- Biomedical Genetics Research Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Debasmita Sadhukhan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Radha Saraswathy
- Biomedical Genetics Research Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
| |
Collapse
|
5
|
Liu W, Zuo B, Liu W, Huo Y, Zhang N, Yang M. Long non-coding RNAs in non-small cell lung cancer: implications for preventing therapeutic resistance. Biochim Biophys Acta Rev Cancer 2023; 1878:188982. [PMID: 37734560 DOI: 10.1016/j.bbcan.2023.188982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
Lung cancer has the highest mortality and morbidity rates among all cancers worldwide. Despite many complex treatment options, including radiotherapy, chemotherapy, targeted drugs, immunotherapy, and combinations of these treatments, efficacy is low in cases of resistance to therapy, metastasis, and advanced disease, contributing to low overall survival. There is a pressing need for the discovery of novel biomarkers and therapeutic targets for the early diagnosis of lung cancer and to determine the efficacy and outcomes of drug treatments. There is now substantial evidence for the diagnostic and prognostic value of long noncoding RNAs (lncRNAs). This review briefly discusses recent findings on the roles and mechanisms of action of lncRNAs in the responses to therapy in non-small cell lung cancer.
Collapse
Affiliation(s)
- Wenjuan Liu
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China
| | - Bingli Zuo
- Human Resources Department, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China
| | - Wenting Liu
- Department of Neurology, Weifang People's Hospital, Weifang, Shandong Province 261041, China
| | - Yanfei Huo
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province 211166, China.
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province 250117, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province 211166, China.
| |
Collapse
|
6
|
García-Olivares V, Muñoz-Barrera A, Rubio-Rodríguez LA, Jáspez D, Díaz-de Usera A, Iñigo-Campos A, Veeramah KR, Alonso S, Thomas MG, Lorenzo-Salazar JM, González-Montelongo R, Flores C. Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data. Comput Struct Biotechnol J 2023; 21:4613-4618. [PMID: 37817776 PMCID: PMC10560978 DOI: 10.1016/j.csbj.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accurate reconstruction of pedigree relationships and retrieval of ancestral information. Using high-throughput sequencing (HTS) data, we present a benchmarking analysis of command-line tools for NRY haplogroup classification. The evaluation was performed using paired Illumina data from whole-genome sequencing (WGS) and whole-exome sequencing (WES) experiments from 50 unrelated donors. Additionally, as a validation, we also used paired WGS/WES datasets of 54 individuals from the 1000 Genomes Project. Finally, we evaluated the tools on data from third-generation HTS obtained from a subset of donors and one reference sample. Our results show that WES, despite typically offering less genealogical resolution than WGS, is an effective method for determining the NRY haplogroup. Y-LineageTracker and Yleaf showed the highest accuracy for WGS data, classifying precisely 98% and 96% of the samples, respectively. Yleaf outperforms all benchmarked tools in the WES data, classifying approximately 90% of the samples. Yleaf, Y-LineageTracker, and pathPhynder can correctly classify most samples (88%) sequenced with third-generation HTS. As a result, Yleaf provides the best performance for applications that use WGS and WES. Overall, our study offers researchers with a guide that allows them to select the most appropriate tool to analyze the NRY region using both second- and third-generation HTS data.
Collapse
Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Krishna R. Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, United States
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
- María Goyri Building, Biotechnology Center, Human Molecular Evolution Lab 2.08 UPV/EHU Science Park, 48940 Leioa, Bizkaia, Spain
| | - Mark G. Thomas
- UCL Genetics Institute, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom
- Research Department of Genetics, Evolution & Environment, University College London (UCL), Darwin Building, Gower Street, London WC1E 6BT, United Kingdom
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| |
Collapse
|
7
|
Zhang Y, Jiang S, He F, Tian Y, Hu H, Gao L, Zhang L, Chen A, Hu Y, Fan L, Yang C, Zhou B, Liu D, Zhou Z, Su Y, Qin L, Wang Y, He H, Lu J, Xiao P, Hu S, Wang QF. Single-cell transcriptomics reveals multiple chemoresistant properties in leukemic stem and progenitor cells in pediatric AML. Genome Biol 2023; 24:199. [PMID: 37653425 PMCID: PMC10472599 DOI: 10.1186/s13059-023-03031-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Cancer patients can achieve dramatic responses to chemotherapy yet retain resistant tumor cells, which ultimately results in relapse. Although xenograft model studies have identified several cellular and molecular features that are associated with chemoresistance in acute myeloid leukemia (AML), to what extent AML patients exhibit these properties remains largely unknown. RESULTS We apply single-cell RNA sequencing to paired pre- and post-chemotherapy whole bone marrow samples obtained from 13 pediatric AML patients who had achieved disease remission, and distinguish AML clusters from normal cells based on their unique transcriptomic profiles. Approximately 50% of leukemic stem and progenitor populations actively express leukemia stem cell (LSC) and oxidative phosphorylation (OXPHOS) signatures, respectively. These clusters have a higher chance of tolerating therapy and exhibit an enhanced metabolic program in response to treatment. Interestingly, the transmembrane receptor CD69 is highly expressed in chemoresistant hematopoietic stem cell (HSC)-like populations (named the CD69+ HSC-like subpopulation). Furthermore, overexpression of CD69 results in suppression of the mTOR signaling pathway and promotion of cell quiescence and adhesion in vitro. Finally, the presence of CD69+ HSC-like cells is associated with unfavorable genetic mutations, the persistence of residual tumor cells in chemotherapy, and poor outcomes in independent pediatric and adult public AML cohorts. CONCLUSIONS Our analysis reveals leukemia stem cell and OXPHOS as two major chemoresistant features in human AML patients. CD69 may serve as a potential biomarker in defining a subpopulation of chemoresistant leukemia stem cells. These findings have important implications for targeting residual chemo-surviving AML cells.
Collapse
Affiliation(s)
- Yongping Zhang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Shuting Jiang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuhong He
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Tian
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Haiyang Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Gao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Lin Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aili Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yixin Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Liyan Fan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Chun Yang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Bi Zhou
- SuZhou Hospital of Anhui Medical University, Suzhou, China
| | - Dan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Zihan Zhou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxun Su
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Qin
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Hailong He
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Jun Lu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Peifang Xiao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Shaoyan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China.
| | - Qian-Fei Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
8
|
Lutshumba J, Wilcock DM, Monson NL, Stowe AM. Sex-based differences in effector cells of the adaptive immune system during Alzheimer's disease and related dementias. Neurobiol Dis 2023; 184:106202. [PMID: 37330146 PMCID: PMC10481581 DOI: 10.1016/j.nbd.2023.106202] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Neurological conditions such as Alzheimer's disease (AD) and related dementias (ADRD) present with many challenges due to the heterogeneity of the related disease(s), making it difficult to develop effective treatments. Additionally, the progression of ADRD-related pathologies presents differently between men and women. With two-thirds of the population affected with ADRD being women, ADRD has presented itself with a bias toward the female population. However, studies of ADRD generally do not incorporate sex-based differences in investigating the development and progression of the disease, which is detrimental to understanding and treating dementia. Additionally, recent implications for the adaptive immune system in the development of ADRD bring in new factors to be considered as part of the disease, including sex-based differences in immune response(s) during ADRD development. Here, we review the sex-based differences of pathological hallmarks of ADRD presentation and progression, sex-based differences in the adaptive immune system and how it changes with ADRD, and the importance of precision medicine in the development of a more targeted and personalized treatment for this devastating and prevalent neurodegenerative condition.
Collapse
Affiliation(s)
- Jenny Lutshumba
- Department of Neurology, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Donna M Wilcock
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States of America; Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Nancy L Monson
- Department of Neurology and Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Ann M Stowe
- Department of Neurology, College of Medicine, University of Kentucky, Lexington, KY, United States of America; Center for Advanced Translational Stroke Science, University of Kentucky, Lexington, KY, United States of America.
| |
Collapse
|
9
|
Rho NY, Mogas T, King WA, Favetta LA. Testis-Specific Protein Y-Encoded (TSPY) Is Required for Male Early Embryo Development in Bos taurus. Int J Mol Sci 2023; 24:ijms24043349. [PMID: 36834761 PMCID: PMC9959854 DOI: 10.3390/ijms24043349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/27/2023] [Accepted: 02/05/2023] [Indexed: 02/10/2023] Open
Abstract
TSPY is a highly conserved multi-copy gene with copy number variation (CNV) among species, populations, individuals and within families. TSPY has been shown to be involved in male development and fertility. However, information on TSPY in embryonic preimplantation stages is lacking. This study aims to determine whether TSPY CNV plays a role in male early development. Using sex-sorted semen from three different bulls, male embryo groups referred to as 1Y, 2Y and 3Y, were produced by in vitro fertilization (IVF). Developmental competency was assessed by cleavage and blastocyst rates. Embryos at different developmental stages were analyzed for TSPY CN, mRNA and protein levels. Furthermore, TSPY RNA knockdown was performed and embryos were assessed as per above. Development competency was only significantly different at the blastocyst stage, with 3Y being the highest. TSPY CNV and transcripts were detected in the range of 20-75 CN for 1Y, 20-65 CN for 2Y and 20-150 CN for 3Y, with corresponding averages of 30.2 ± 2.5, 33.0 ± 2.4 and 82.3 ± 3.6 copies, respectively. TSPY transcripts exhibited an inverse logarithmic pattern, with 3Y showing significantly higher TSPY. TSPY proteins, detected only in blastocysts, were not significantly different among groups. TSPY knockdown resulted in a significant TSPY depletion (p < 0.05), with no development observed after the eight-cell stage in male embryos, suggesting that TSPY is required for male embryo development.
Collapse
Affiliation(s)
- Na-Young Rho
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Teresa Mogas
- Department of Medicine and Animal Surgery, Autonomous University of Barcelona, Cerdanyola del Vallés, 08193 Barcelona, Spain
| | - W. Allan King
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
- Karyotekk Inc., Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Laura A. Favetta
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence:
| |
Collapse
|
10
|
García-Fernández C, Lizano E, Telford M, Olalde Í, de Cid R, Larmuseau MHD, M. de Pancorbo M, Calafell F. Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition. Sci Rep 2022; 12:20708. [PMID: 36456614 PMCID: PMC9715704 DOI: 10.1038/s41598-022-25200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.9 Mbp or 0.14% of a diploid human genome. Consequently, investing in whole-genome sequencing to resolve Y-chromosome questions is poorly efficient. Here we use, as an alternative, target enrichment technology to greatly increase sequencing effectiveness, validating and applying the technique to 181 males, for 162 of whom we obtained a positive result. Additionally, 75 samples sequenced for the whole genome were also included, for a total sample size of 237. These samples were chosen for their Y chromosome haplogroup: R1b-DF27. In the context of European populations, and particularly in Iberia, this haplogroup stands out for its high frequency and its demographic history. Current evidence indicates that the diffusion of this haplogroup is related to the population movements that mark the cultural Bronze Age transition, making it remarkably interesting for population geneticists. The results of this study show the effects of the rapid radiation of the haplogroup in Spain, as even with the higher discriminating power of whole sequences, most haplotypes still fall within the R1b-DF27* paragroup rather than in the main derived branches. However, we were able to refine the ISOGG 2019-2020 phylogeny, and its two main subbranches, namely L176.2 and Z272, which present geographical differentiation between the Atlantic and Mediterranean coasts of Iberia.
Collapse
Affiliation(s)
- Carla García-Fernández
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Esther Lizano
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain ,grid.7080.f0000 0001 2296 0625Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marco Telford
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Íñigo Olalde
- grid.11480.3c0000000121671098BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain ,grid.424810.b0000 0004 0467 2314Ikerbasque—Basque Foundation of Science, Bilbao, Spain
| | - Rafael de Cid
- grid.429186.00000 0004 1756 6852Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Maarten H. D. Larmuseau
- grid.5596.f0000 0001 0668 7884Laboratory of Human Genetic Genealogy, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.5284.b0000 0001 0790 3681ARCHES–Antwerp Cultural Heritage Sciences, Faculty of Design Sciences, University of Antwerp, Antwerp, Belgium ,Histories Vzw, Gent, Belgium
| | - Marian M. de Pancorbo
- grid.11480.3c0000000121671098BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesc Calafell
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| |
Collapse
|
11
|
Pei S, Xu H, Wang L, Li F, Li W, Yue X. Copy number variation of ZNF280BY across eight sheep breeds and its association with testicular size of Hu sheep. J Anim Sci 2022; 100:6624001. [PMID: 35775620 DOI: 10.1093/jas/skac232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
ZNF280BY, a bovid-specific Y chromosome gene, was firstly found to be highly expressed in bovine testis, indicating it may play important roles in testicular development and male fertility. In this study, we firstly cloned the full-length cDNA of ovine ZNF280BY containing 1993 bp, and with a 1632 bp open reading frame. ZNF280BY was predominantly expressed in the testis, and its expression level was significantly higher in large testis than in small testis in Hu sheep at 6 months of age. In addition, the expression level of ZNF280BY significantly increased during testicular development, showing the highest expression level at 12 months of age. ZNF280BY showed copy number variation (CNV) in 723 rams from eight sheep breeds, ranging from 17 to 514 copies, with a median copy number of 188. Pearson correlation analysis showed that the CNV of ZNF280BY was negatively correlated with testis size in Hu sheep. Furthermore, its mRNA expression level in testis had no significant correlation with the CNV but was significantly correlated with testis size. This study concluded that the expression of ZNF280BY was closely related to testicular development, and the CNV of ZNF280BY could be used as an important genetic marker to evaluate the ram reproductive capacity at an early stage in Hu sheep.
Collapse
Affiliation(s)
- Shengwei Pei
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Haiyue Xu
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Li Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Fadi Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Wanhong Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| |
Collapse
|
12
|
Hadi S, Yao J, Adnan A. Editorial: Role of Y Chromosome in Molecular Anthropology, Forensics, and Genetic Genealogy. Front Genet 2022; 13:863455. [PMID: 35754810 PMCID: PMC9218708 DOI: 10.3389/fgene.2022.863455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/09/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Jun Yao
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
| | - Atif Adnan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
| |
Collapse
|
13
|
Gomes-Duarte A, Venø MT, de Wit M, Senthilkumar K, Broekhoven MH, van den Herik J, Heeres FR, van Rossum D, Rybiczka-Tesulov M, Legnini I, van Rijen PC, van Eijsden P, Gosselaar PH, Rajewsky N, Kjems J, Vangoor VR, Pasterkamp RJ. Expression of Circ_Satb1 Is Decreased in Mesial Temporal Lobe Epilepsy and Regulates Dendritic Spine Morphology. Front Mol Neurosci 2022; 15:832133. [PMID: 35310884 PMCID: PMC8927295 DOI: 10.3389/fnmol.2022.832133] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/10/2022] [Indexed: 11/24/2022] Open
Abstract
Mesial temporal lobe epilepsy (mTLE) is a chronic disease characterized by recurrent seizures that originate in the temporal lobes of the brain. Anti-epileptic drugs (AEDs) are the standard treatment for managing seizures in mTLE patients, but are frequently ineffective. Resective surgery is an option for some patients, but does not guarantee a postoperative seizure-free period. Therefore, further insight is needed into the pathogenesis of mTLE to enable the design of new therapeutic strategies. Circular RNAs (circRNAs) have been identified as important regulators of neuronal function and have been implicated in epilepsy. However, the mechanisms through which circRNAs contribute to epileptogenesis remain unknown. Here, we determine the circRNA transcriptome of the hippocampus and cortex of mTLE patients by using RNA-seq. We report 333 differentially expressed (DE) circRNAs between healthy individuals and mTLE patients, of which 23 circRNAs displayed significant adjusted p-values following multiple testing correction. Interestingly, hippocampal expression of circ_Satb1, a circRNA derived from special AT-rich sequence binding protein 1 (SATB1), is decreased in both mTLE patients and in experimental epilepsy. Our work shows that circ_Satb1 displays dynamic patterns of neuronal expression in vitro and in vivo. Further, circ_Satb1-specific knockdown using CRISPR/CasRx approaches in hippocampal cultures leads to defects in dendritic spine morphology, a cellular hallmark of mTLE. Overall, our results identify a novel epilepsy-associated circRNA with disease-specific expression and previously unidentified cellular effects that are relevant for epileptogenesis.
Collapse
Affiliation(s)
- Andreia Gomes-Duarte
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Morten T. Venø
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Omiics ApS, Aarhus, Denmark
| | - Marina de Wit
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ketharini Senthilkumar
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mark H. Broekhoven
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Joëlle van den Herik
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Fleur R. Heeres
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Daniëlle van Rossum
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mateja Rybiczka-Tesulov
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ivano Legnini
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Peter C. van Rijen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Pieter van Eijsden
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Peter H. Gosselaar
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Vamshidhar R. Vangoor
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - R. Jeroen Pasterkamp
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: R. Jeroen Pasterkamp,
| |
Collapse
|
14
|
Li M, Ji Y, Wang D, Zhang Y, Zhang H, Tang Y, Lin G, Hu L. Evaluation of Laser Confocal Raman Spectroscopy as a Non-Invasive Method for Detecting Sperm DNA Contents. Front Physiol 2022; 13:827941. [PMID: 35211034 PMCID: PMC8861532 DOI: 10.3389/fphys.2022.827941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/13/2022] [Indexed: 11/13/2022] Open
Abstract
RESEARCH QUESTION Is Raman spectroscopy an efficient and accurate method to detect sperm chromosome balance state by DNA content differences? DESIGN Semen samples were provided by diploid healthy men, and the analysis parameters met the current World Health Organization standards. The DNA content was assessed by analysis of the corresponding spectra obtained from a laser confocal Raman spectroscope. The sperm sex chromosome information was obtained by fluorescence in situ hybridization (FISH). Comparative analysis was performed between FISH results and Raman spectral analysis results. RESULTS Different parts of the sperm head showed different spectral signal intensities, which indicated that there were different chemical components. Standard principal component analysis (PCA) can preliminarily classify sperm with different DNA contents into two groups. Further analysis showed that there were significant differences in the 785 DNA backbone peaks and 714-1,162 cm-1 DNA skeleton regions among sperm with different DNA contents. The peak and regional peak of the DNA skeleton of X sperm were significantly higher than those of Y sperm (X vs. Y, p < 0.05). The above sperm types were confirmed by FISH. ROC curve analysis shows that there is a correlation between the Raman spectrum data and FISH results. CONCLUSION Raman spectroscopy can identify X and Y sperms by analyzing the DNA content difference. However, the accuracy of the detection still needs to be improved. Nevertheless, Raman spectroscopy has a potential application value in the field of sperm aneuploidy detection and may even be used as a non-invasive predictor of sperm aneuploid state in preimplantation genetic testing (PGT-A).
Collapse
Affiliation(s)
- Mengge Li
- National Engineering and Research Center of Human Stem Cells, Changsha, China.,Hunan Guangxiu Hospital, Changsha, China
| | - Yaxing Ji
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | | | | | - Huan Zhang
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
| | - Yi Tang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
| | - Ge Lin
- National Engineering and Research Center of Human Stem Cells, Changsha, China.,NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
| | - Liang Hu
- National Engineering and Research Center of Human Stem Cells, Changsha, China.,NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, China
| |
Collapse
|
15
|
Maier MC, McInerney MRA, Graves JAM, Charchar FJ. Noncoding Genes on Sex Chromosomes and Their Function in Sex Determination, Dosage Compensation, Male Traits, and Diseases. Sex Dev 2021; 15:432-440. [PMID: 34794153 DOI: 10.1159/000519622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022] Open
Abstract
The mammalian Y chromosome has evolved in many species into a specialized chromosome that contributes to sex development among other male phenotypes. This function is well studied in terms of protein-coding genes. Less is known about the noncoding genome on the Y chromosome and its contribution to both sex development and other traits. Once considered junk genetic material, noncoding RNAs are now known to contribute to the regulation of gene expression and to play an important role in refining cellular functions. The prime examples are noncoding genes on the X chromosome, which mitigate the differential dosage of genes on sex chromosomes. Here, we discuss the evolution of noncoding RNAs on the Y chromosome and the emerging evidence of how micro, long, and circular noncoding RNAs transcribed from the Y chromosome contribute to sex differentiation. We briefly touch on emerging evidence that these noncoding RNAs also contribute to some other important clinical phenotypes in humans.
Collapse
Affiliation(s)
- Michelle C Maier
- Health Innovation & Transformation Centre, Federation University, Mt Helen, Victoria, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia
| | - Molly-Rose A McInerney
- Health Innovation & Transformation Centre, Federation University, Mt Helen, Victoria, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia
| | | | - Fadi J Charchar
- Health Innovation & Transformation Centre, Federation University, Mt Helen, Victoria, Australia.,Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
16
|
Rooda I, Kaselt B, Liivrand M, Smolander OP, Salumets A, Velthut-Meikas A. Hsa-mir-548 family expression in human reproductive tissues. BMC Genom Data 2021; 22:40. [PMID: 34625017 PMCID: PMC8501715 DOI: 10.1186/s12863-021-00997-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Hsa-miR-548ba expressed in ovarian granulosa cells targets PTEN and LIFR, which are essential for ovarian follicle activation and growth. The expression pattern of hsa-miR-548ba correlates with its host gene follicle-stimulating hormone receptor (FSHR), and FSH has a positive influence on hsa-miR-548ba expression. However, hsa-miR-548ba is a member of a large hsa-mir-548 family with potentially overlapping targets. The current study aims to investigate the co-expression of hsa-mir-548 family members in FSHR-positive reproductive tissues and to explore the potential co-regulation of pathways. RESULTS For the above-described analysis, small RNA sequencing data from public data repositories were used. Sequencing results revealed that hsa-miR-548ba was expressed at the highest level in the ovarian granulosa cells and uterine myometrial samples together with another twelve and one hsa-miR-548 family members, respectively. Pathway enrichment analysis of microRNA targets in the ovarian samples revealed the hsa-miR-548ba and hsa-miR-548b-5p co-regulation of RAB geranylgeranylation in mural granulosa cells. Moreover, other hsa-mir-548 family members co-regulate pathways essential for ovarian functions (PIP3 activates AKT signalling and signalling by ERBB4). In addition to hsa-miR-548ba, hsa-miR-548o-3p is expressed in the myometrium, which separately targets the peroxisome proliferator-activated receptor alpha (PPARA) pathway. CONCLUSION This study reveals that hsa-mir-548 family members are expressed in variable combinations in the reproductive tract, where they potentially fulfil different regulatory roles. The results provide a reference for further studies of the hsa-mir-548 family role in the reproductive tract.
Collapse
Affiliation(s)
- Ilmatar Rooda
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.
- Competence Centre on Health Technologies, Teaduspargi 13, 50411, Tartu, Estonia.
| | - Birgitta Kaselt
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Maria Liivrand
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Olli-Pekka Smolander
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Teaduspargi 13, 50411, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 14186, Stockholm, Sweden
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa St. 8, 50406, Tartu, Estonia
- Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Agne Velthut-Meikas
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| |
Collapse
|
17
|
The Y chromosome and its use in forensic DNA analysis. Emerg Top Life Sci 2021; 5:427-441. [PMID: 34533187 PMCID: PMC8457770 DOI: 10.1042/etls20200339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022]
Abstract
Originally relatively ignored in forensic investigations because its genetic analysis lacks inference of individual identification, the value of Y chromosome analysis has been proven in cases of sexual assault, particularly where the amount of material left by a male assailant is limited in comparison with female DNA. All routine analysis of autosomal DNA, however, targets a gene (AMELY) on the Y chromosome in order to identify the sex of the DNA source and this is discussed in the context of the genetic structure of this male-specific chromosome. Short-tandem repeat markers on the chromosome are tested in dedicated multiplexes that have developed over time and these are described alongside international guidance as to their use in a forensic setting. As a marker of lineage, the Y chromosome provides additional tools to assist in the inference of ancestry, both geographical and familial and the value of Y chromosome testing is illustrated through descriptions of cases of criminal and historical interest. A decision to analyse the Y chromosome has to be considered in the context, not only of the circumstances of the case, but also with regard to the ethical questions it might raise, and these are discussed in relation to the cases that have been described in more detail in the accompanying online supplementary material.
Collapse
|
18
|
Yuen W, Golin AP, Flannigan R, Schlegel PN. Histology and sperm retrieval among men with Y chromosome microdeletions. Transl Androl Urol 2021; 10:1442-1456. [PMID: 33850779 PMCID: PMC8039602 DOI: 10.21037/tau.2020.03.35] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
In this review of Y chromosome microdeletions, azoospermia factor (AZF) deletion subtypes, histological features and microTESE sperm retrieval rates are summarized after a systematic literature review. PubMed was searched and papers were identified using Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Approximately half of infertile couples have a male factor contributing to their infertility. One of the most common genetic etiologies are Y chromosome microdeletions. Men with Y chromosome microdeletions may have rare sperm available in the ejaculate or undergo surgical sperm retrieval and subsequent intracytoplasmic sperm injection to produce offspring. Azoospermia or severe oligozoospermia are the most common semen analysis findings found in men with Y chromosome microdeletions, associated with impaired spermatogenesis. Men with complete deletions of azoospermia factor a, b, or a combination of any loci have severely impaired spermatogenesis and are nearly always azoospermic with no sperm retrievable from the testis. Deletions of the azoospermia factor c or d often have sperm production and the highest likelihood of a successful sperm retrieval. In men with AZFc deletions, histologically, 46% of men demonstrate Sertoli cell only syndrome on biopsy, whereas 38.2% have maturation arrest and 15.7% have hypospermatogenesis. The microTESE sperm retrieval rates in AZFc-deleted men range from 13-100% based on the 32 studies analyzed, with a mean sperm retrieval rate of 47%.
Collapse
Affiliation(s)
- Wallace Yuen
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Andrew P Golin
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ryan Flannigan
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Urology, Weill Cornell Medicine, New York, NY, USA
| | - Peter N Schlegel
- Department of Urology, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
19
|
Gomes-Duarte A, Bauer S, Venø MT, Norwood BA, Henshall DC, Kjems J, Rosenow F, Vangoor VR, Pasterkamp RJ. Enrichment of Circular RNA Expression Deregulation at the Transition to Recurrent Spontaneous Seizures in Experimental Temporal Lobe Epilepsy. Front Genet 2021; 12:627907. [PMID: 33584828 PMCID: PMC7876452 DOI: 10.3389/fgene.2021.627907] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Mesial temporal lobe epilepsy (mTLE) is a common form of epilepsy and is characterized by recurrent spontaneous seizures originating from the temporal lobe. The majority of mTLE patients develop pharmacoresistance to available anti-epileptic drugs (AEDs) while exhibiting severe pathological changes that can include hippocampal atrophy, neuronal death, gliosis and chronic seizures. The molecular mechanisms leading to mTLE remain incompletely understood, but are known to include defects in post-transcriptional gene expression regulation, including in non-coding RNAs (ncRNAs). Circular RNAs (circRNAs) are a class of recently rediscovered ncRNAs with high levels of expression in the brain and proposed roles in diverse neuronal processes. To explore a potential role for circRNAs in epilepsy, RNA-sequencing (RNA-seq) was performed on hippocampal tissue from a rat perforant pathway stimulation (PPS) model of TLE at different post-stimulation time points. This analysis revealed 218 differentially expressed (DE) circRNAs. Remarkably, the majority of these circRNAs were changed at the time of the occurrence of the first spontaneous seizure (DOFS). The expression pattern of two circRNAs, circ_Arhgap4 and circ_Nav3, was further validated and linked to miR-6328 and miR-10b-3p target regulation, respectively. This is the first study to examine the regulation of circRNAs during the development of epilepsy. It reveals an intriguing link between circRNA deregulation and the transition of brain networks into the state of spontaneous seizure activity. Together, our results provide a molecular framework for further understanding the role and mechanism-of-action of circRNAs in TLE.
Collapse
Affiliation(s)
- Andreia Gomes-Duarte
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Sebastian Bauer
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University Frankfurt, Frankfurt, Germany
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
| | - Morten T. Venø
- Interdisciplinary Nanoscience Centre, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Omiics ApS, Aarhus, Denmark
| | - Braxton A. Norwood
- Department of Neuroscience, Expesicor Inc., Kalispell, MT, United States
- Diagnostics Development, FYR Diagnostics, Missoula, MT, United States
| | - David C. Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- FutureNeuro, The Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Centre, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Felix Rosenow
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University Frankfurt, Frankfurt, Germany
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
| | - Vamshidhar R. Vangoor
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - R. Jeroen Pasterkamp
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
20
|
Rausch C, Weber P, Prorok P, Hörl D, Maiser A, Lehmkuhl A, Chagin VO, Casas-Delucchi CS, Leonhardt H, Cardoso MC. Developmental differences in genome replication program and origin activation. Nucleic Acids Res 2021; 48:12751-12777. [PMID: 33264404 PMCID: PMC7736824 DOI: 10.1093/nar/gkaa1124] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
To ensure error-free duplication of all (epi)genetic information once per cell cycle, DNA replication follows a cell type and developmental stage specific spatio-temporal program. Here, we analyze the spatio-temporal DNA replication progression in (un)differentiated mouse embryonic stem (mES) cells. Whereas telomeres replicate throughout S-phase, we observe mid S-phase replication of (peri)centromeric heterochromatin in mES cells, which switches to late S-phase replication upon differentiation. This replication timing reversal correlates with and depends on an increase in condensation and a decrease in acetylation of chromatin. We further find synchronous duplication of the Y chromosome, marking the end of S-phase, irrespectively of the pluripotency state. Using a combination of single-molecule and super-resolution microscopy, we measure molecular properties of the mES cell replicon, the number of replication foci active in parallel and their spatial clustering. We conclude that each replication nanofocus in mES cells corresponds to an individual replicon, with up to one quarter representing unidirectional forks. Furthermore, with molecular combing and genome-wide origin mapping analyses, we find that mES cells activate twice as many origins spaced at half the distance than somatic cells. Altogether, our results highlight fundamental developmental differences on progression of genome replication and origin activation in pluripotent cells.
Collapse
Affiliation(s)
- Cathia Rausch
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Patrick Weber
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Paulina Prorok
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - David Hörl
- Department of Biology II, LMU Munich, 81377 Munich, Germany
| | - Andreas Maiser
- Department of Biology II, LMU Munich, 81377 Munich, Germany
| | - Anne Lehmkuhl
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Vadim O Chagin
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.,Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
21
|
Pandey A, Jaiswal A, Tiwari M, Ali A, Sharma R. Yq AZF microdeletions in male infertility: An update on the phenotypic spectrum, epidemiology and diagnostics. ASIAN PACIFIC JOURNAL OF REPRODUCTION 2021. [DOI: 10.4103/2305-0500.326718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
22
|
Uno N, Kaku N, Morinaga Y, Hasegawa H, Yanagihara K. Flow cytometry assay for the detection of single-copy DNA in human lymphocytes. Nucleic Acids Res 2020; 48:e86. [PMID: 32544240 PMCID: PMC7470942 DOI: 10.1093/nar/gkaa515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/09/2020] [Accepted: 06/05/2020] [Indexed: 11/23/2022] Open
Abstract
Specific nucleic acid sequences can be detected in individual cells by in situ hybridization. However, when very few copies of a target sequence are present per cell, its signal is undetectable by flow cytometry. Although various approaches have been developed to increase fluorescence signals for in situ hybridization, flow cytometric detection of specific genomic DNA sequences has not been established. Here, we present a flow cytometry assay for detection of single-copy genomic sequences in human lymphocytes using in situ PCR with universal energy transfer-labelled primers.
Collapse
Affiliation(s)
- Naoki Uno
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| | - Norihito Kaku
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| | - Yoshitomo Morinaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences. Nagasaki 852-8501, Japan
| |
Collapse
|
23
|
Navarro-Romero MT, Muñoz MDL, Alcala-Castañeda E, Terreros-Espinosa E, Domínguez-de-la-Cruz E, García-Hernández N, Moreno-Galeana MÁ. A novel method of male sex identification of human ancient skeletal remains. Chromosome Res 2020; 28:277-291. [PMID: 32621020 DOI: 10.1007/s10577-020-09634-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 10/23/2022]
Abstract
Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in subadult, or fragmented, incomplete skeletons or when the DNA is highly degraded. Most of the methods include the identification of the male and female sexes, but the absence of a specific marker for the males does not mean that the sample obtained was from a female. This study aims (1) to identify new male-specific regions that allow male identification; (2) to contrast the effectiveness of these markers against AMELX/AMELY and anthropometric measurement procedures; and (3) to test the efficacy of these markers in archaeological samples. For the first two aims, we used known sex samples, and for the third aim, we used samples from different archaeological sites. A novel molecular technique to identify male-specific regions by amplification of TTTY7, TSPY3, TTTY2, and TTTY22 genes of the human Y chromosome was developed. The results showed amplification of the specific DNA regions of Y chromosome in male individuals, with no amplification being observed in any of the female samples, confirming their specificity for male individuals. This approach complements the current procedures, such as the AMELX/AMELY test and anthropometric principle.
Collapse
Affiliation(s)
- María Teresa Navarro-Romero
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, C.P. 7360, Mexico City, Mexico
| | - María de Lourdes Muñoz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, C.P. 7360, Mexico City, Mexico.
| | - Enrique Alcala-Castañeda
- Department of Archaeological Studies, Instituto Nacional de Antropología e Historia, Lic. Verdad 3, Centro Histórico, 06000, Mexico City, Mexico
| | - Eladio Terreros-Espinosa
- Templo Mayor Museum, Instituto Nacional de Antropología e Historia, Seminario 8, Centro Histórico, 06060, Mexico City, Mexico
| | - Eduardo Domínguez-de-la-Cruz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, C.P. 7360, Mexico City, Mexico
| | - Normand García-Hernández
- Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad Hospital de Pediatría "Dr. Silvestre Frenk Freud", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Av. Cuauhtémoc 330, Doctores, 06720, Mexico City, Mexico
| | - Miguel Ángel Moreno-Galeana
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, C.P. 7360, Mexico City, Mexico
| |
Collapse
|
24
|
Brownmiller T, Juric JA, Ivey AD, Harvey BM, Westemeier ES, Winters MT, Stevens AM, Stanley AN, Hayes KE, Sprowls SA, Ammer ASG, Walker M, Bey EA, Wu X, Lim ZF, Zhu L, Wen S, Hu G, Ma PC, Martinez I. Y Chromosome LncRNA Are Involved in Radiation Response of Male Non-Small Cell Lung Cancer Cells. Cancer Res 2020; 80:4046-4057. [PMID: 32616503 DOI: 10.1158/0008-5472.can-19-4032] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/01/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022]
Abstract
Numerous studies have implicated changes in the Y chromosome in male cancers, yet few have investigated the biological importance of Y chromosome noncoding RNA. Here we identify a group of Y chromosome-expressed long noncoding RNA (lncRNA) that are involved in male non-small cell lung cancer (NSCLC) radiation sensitivity. Radiosensitive male NSCLC cell lines demonstrated a dose-dependent induction of linc-SPRY3-2/3/4 following irradiation, which was not observed in radioresistant male NSCLC cell lines. Cytogenetics revealed the loss of chromosome Y (LOY) in the radioresistant male NSCLC cell lines. Gain- and loss-of-function experiments indicated that linc-SPRY3-2/3/4 transcripts affect cell viability and apoptosis. Computational prediction of RNA binding proteins (RBP) motifs and UV-cross-linking and immunoprecipitation (CLIP) assays identified IGF2BP3, an RBP involved in mRNA stability, as a binding partner for linc-SPRY3-2/3/4 RNA. The presence of linc-SPRY3-2/3/4 reduced the half-life of known IGF2BP3 binding mRNA, such as the antiapoptotic HMGA2 mRNA, as well as the oncogenic c-MYC mRNA. Assessment of Y chromosome in NSCLC tissue microarrays and expression of linc-SPRY3-2/3/4 in NSCLC RNA-seq and microarray data revealed a negative correlation between the loss of the Y chromosome or linc-SPRY3-2/3/4 and overall survival. Thus, linc-SPRY3-2/3/4 expression and LOY could represent an important marker of radiotherapy in NSCLC. SIGNIFICANCE: This study describes previously unknown Y chromosome-expressed lncRNA regulators of radiation response in male NSCLC and show a correlation between loss of chromosome Y and radioresistance. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/19/4046/F1.large.jpg.
Collapse
Affiliation(s)
- Tayvia Brownmiller
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Jamie A Juric
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Abby D Ivey
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Brandon M Harvey
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Emily S Westemeier
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Michael T Winters
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Alyson M Stevens
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Alana N Stanley
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Karen E Hayes
- Modulation Therapeutics, West Virginia University, Morgantown, West Virginia
| | - Samuel A Sprowls
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia
| | - Amanda S Gatesman Ammer
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Mackenzee Walker
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Erik A Bey
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, Indiana
| | - Xiaoliang Wu
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Zuan-Fu Lim
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania.,Cancer Cell Biology Program, West Virginia University School of Graduate Studies, West Virginia University, Morgantown, West Virginia
| | - Lin Zhu
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Sijin Wen
- Department of Biostatistics, School of Public Health, West Virginia University, Morgantown, West Virginia
| | - Gangqing Hu
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia.,Bioinformatics Core, West Virginia University, Morgantown, West Virginia
| | - Patrick C Ma
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Ivan Martinez
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia.
| |
Collapse
|
25
|
Bush SJ, Connor TR, Peto TE, Crook DW, Walker AS. Evaluation of methods for detecting human reads in microbial sequencing datasets. Microb Genom 2020; 6:mgen000393. [PMID: 32558637 PMCID: PMC7478626 DOI: 10.1099/mgen.0.000393] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Sequencing data from host-associated microbes can often be contaminated by the body of the investigator or research subject. Human DNA is typically removed from microbial reads either by subtractive alignment (dropping all reads that map to the human genome) or by using a read classification tool to predict those of human origin, and then discarding them. To inform best practice guidelines, we benchmarked eight alignment-based and two classification-based methods of human read detection using simulated data from 10 clinically prevalent bacteria and three viruses, into which contaminating human reads had been added. While the majority of methods successfully detected >99 % of the human reads, they were distinguishable by variance. The most precise methods, with negligible variance, were Bowtie2 and SNAP, both of which misidentified few, if any, bacterial reads (and no viral reads) as human. While correctly detecting a similar number of human reads, methods based on taxonomic classification, such as Kraken2 and Centrifuge, could misclassify bacterial reads as human, although the extent of this was species-specific. Among the most sensitive methods of human read detection was BWA, although this also made the greatest number of false positive classifications. Across all methods, the set of human reads not identified as such, although often representing <0.1 % of the total reads, were non-randomly distributed along the human genome with many originating from the repeat-rich sex chromosomes. For viral reads and longer (>300 bp) bacterial reads, the highest performing approaches were classification-based, using Kraken2 or Centrifuge. For shorter (c. 150 bp) bacterial reads, combining multiple methods of human read detection maximized the recovery of human reads from contaminated short read datasets without being compromised by false positives. A particularly high-performance approach with shorter bacterial reads was a two-stage classification using Bowtie2 followed by SNAP. Using this approach, we re-examined 11 577 publicly archived bacterial read sets for hitherto undetected human contamination. We were able to extract a sufficient number of reads to call known human SNPs, including those with clinical significance, in 6 % of the samples. These results show that phenotypically distinct human sequence is detectable in publicly archived microbial read datasets.
Collapse
Affiliation(s)
- Stephen J. Bush
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas R. Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, UK
- Public Health Wales, University Hospital of Wales, Cardiff, UK
| | - Tim E.A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Research Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| |
Collapse
|
26
|
Kloc M, Ghobrial RM, Kubiak JZ. The Role of Genetic Sex and Mitochondria in Response to COVID-19 Infection. Int Arch Allergy Immunol 2020; 181:629-634. [PMID: 32564017 PMCID: PMC7360490 DOI: 10.1159/000508560] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/08/2020] [Indexed: 12/14/2022] Open
Abstract
The difference between the female and male immune response to COVID-19 infection, and infections in general, is multifactorial. The well-known determiners of the immune response, such as X and Y chromosomes, sex hormones, and microbiota, are functionally interconnected and influence each other in shaping the organism's immunity. We focus our commentary on the interplay between the genetic sex and mitochondria and how this may affect a sex-dependent immune response in COVID-19 infection. Realizing the existence of these interactions may help in designing novel methods or fine-tuning the existing and routine therapies to fight COVID-19 and other infections.
Collapse
Affiliation(s)
- Malgorzata Kloc
- The Houston Methodist Research Institute, Houston, Texas, USA,
- Department of Surgery, The Houston Methodist Hospital, Houston, Texas, USA,
- Department of Genetics, M.D. Anderson Cancer Center, The University of Texas, Houston, Texas, USA,
| | - Rafik Mark Ghobrial
- The Houston Methodist Research Institute, Houston, Texas, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, Texas, USA
| | - Jacek Z Kubiak
- Laboratory of Regenerative Medicine and Cell Biology, Military Institute of Hygiene and Epidemiology (WIHE), Warsaw, Poland
- UnivRennes, UMR 6290, CNRS, Institute of Genetics and Development of Rennes, Cell Cycle Group, Faculty of Medicine, Rennes, France
| |
Collapse
|
27
|
Sampathkumar NK, Bravo JI, Chen Y, Danthi PS, Donahue EK, Lai RW, Lu R, Randall LT, Vinson N, Benayoun BA. Widespread sex dimorphism in aging and age-related diseases. Hum Genet 2020; 139:333-356. [PMID: 31677133 PMCID: PMC7031050 DOI: 10.1007/s00439-019-02082-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/26/2019] [Indexed: 02/07/2023]
Abstract
Although aging is a conserved phenomenon across evolutionary distant species, aspects of the aging process have been found to differ between males and females of the same species. Indeed, observations across mammalian studies have revealed the existence of longevity and health disparities between sexes, including in humans (i.e. with a female or male advantage). However, the underlying mechanisms for these sex differences in health and lifespan remain poorly understood, and it is unclear which aspects of this dimorphism stem from hormonal differences (i.e. predominance of estrogens vs. androgens) or from karyotypic differences (i.e. XX vs. XY sex chromosome complement). In this review, we discuss the state of the knowledge in terms of sex dimorphism in various aspects of aging and in human age-related diseases. Where the interplay between sex differences and age-related differences has not been explored fully, we present the state of the field to highlight important future research directions. We also discuss various dietary, drug or genetic interventions that were shown to improve longevity in a sex-dimorphic fashion. Finally, emerging tools and models that can be leveraged to decipher the mechanisms underlying sex differences in aging are also briefly discussed.
Collapse
Affiliation(s)
- Nirmal K Sampathkumar
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, 90089, USA
| | - Yilin Chen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Masters Program in Nutrition, Healthspan, and Longevity, University of Southern California, Los Angeles, CA, 90089, USA
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Erin K Donahue
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rochelle W Lai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ryan Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, 90089, USA
| | - Lewis T Randall
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, 90089, USA
| | - Nika Vinson
- Department of Urology, Pelvic Medicine and Reconstructive Surgery, UCLA David Geffen School of Medicine, Los Angeles, CA, 90024, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, 90089, USA.
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA.
| |
Collapse
|
28
|
Dash HR, Rawat N, Das S. Alternatives to amelogenin markers for sex determination in humans and their forensic relevance. Mol Biol Rep 2020; 47:2347-2360. [DOI: 10.1007/s11033-020-05268-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
|
29
|
The Role of Number of Copies, Structure, Behavior and Copy Number Variations (CNV) of the Y Chromosome in Male Infertility. Genes (Basel) 2019; 11:genes11010040. [PMID: 31905733 PMCID: PMC7016774 DOI: 10.3390/genes11010040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
The World Health Organization (WHO) defines infertility as the inability of a sexually active, non-contracepting couple to achieve spontaneous pregnancy within one year. Statistics show that the two sexes are equally at risk. Several causes may be responsible for male infertility; however, in 30–40% of cases a diagnosis of idiopathic male infertility is made in men with normal urogenital anatomy, no history of familial fertility-related diseases and a normal panel of values as for endocrine, genetic and biochemical markers. Idiopathic male infertility may be the result of gene/environment interactions, genetic and epigenetic abnormalities. Numerical and structural anomalies of the Y chromosome represent a minor yet significant proportion and are the topic discussed in this review. We searched the PubMed database and major search engines for reports about Y-linked male infertility. We present cases of Y-linked male infertility in terms of (i) anomalies of the Y chromosome structure/number; (ii) Y chromosome misbehavior in a normal genetic background; (iii) Y chromosome copy number variations (CNVs). We discuss possible explanations of male infertility caused by mutations, lower or higher number of copies of otherwise wild type, Y-linked sequences. Despite Y chromosome structural anomalies are not a major cause of male infertility, in case of negative results and of normal DNA sequencing of the ascertained genes causing infertility and mapping on this chromosome, we recommend an analysis of the karyotype integrity in all cases of idiopathic fertility impairment, with an emphasis on the structure and number of this chromosome.
Collapse
|
30
|
Sun T, Hanif Q, Chen H, Lei C, Dang R. Copy Number Variations of Four Y-Linked Genes in Swamp Buffaloes. Animals (Basel) 2019; 10:ani10010031. [PMID: 31877875 PMCID: PMC7023270 DOI: 10.3390/ani10010031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 12/18/2019] [Indexed: 12/25/2022] Open
Abstract
Simple Summary The amplification of the male-specific region of the Y chromosome was a unique phenomenon during mammalian sex chromosome evolution. The Y-linked copy number variations of many species have been confirmed. However, the Y-linked copy number variations (CNVs) in water buffalo are still unknown. In this study, we investigated the copy number variations of four Y-linked genes (SRY, UTY, DBY, and OFD1Y) in buffalo. Our results showed that UTY was a single-copy gene in buffalo, while DBY, OFD1Y, and SRY exhibited copy number variations in buffalo. Abstract Copy number variation (CNV), a significant source of genetic diversity in the mammalian Y chromosome, is associated with the development of many complex phenotypes, such as spermatogenesis and male fertility. The contribution of Y-linked CNVs has been studied in various species, however, water buffalo has not been explored in this area and the genetic information still remains unknown. The aim of the current study was to investigate the CNVs of four Y-linked genes, including, sex determining Region of Y-Chromosome (SRY), ubiquitously transcribed tetratricopeptide repeat gene protein on the chromosome Y (UTY), DEAD-box helicase 3 Y-linked (DDX3Y, also known as DBY), and oral-facial-digital syndrome 1 Y-linked (OFD1Y) in 254 swamp buffaloes from 15 populations distributed across China, Vietnam, and Laos using quantitative real-time PCR (qPCR). Our results revealed the prevalence of a single-copy UTY gene in buffaloes. The DBY and OFD1Y represented CNVs among and within different buffalo breeds. The SRY showed CNVs only in Vietnamese and Laotian buffaloes. In conclusion, this study indicated that DBY, OFD1Y, and SRY showed CNVs, while the UTY was a single-copy gene in swamp buffaloes.
Collapse
Affiliation(s)
- Ting Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad 577, Pakistan
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
- Correspondence: ; Tel.: +86-153-8862-7637
| |
Collapse
|
31
|
Wu Y, Zhang WX, Zuo F, Zhang GW. Comparison of mRNA expression from Y-chromosome X-degenerate region genes in taurine cattle, yaks and interspecific hybrid bulls. Anim Genet 2019; 50:740-743. [PMID: 31475374 DOI: 10.1111/age.12841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2019] [Indexed: 12/13/2022]
Abstract
The yattle (dzo) is an interspecific hybrid of the taurine cattle (Bos taurus) and the domestic yak (Bos grunniens). F1 hybrid yattle bulls are sterile due to spermatogenic arrest and have misregulation of spermatogenesis genes in the testes. However, the expression pattern of Y chromosome-linked genes in cattle, yaks and yattle testes is still unknown. In this study, we analyzed the mRNA expression pattern of 10 genes known to be present as single copies in the X-degenerate region of the bovine male-specific region of the Y chromosome. Using male-specific primers and reverse transcription quantitative PCR, the ubiquitously transcribed tetratricopeptide repeat gene, Y-linked (UTY), oral-facial-digital syndrome 1, Y-linked (OFD1Y) and ubiquitin specific peptidase 9, Y-linked (USP9Y) genes were ubiquitously expressed and significantly more highly expressed in yattle than in cattle and yaks testes (P < 0.001). RNA binding motif protein, Y-linked (RBMY) had testes-specific expression, and eukaryotic translation initiation factor 1A, Y-linked (EIF1AY) was expressed mainly in testis, whereas yattle and cattle did not show significant differences with respect to the expression of RBMY and EIF1AY. Thus, based on the model of yattle bull sterility, the high expression of UTY, OFD1Y and USP9Y may be associated with yattle infertility.
Collapse
Affiliation(s)
- Y Wu
- College of Animal Science, Southwest University, Rongchang, Chongqing, 402460, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, 402460, China
| | - W-X Zhang
- Animal Husbandry and Veterinary Bureau of Rongchang, Rongchang, Chongqing, 402460, China
| | - F Zuo
- College of Animal Science, Southwest University, Rongchang, Chongqing, 402460, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, 402460, China
| | - G-W Zhang
- College of Animal Science, Southwest University, Rongchang, Chongqing, 402460, China.,Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, 402460, China
| |
Collapse
|
32
|
Fan H, Hu Y, Shan L, Yu L, Wang B, Li M, Wu Q, Wei F. Synteny search identifies carnivore Y chromosome for evolution of male specific genes. Integr Zool 2019; 14:224-234. [PMID: 30019860 DOI: 10.1111/1749-4877.12352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The explosive accumulation of mammalian genomes has provided a valuable resource to characterize the evolution of the Y chromosome. Unexpectedly, the Y-chromosome sequence has been characterized in only a small handful of species, with the majority being model organisms. Thus, identification of Y-linked scaffolds from unordered genome sequences is becoming more important. Here, we used a syntenic-based approach to generate the scaffolds of the male-specific region of the Y chromosome (MSY) from the genome sequence of 6 male carnivore species. Our results identified 14, 15, 9, 28, 14 and 11 Y-linked scaffolds in polar bears, pacific walruses, red pandas, cheetahs, ferrets and tigers, covering 1.55 Mbp, 2.62 Mbp, 964 Kb, 1.75 Mb, 2.17 Mbp and 1.84 Mb MSY, respectively. All the candidate Y-linked scaffolds in 3 selected species (red pandas, polar bears and tigers) were successfully verified using polymerase chain reaction. We re-annotated 8 carnivore MSYs including these 6 Y-linked scaffolds and domestic dog and cat MSY; a total of 11 orthologous genes conserved in at least 7 of the 8 carnivores were identified. These 11 Y-linked genes have significantly higher evolutionary rates compared with their X-linked counterparts, indicating less purifying selection for MSY genes. Taken together, our study shows that the approach of synteny search is a reliable and easily affordable strategy to identify Y-linked scaffolds from unordered carnivore genomes and provides a preliminary evolutionary study for carnivore MSY genes.
Collapse
Affiliation(s)
- Huizhong Fan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Lei Shan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lijun Yu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Min Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
33
|
Zhang GW, Wu Y, Luo Z, Guan J, Wang L, Luo X, Zuo F. Comparison of Y-chromosome-linked TSPY, TSPY2, and PRAMEY genes in Taurus cattle, yaks, and interspecific hybrid bulls. J Dairy Sci 2019; 102:6263-6275. [PMID: 31103297 DOI: 10.3168/jds.2018-15680] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 03/20/2019] [Indexed: 12/28/2022]
Abstract
Domestic yaks (Bos grunniens) and domestic Taurus cattle (Bos taurus) are closely related. An interesting phenomenon in interspecific crossings is male sterility in the F1 hybrid (yattle) and F2 backcross, with no late meiotic cells or spermatids in the seminiferous tubules. The mammalian Y chromosome is crucial for spermatogenesis and male fertility. This study investigated the copy number variations and mRNA of Y-transitional region genes TSPY2 (testis specific protein, Y-linked 2 and testis-specific Y-encoded protein 3-like) and PRAMEY (preferentially expressed antigen in melanoma, Y-linked), and Y-ampliconic region genes TSPY (testis-specific Y-encoded protein 1-like), ZNF280BY (zinc finger protein 280B, Y-linked) and HSFY (heat-shock transcription factor, Y-linked) in mature testes from Taurus cattle, yaks, and yattle. Phylogenetic trees divided 33 copies of TSPY into major 2 types (TSPY-T1 and TSPY-T2), 19 copies of TSPY2 into 2 types (TSPY2-T1 and T2), and 8 copies of PRAMEY into 4 types (PRAMEY-T1 to T4). Searching by the Basic Local Alignment Search Tool of the TSPY2 coding sequences in GenBank revealed that TSPY2 was conserved in Bovidae. The TSPY2-T2 sequences were absent, whereas PRAMEY-T2 and PRAMEY-T4 were amplified on the yak Y chromosome. The average copy numbers of TSPY-T2 and ZNF280BY were significantly different between cattle and yaks. The TSPY-T2, TSPY2, PRAMEY, ZNF280BY, and HSFY genes were uniquely or predominantly expressed in testes. Reverse-transcription quantitative PCR showed that the TSPY-T2, PRAMEY-T2, HSFY, ZNF280BY, protamine 1 (PRM1), and protamine 2 (PRM2) genes were almost not expressed in yattle. The PRM1 and PRM2 genes are used as positive markers for spermatozoa. Thus, our results showed that the genomic structure of the Y-transitional and Y-ampliconic region differed between Taurus cattle and yaks. Dysregulated expression of Y-ampliconic region genes TSPY-T2, HSPY, ZNF280BY, and Y-transitional region gene PRAMEY-T2 may be associated with hybrid male sterility in yattle.
Collapse
Affiliation(s)
- Gong-Wei Zhang
- College of Animal Science, Southwest University, Rongchang, Chongqing, China 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China 402460.
| | - Yuhui Wu
- College of Animal Science, Southwest University, Rongchang, Chongqing, China 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China 402460
| | - Zonggang Luo
- College of Animal Science, Southwest University, Rongchang, Chongqing, China 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China 402460
| | - Jiuqiang Guan
- Yak Research Institution, Sichuan Academy of Grassland Science, Chengdu, Sichuan, China 611731
| | - Ling Wang
- College of Animal Science, Southwest University, Rongchang, Chongqing, China 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China 402460
| | - Xiaolin Luo
- Yak Research Institution, Sichuan Academy of Grassland Science, Chengdu, Sichuan, China 611731
| | - Fuyuan Zuo
- College of Animal Science, Southwest University, Rongchang, Chongqing, China 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China 402460.
| |
Collapse
|
34
|
Matsumura T, Endo T, Isotani A, Ogawa M, Ikawa M. An azoospermic factor gene, Ddx3y and its paralog, Ddx3x are dispensable in germ cells for male fertility. J Reprod Dev 2019; 65:121-128. [PMID: 30613052 PMCID: PMC6473106 DOI: 10.1262/jrd.2018-145] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
About 10% of male infertile patients show abnormalities in spermatogenesis. The microdeletion of azoospermia factor a (AZFa) region of the Y chromosome is thought to be a
cause of spermatogenic failure. However, candidate gene responsible for the spermatogenic failure in AZFa deleted patients has not been elucidated yet. Using mice, we
explored the function of Ddx3y, a strong candidate gene in the Azfa region, and Ddx3x, a Ddx3y paralog on the X
chromosome, in spermatogenesis. We first generated Ddx3y KO male mice using CRISPR/Cas9 and found that the Ddx3y KO male mice show normal spermatogenesis,
produce morphologically normal spermatozoa, and sire healthy offspring. Because Ddx3x KO males were embryonic lethal, we next generated chimeric mice, which contain
Ddx3x and Ddx3y double KO (dKO) germ cells, and found that the dKO germ cells can differentiate into spermatozoa and transmit their mutant alleles to
offspring by normal mating. We conclude that Ddx3x and Ddx3y are dispensable for spermatogenesis at least in mice. Unlike human, mice have an additional
Ddx3y paralog D1pas1, that has been reported to be essential for spermatogenesis. These findings suggest that human and mouse DDX3 related proteins have
distinct differences in their functions.
Collapse
Affiliation(s)
- Takafumi Matsumura
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Tsutomu Endo
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Ayako Isotani
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Masaki Ogawa
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan.,Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| |
Collapse
|
35
|
Zhang B, Miller VM, Miller JD. Influences of Sex and Estrogen in Arterial and Valvular Calcification. Front Endocrinol (Lausanne) 2019; 10:622. [PMID: 31620082 PMCID: PMC6763561 DOI: 10.3389/fendo.2019.00622] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/27/2019] [Indexed: 01/14/2023] Open
Abstract
Vascular and cardiac valvular calcification was once considered to be a degenerative and end stage product in aging cardiovascular tissues. Over the past two decades, however, a critical mass of data has shown that cardiovascular calcification can be an active and highly regulated process. While the incidence of calcification in the coronary arteries and cardiac valves is higher in men than in age-matched women, a high index of calcification associates with increased morbidity, and mortality in both sexes. Despite the ubiquitous portending of poor outcomes in both sexes, our understanding of mechanisms of calcification under the dramatically different biological contexts of sex and hormonal milieu remains rudimentary. Understanding how the critical context of these variables inform our understanding of mechanisms of calcification-as well as innovative strategies to target it therapeutically-is essential to advancing the fields of both cardiovascular disease and fundamental mechanisms of aging. This review will explore potential sex and sex-steroid differences in the basic biological pathways associated with vascular and cardiac valvular tissue calcification, and potential strategies of pharmacological therapy to reduce or slow these processes.
Collapse
Affiliation(s)
- Bin Zhang
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, United States
| | - Virginia M. Miller
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
| | - Jordan D. Miller
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, United States
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
- Department of Cardiovascular Surgery, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Jordan D. Miller
| |
Collapse
|
36
|
Wong JYY, Margolis HG, Machiela M, Zhou W, Odden MC, Psaty BM, Robbins J, Jones RR, Rotter JI, Chanock SJ, Rothman N, Lan Q, Lee JS. Outdoor air pollution and mosaic loss of chromosome Y in older men from the Cardiovascular Health Study. ENVIRONMENT INTERNATIONAL 2018; 116:239-247. [PMID: 29698900 PMCID: PMC5971001 DOI: 10.1016/j.envint.2018.04.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/09/2018] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Mosaic loss of chromosome Y (mLOY) can occur in a fraction of cells as men age, which is potentially linked to increased mortality risk. Smoking is related to mLOY; however, the contribution of air pollution is unclear. OBJECTIVE We investigated whether exposure to outdoor air pollution, age, and smoking were associated with mLOY. METHODS We analyzed baseline (1989-1993) blood samples from 933 men ≥65 years of age from the prospective Cardiovascular Health Study. Particulate matter ≤10 μm (PM10), carbon monoxide, nitrogen dioxide, sulfur dioxide, and ozone data were obtained from the U.S. EPA Aerometric Information Retrieval System for the year prior to baseline. Inverse-distance weighted air monitor data were used to estimate each participants' monthly residential exposure. mLOY was detected with standard methods using signal intensity (median log-R ratio (mLRR)) of the male-specific chromosome Y regions from Illumina array data. Linear regression models were used to evaluate relations between mean exposure in the prior year, age, smoking and continuous mLRR. RESULTS Increased PM10 was associated with mLOY, namely decreased mLRR (p-trend = 0.03). Compared with the lowest tertile (≤28.5 μg/m3), the middle (28.5-31.0 μg/m3; β = -0.0044, p = 0.09) and highest (≥31 μg/m3; β = -0.0054, p = 0.04) tertiles had decreased mLRR, adjusted for age, clinic, race/cohort, smoking status and pack-years. Additionally, increasing age (β = -0.00035, p = 0.06) and smoking pack-years (β = -0.00011, p = 1.4E-3) were associated with decreased mLRR, adjusted for each other and race/cohort. No significant associations were found for other pollutants. CONCLUSIONS PM10 may increase leukocyte mLOY, a marker of genomic instability. The sample size was modest and replication is warranted.
Collapse
Affiliation(s)
- Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
| | - Helene G Margolis
- Department of Internal Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Mitchell Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research Inc., Bethesda, MD, USA
| | - Michelle C Odden
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA.; Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - John Robbins
- Department of Internal Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Rena R Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles BioMedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jennifer S Lee
- Division of Endocrinology, Gerontology, and Metabolism, Department of Medicine, and Division of Epidemiology, Department of Health Research and Policy, School of Medicine, Stanford University, Stanford, CA, USA; Medical Services, Veteran Affairs, Palo Alto, Health Care System, CA, USA
| |
Collapse
|
37
|
Methodology for Y Chromosome Capture: A complete genome sequence of Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads. Sci Rep 2018; 8:9436. [PMID: 29930304 PMCID: PMC6013464 DOI: 10.1038/s41598-018-27819-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 06/01/2018] [Indexed: 12/13/2022] Open
Abstract
This study is a comparison of the efficiency of three technologies used for Y chromosome capture and the next-generation sequencing (NGS) technologies applied for determining its whole sequence. Our main findings disclose that streptavidin-biotin magnetic particle-based capture methodology offers better and a deeper sequence coverage for Y chromosome capture, compared to chromosome sorting and microdissection procedures. Moreover, this methodology is less time consuming and the most selective for capturing only Y chromosomal material, in contrast with other methodologies that result in considerable background material from other, non-targeted chromosomes. NGS results compared between two platforms, NextSeq 500 and SOLID 5500xl, produce the same coverage results. This is the first study to explore a methodological comparison of Y chromosome capture and genetic analysis. Our results indicate an improved strategy for Y chromosome research with applications in several scientific fields where this chromosome plays an important role, such as forensics, medical sciences, molecular anthropology and cancer sciences.
Collapse
|
38
|
Bikel S, Jacobo-Albavera L, Sánchez-Muñoz F, Cornejo-Granados F, Canizales-Quinteros S, Soberón X, Sotelo-Mundo RR, Del Río-Navarro BE, Mendoza-Vargas A, Sánchez F, Ochoa-Leyva A. A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data. PeerJ 2017; 5:e4133. [PMID: 29230367 PMCID: PMC5724404 DOI: 10.7717/peerj.4133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022] Open
Abstract
Background In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays. Methods We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6-10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR). Results From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment. Discussion Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments.
Collapse
Affiliation(s)
- Shirley Bikel
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, México
| | - Leonor Jacobo-Albavera
- Instituto Nacional de Medicina Genómica, Instituto Nacional de Medicina Genómica, México City, México
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez (INCICh), México City, México
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, México
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada la Salud, Instituto Nacional de Medicina Genómica, México City, México
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Instituto Nacional de Medicina Genómica, México City, México.,Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora, México
| | | | - Alfredo Mendoza-Vargas
- Instituto Nacional de Medicina Genómica, Instituto Nacional de Medicina Genómica, México City, México
| | - Filiberto Sánchez
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, México
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Universidad Nacional Autónoma de México, Instituto de Biotecnología, Cuernavaca, Morelos, México
| |
Collapse
|
39
|
Kim KE, Kim YJ, Jung MK, Chae HW, Kwon AR, Lee WJ, Kim DH, Kim HS. A boy with 46,X,+mar presenting gynecomastia and short stature. Ann Pediatr Endocrinol Metab 2017; 22:266-271. [PMID: 29301188 PMCID: PMC5769836 DOI: 10.6065/apem.2017.22.4.266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/12/2017] [Accepted: 06/17/2017] [Indexed: 01/22/2023] Open
Abstract
A 15-year-old boy was referred due to gynecomastia and short stature. He was overweight and showed the knuckle-dimple sign on the left hand, a short fourth toe on the left foot, and male external genitalia with a small phallus. His levels of estradiol and follicle-stimulating hormone were increased, and his testosterone concentration was normal. Other hormonal tests were within the normal range. Radiographs showed short fourth and fifth metacarpals and fourth metatarsal bones. The karyotype was reported as 46,X,+mar, and the marker chromosome was shown to originate from the Y chromosome, which was identified by fluorescence in situ hybridization. Polymerase chain reaction and direct sequencing were used to clarify the deleted loci of the Y chromosome by making use of Y-specific sequence-tagged sites (STSs). The sex-determining region Y and centromere were verified, and there were microdeletions on the long arm of the Y chromosome. The azoospermia factor (AZF) b region was partially deleted, and AZFa and AZFc were completely deleted. Two STS probes of sY143 and the Y chromosome RNA recognition motif in AZFb showed positive signals corresponding to Yq11.223. The karyotype of the patient was interpreted as 46,X,der(Y)del(Y)(q11.21q11.222)del(Y)(q11.23qter). Herein, we report a rare case of a boy presenting with gynecomastia and short stature with 46, X, +mar, which originated from the Y chromosome, which was identified to have Yq microdeletions.
Collapse
Affiliation(s)
- Ki Eun Kim
- Department of Pediatrics, CHA Gangnam Medical Center, CHA University, Seoul, Korea
| | - Ye Jin Kim
- Division of Pediatric Endocrinology, Department of Pediatrics, Endocrine Research Institute, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Mo Kyoung Jung
- Division of Pediatric Endocrinology, Department of Pediatrics, Endocrine Research Institute, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun-Wook Chae
- Division of Pediatric Endocrinology, Department of Pediatrics, Endocrine Research Institute, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Ah Reum Kwon
- Division of Pediatric Endocrinology, Department of Pediatrics, Endocrine Research Institute, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Woo Jung Lee
- Division of Pediatric Endocrinology, Department of Pediatrics, Endocrine Research Institute, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Duk-Hee Kim
- Department of Pediatrics, Sowha Children’s Hospital, Seoul, Korea
| | - Ho-Seong Kim
- Division of Pediatric Endocrinology, Department of Pediatrics, Endocrine Research Institute, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Korea,Address for correspondence: Ho-Seong Kim, MD, PhD https://orcid.org/0000-0003-1135-099X Division of Pediatrics Endocrinology, Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea Tel: +82-2-2228-2069 Fax: +82-2-393-9118 E-mail:
| |
Collapse
|
40
|
Han H, Zhao X, Xia X, Chen H, Lei C, Dang R. Copy number variations of five Y chromosome genes in donkeys. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-391-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. In mammals, the Y chromosome plays a pivotal role in male sex determination and is essential for normal sperm production. A number of studies were conducted on Y chromosome genes of various species and identified single-copy and multi-copy genes. However, limited studies about donkey Y chromosome genes have been done. In this study, 263 male samples from 13 Chinese donkey breeds were collected to analyze the copy number variations (CNVs) of five Y chromosome genes using the quantitative PCR (qPCR) method. These five genes (cullin 4 B Y (CUL4BY), equus testis-specific transcript y1 (ETSTY1), equus testis-specific transcript y4 (ETSTY4), equus testis-specific transcript Y 5 (ETSTY5), and sex-determining region Y (SRY) were identified as multi-copy, whose median copy numbers (MCNs) were 5, 45, 2, and 2, and 13 with CNV ranges of 1–57, 1–227, 1–37, 1–86 and 1–152, respectively. The CNVs of these five genes were shared in different breeds. Compared to previous studies, the copy numbers of five genes showed some distinct consequences in this study. In particular, the well-known single-copy SRY gene showed CNVs in donkeys. Our results provided genetic variations of donkey Y chromosome genes.
Collapse
|
41
|
Kumar P, Jain M, Kalsi AK, Halder A. Molecular characterisation of a case of dicentric Y presented as nonobstructive azoospermia with testicular early maturation arrest. Andrologia 2017; 50. [PMID: 28836280 DOI: 10.1111/and.12886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2017] [Indexed: 12/28/2022] Open
Abstract
The dicentric Y chromosome is the most common cytogenetically visible structural abnormality of Y chromosome. The sites of break and fusion of dicentric Y are variable, but break and fusion at Yq12 (proximal to the pseudoautosomal region 2/PAR 2) is very rare. Dicentric Y chromosome is unstable during cell division and likely to generate chromosomal mosaicism. Here, we report a case of infertile male with nonmosaic 46,XY where chromosome Y was dicentric with break and fusion at Yq12 (proximal to PAR 2). Clinical presentation of the case was nonobstructive azoospermia due to early maturation arrest at the primary spermatocyte stage. Various molecular techniques such as FISH, STS-PCR and DNA microarray were carried out to characterise genetic defect leading to testicular maturation arrest in the patient. The break and fusion was found at Yq12 (proximal to PAR 2) and resulted in near total duplication of Y chromosome (excluding PAR 2). The reason for maturation arrest seems due to CNVs of PARs (gain in PAR 1 and loss of PAR 2) and azoospermia factors (gain).
Collapse
Affiliation(s)
- P Kumar
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - M Jain
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - A K Kalsi
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| | - A Halder
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
42
|
Zhang GW, Guan JQ, Luo ZG, Zhang WX, Wang L, Luo XL, Zuo FY. A tremendous expansion of copy number in crossbred bulls ( × ). J Anim Sci 2017; 94:1398-407. [PMID: 27135999 DOI: 10.2527/jas.2015-9983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Crossbreeding between cattle () and yak () exhibits significant hybrid advantages in milk yield and meat production. By contrast, cattle-yak F hybrid bulls are sterile. Copy number variations (CNV) of multicopy gene families in male-specific regions of the mammalian Y chromosome (MSY) affect human and animal fertility. The present study investigated CNV of (), (), (), and () in 5 yak breed bulls ( = 63), cattle-yak F ( = 22) and F ( = 2) hybrid bulls, and Chinese Yellow (CY) cattle bulls ( = 10) by quantitative real-time PCR. showed restricted amplification in yak bulls in that the average geometric mean copy number (CN) was estimated to be 4 copies. The most compelling finding is that there is a tremendous expansion of CN in F hybrids (385 copies; 95% confidence interval [CI] = 351-421) and F hybrids (356 copies) compared with the male parent breed CY cattle (142 copies; 95% CI = 95-211). Copy numbers of and were also extensively expanded on the Y chromosome in yak and CY cattle bulls. The geometric mean CN of and were estimated to be 123 (95% CI = 114-132) and 250 copies (95% CI = 233-268) in yak bulls and 71 (95% CI = 61-82) and 133 (95% CI = 107-164) copies in CY cattle, respectively. Yak and CY cattle have 2 copies of the gene on the Y chromosome. Similarly to gene, the F and F hybrid bulls have higher CN of , , and than CY cattle ( < 0.01). These results indicated that the MSY of yak and cattle-yak crossbred hybrids was fundamentally different from cattle MSY in the context of genomic organization. Based on the model of cattle-yak F and F hybrid bull sterility, the CNV of may serve as a potential risk factor for crossbred bull ( × ) infertility. To our knowledge, this is the first study to examine differences in multicopy genes in MSY between yak and cattle-yak bulls.
Collapse
|
43
|
Halder A, Kumar P, Jain M, Iyer VK. Copy number variations in testicular maturation arrest. Andrology 2017; 5:460-472. [DOI: 10.1111/andr.12330] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/13/2016] [Accepted: 12/28/2016] [Indexed: 01/01/2023]
Affiliation(s)
- A. Halder
- Department of Reproductive Biology; All India Institute of Medical Sciences; New Delhi India
| | - P. Kumar
- Department of Reproductive Biology; All India Institute of Medical Sciences; New Delhi India
| | - M. Jain
- Department of Reproductive Biology; All India Institute of Medical Sciences; New Delhi India
| | - V. K. Iyer
- Department of Pathology; All India Institute of Medical Sciences; New Delhi India
| |
Collapse
|
44
|
Kirk IK, Weinhold N, Belling K, Skakkebæk NE, Jensen TS, Leffers H, Juul A, Brunak S. Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations. Cell Syst 2017; 4:357-364.e3. [PMID: 28215527 DOI: 10.1016/j.cels.2017.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 10/23/2016] [Accepted: 01/05/2017] [Indexed: 10/20/2022]
Abstract
Gene copy-number changes influence phenotypes through gene-dosage alteration and subsequent changes of protein complex stoichiometry. Human trisomies where gene copy numbers are increased uniformly over entire chromosomes provide generic cases for studying these relationships. In most trisomies, gene and protein level alterations have fatal consequences. We used genome-wide protein-protein interaction data to identify chromosome-specific patterns of protein interactions. We found that some chromosomes encode proteins that interact infrequently with each other, chromosome 21 in particular. We combined the protein interaction data with transcriptome data from human brain tissue to investigate how this pattern of global interactions may affect cellular function. We identified highly connected proteins that also had coordinated gene expression. These proteins were associated with important neurological functions affecting the characteristic phenotypes for Down syndrome and have previously been validated in mouse knockout experiments. Our approach is general and applicable to other gene-dosage changes, such as arm-level amplifications in cancer.
Collapse
Affiliation(s)
- Isa Kristina Kirk
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nils Weinhold
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kirstine Belling
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Niels Erik Skakkebæk
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thomas Skøt Jensen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Henrik Leffers
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Brunak
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| |
Collapse
|
45
|
Babić N, Dogan S, Čakar J, Pilav A, Marjanović D, Hadžiavdić V. Molecular diversity of 23 Y-chromosome short tandem repeat loci in the population of Tuzla Canton, Bosnia and Herzegovina. Ann Hum Biol 2016; 44:419-426. [PMID: 27826995 DOI: 10.1080/03014460.2016.1259430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Tuzla Canton is the most populated region in the ethnically mixed territory of Bosnia and Herzegovina, whose genetic analysis could provide an insight into past demographic events. AIM Analysis of 23 Y-chromosome STR markers in the population of Tuzla Canton and investigation of the genetic relationship of the male population of the Tuzla Canton and that of the larger Bosnian and Herzegovinian population as well as neighbouring and other European populations. SUBJECTS AND METHODS The study was conducted among 100 unrelated healthy adult males from Tuzla Canton that have been genotyped using 23 Y-STR loci included in the PowerPlex Y23 kit. Statistical parameters such as haplotype diversity and allele frequencies were calculated, as well as the Rst-based genetic distances between the new dataset and those from Bosnia and Herzegovina and elsewhere, which were then visualised through multi-dimensional scaling plot and neighbour-joining phylogenetic tree analyses. RESULTS The PowerPlex Y23 kit has shown high discrimination capacity, as all 100 individuals have unique haplotypes. The newly incorporated loci seem to be highly informative. Population comparison reveals no statistically significant differences between the study population and the general Bosnian-Herzegovinian population, and between the study population and neighbouring populations. CONCLUSION These results could be used as an additional investigation of the genetic relationship between the regional populations in Bosnia and Herzegovina and neighbouring human populations, as well as for further human population and forensic genetics studies.
Collapse
Affiliation(s)
- Naida Babić
- a Department of Biology, Faculty of Natural Sciences and Mathematics , University of Tuzla , Tuzla , Bosnia and Herzegovina
| | - Serkan Dogan
- b Department of Genetics and Bioengineering , International Burch University , Sarajevo , Bosnia and Herzegovina
| | - Jasmina Čakar
- c Institute for Genetic Engineering and Biotechnology, University of Sarajevo , Sarajevo , Bosnia and Herzegovina
| | - Amela Pilav
- c Institute for Genetic Engineering and Biotechnology, University of Sarajevo , Sarajevo , Bosnia and Herzegovina
| | - Damir Marjanović
- b Department of Genetics and Bioengineering , International Burch University , Sarajevo , Bosnia and Herzegovina.,d Institute for Anthropological Researches , Zagreb , Croatia
| | - Vesna Hadžiavdić
- a Department of Biology, Faculty of Natural Sciences and Mathematics , University of Tuzla , Tuzla , Bosnia and Herzegovina
| |
Collapse
|
46
|
The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research. Hum Genet 2016; 136:559-573. [DOI: 10.1007/s00439-016-1740-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
|
47
|
FISH and array CGH characterization of de novo derivative Y chromosome (Yq duplication and partial Yp deletion) in an azoospermic male. Reprod Biomed Online 2015; 31:217-24. [PMID: 26096031 DOI: 10.1016/j.rbmo.2015.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 12/12/2022]
Abstract
This study presents a 28-year-old infertile male who was referred to the cytogenetic laboratory for chromosomal analysis after 4 years of regular unprotected intercourse in whom non-obstructive azoospermia was revealed. Standard cytogenetic G-banding was performed on metaphase spreads and a de-novo karyotype 46,X,der(Y)(q11.22;p11.3) was identified. This analysis was followed by flourescence in-situ hybridization(FISH) and array comparative genomic hybridization (aCGH). Finally, the patient's karyotype was identified as 46,X,der(Y)(qter→q11.221::p11.31→qter).ish der(Y) (qter+,pter-,SHOX+,SRY+,Ycen+,DYZ3+;DYZ1+,qter+).arrYq11.221q12(14,448,863-59,288,511) x2, Yp11.32p11.31(104,062-266,388) x0. It is proposed that de-novo derivative monocentric Y chromosome with duplicated region Y qter→q11.221::p11.31→qter with partial deletion of Yp PAR1 region most probably can perturb the conjugation of sex chromosomes during first meiotic division of spermatogenic arrested differentiation (development).
Collapse
|
48
|
Sehgal N, Fritz AJ, Morris K, Torres I, Chen Z, Xu J, Berezney R. Gene density and chromosome territory shape. Chromosoma 2014; 123:499-513. [PMID: 25106753 DOI: 10.1007/s00412-014-0480-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/15/2014] [Accepted: 07/17/2014] [Indexed: 12/16/2022]
Abstract
Despite decades of study of chromosome territories (CT) in the interphase nucleus of mammalian cells, our understanding of the global shape and 3-D organization of the individual CT remains very limited. Past microscopic analysis of CT suggested that while many of the CT appear to be very regular ellipsoid-like shapes, there were also those with more irregular shapes. We have undertaken a comprehensive analysis to determine the degree of shape regularity of different CT. To be representative of the whole human genome, 12 different CT (~41 % of the genome) were selected that ranged from the largest (CT 1) to the smallest (CT 21) in size and from the highest (CT 19) to lowest (CT Y) in gene density. Using both visual inspection and algorithms that measure the degree of shape ellipticity and regularity, we demonstrate a strong inverse correlation between the degree of regular CT shape and gene density for those CT that are most gene-rich (19, 17, 11) and gene-poor (18, 13, Y). CT more intermediate in gene density showed a strong negative correlation with shape regularity, but not with ellipticity. An even more striking correlation between gene density and CT shape was determined for the nucleolar-associated NOR-CT. Correspondingly, striking differences in shape between the X active and inactive CT implied that aside from gene density, the overall global level of gene transcription on individual CT is also an important determinant of chromosome territory shape.
Collapse
Affiliation(s)
- Nitasha Sehgal
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | | | | | | | | | | | | |
Collapse
|
49
|
Shah K, McCormack CE, Bradbury NA. Do you know the sex of your cells? Am J Physiol Cell Physiol 2014; 306:C3-18. [PMID: 24196532 PMCID: PMC3919971 DOI: 10.1152/ajpcell.00281.2013] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/31/2013] [Indexed: 11/22/2022]
Abstract
Do you know the sex of your cells? Not a question that is frequently heard around the lab bench, yet thanks to recent research is probably one that should be asked. It is self-evident that cervical epithelial cells would be derived from female tissue and prostate cells from a male subject (exemplified by HeLa and LnCaP, respectively), yet beyond these obvious examples, it would be true to say that the sex of cell lines derived from non-reproductive tissue, such as lung, intestine, kidney, for example, is given minimal if any thought. After all, what possible impact could the presence of a Y chromosome have on the biochemistry and cell biology of tissues such as the exocrine pancreatic acini? Intriguingly, recent evidence has suggested that far from being irrelevant, genes expressed on the sex chromosomes can have a marked impact on the biology of such diverse tissues as neurons and renal cells. It is also policy of AJP-Cell Physiology that the source of all cells utilized (species, sex, etc.) should be clearly indicated when submitting an article for publication, an instruction that is rarely followed (http://www.the-aps.org/mm/Publications/Info-For-Authors/Composition). In this review we discuss recent data arguing that the sex of cells being used in experiments can impact the cell's biology, and we provide a table outlining the sex of cell lines that have appeared in AJP-Cell Physiology over the past decade.
Collapse
Affiliation(s)
- Kalpit Shah
- Department of Physiology and Biophysics, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois
| | | | | |
Collapse
|
50
|
Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development. Proc Natl Acad Sci U S A 2013; 110:12373-8. [PMID: 23842086 DOI: 10.1073/pnas.1221104110] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The male-specific region of the mammalian Y chromosome (MSY) contains clusters of genes essential for male reproduction. The highly repetitive and degenerative nature of the Y chromosome impedes genomic and transcriptomic characterization. Although the Y chromosome sequence is available for the human, chimpanzee, and macaque, little is known about the annotation and transcriptome of nonprimate MSY. Here, we investigated the transcriptome of the MSY in cattle by direct testis cDNA selection and RNA-seq approaches. The bovine MSY differs radically from the primate Y chromosomes with respect to its structure, gene content, and density. Among the 28 protein-coding genes/families identified on the bovine MSY (12 single- and 16 multicopy genes), 16 are bovid specific. The 1,274 genes identified in this study made the bovine MSY gene density the highest in the genome; in comparison, primate MSYs have only 31-78 genes. Our results, along with the highly transcriptional activities observed from these Y-chromosome genes and 375 additional noncoding RNAs, challenge the widely accepted hypothesis that the MSY is gene poor and transcriptionally inert. The bovine MSY genes are predominantly expressed and are differentially regulated during the testicular development. Synonymous substitution rate analyses of the multicopy MSY genes indicated that two major periods of expansion occurred during the Miocene and Pliocene, contributing to the adaptive radiation of bovids. The massive amplification and vigorous transcription suggest that the MSY serves as a genomic niche regulating male reproduction during bovid expansion.
Collapse
|