1
|
An J, Wang J, Kong S, Song S, Chen W, Yuan P, He Q, Chen Y, Li Y, Yang Y, Wang W, Li R, Yan L, Yan Z, Qiao J. GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad004. [PMID: 38862425 DOI: 10.1093/gpbjnl/qzad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 09/20/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
Gametogenesis plays an important role in the reproduction and evolution of species. The transcriptomic and epigenetic alterations in this process can influence the reproductive capacity, fertilization, and embryonic development. The rapidly increasing single-cell studies have provided valuable multi-omics resources. However, data from different layers and sequencing platforms have not been uniformed and integrated, which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and spermatogenesis. Here, we develop GametesOmics, a comprehensive database that integrates the data of gene expression, DNA methylation, and chromatin accessibility during oogenesis and spermatogenesis in humans and mice. GametesOmics provides a user-friendly website and various tools, including Search and Advanced Search for querying the expression and epigenetic modification(s) of each gene; Tools with Differentially expressed gene (DEG) analysis for identifying DEGs, Correlation analysis for demonstrating the genetic and epigenetic changes, Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors (TFs), and MethylView for studying the genomic distribution of epigenetic modifications. GametesOmics also provides Genome Browser and Ortholog for tracking and comparing gene expression, DNA methylation, and chromatin accessibility between humans and mice. GametesOmics offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development, and can be accessed at http://gametesomics.cn/.
Collapse
Affiliation(s)
- Jianting An
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jing Wang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Siming Kong
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shi Song
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Wei Chen
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Peng Yuan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Qilong He
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yidong Chen
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ye Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yi Yang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Wei Wang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rong Li
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Liying Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Zhiqiang Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100191, China
| |
Collapse
|
2
|
Alipanah M, Mazloom SM, Gharari F. Detection of selective sweep in European wild sheep breeds. 3 Biotech 2024; 14:122. [PMID: 38560387 PMCID: PMC10978567 DOI: 10.1007/s13205-024-03964-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
In wild animal populations, there is a differentiation between populations due to natural selection. The direction and pressure of natural selection in the wild sheep are different in the various geographic areas. Linkage disequilibrium studies showed that regions of the genome in whole wild sheep are under natural selection and that natural selection can affect immune or reproductive or metabolic traits. The study aimed to identify genomic regions under natural selection in wild sheep. For this purpose, the genetic information of 24 European wild sheep and 24 Sardinian wild sheep was used. The genotypes were determined using Illumina 50 K SNPChip arrays based on Oar_4.0 version of the sheep genome. After quality control steps, finally, 31,560 SNP markers were analyzed. The value of LD was calculated by calculating the r2 statistic between all pairs of locations through PLINK software. To identify signs of selection based on linkage disequilibrium methods, an extended haplotype homozygosity test of XP-EHH crossing population and iHS intrapopulation was used. The results of iHS studies showed that in European and Sardinian wild sheep, the highest iHS coefficient under natural selection was observed on 3 and 2 chromosome numbers, respectively. Also, the results of XP-EHH studies showed that the largest XP-EHH coefficients under natural selection in European wild sheep compared to Sardinian and vice versa in Sardinian wild sheep compared to European wild sheep were observed on 3 and 16 chromosome numbers, respectively. In addition, the results of gene cycle studies showed that COPB1, SEC24D, ZDHHC17, BBS4, RFX3, SLC26A8, CAMK2D, GRIA1, GRM1, GRID2, PPP2R1A, CPEB4, PLEKHA5 and KIF13A, VPS39, VPS53, DTNBP1, DYNC1I1, FAM91A genes are under natural selection in Sardinian and European wild sheeps, respectively. The direction and selection pressure of natural selection in the two breeds of wild sheep is different due to different geographic conditions.
Collapse
Affiliation(s)
- Masoud Alipanah
- Department of Plant Production, University of Torbat Heydarieh, Torbat Heydarieh, 9516168595 Iran
| | - Seyed Mostafa Mazloom
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, 9177948974 Iran
| | - Faezeh Gharari
- Department of Plant Production, University of Torbat Heydarieh, Torbat Heydarieh, 9516168595 Iran
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, 9177948974 Iran
| |
Collapse
|
3
|
Coschiera A, Yoshihara M, Lauter G, Ezer S, Pucci M, Li H, Kavšek A, Riedel CG, Kere J, Swoboda P. Primary cilia promote the differentiation of human neurons through the WNT signaling pathway. BMC Biol 2024; 22:48. [PMID: 38413974 PMCID: PMC10900739 DOI: 10.1186/s12915-024-01845-w] [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: 07/18/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell's immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce. RESULTS We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and in RFX2 -/- mutant neurons with altered cilia, we discovered an early-differentiation "ciliary time window" during which transient cilia promote axon outgrowth, branching and arborization. Experiments in neurons with IFT88 and IFT172 ciliary gene knockdowns, leading to shorter cilia, confirm these results. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes. CONCLUSIONS We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in "mild" impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.
Collapse
Affiliation(s)
- Andrea Coschiera
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba, Japan
- Chiba University, Chiba, Japan
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
- Uppsala University, Uppsala, Sweden
| | - Sini Ezer
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Mariangela Pucci
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Bioscience and Technology for Food, Agriculture and Environment, Teramo, Italy
- University of Teramo, Teramo, Italy
| | - Haonan Li
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Alan Kavšek
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
| |
Collapse
|
4
|
Adams M, Vollmers C. Generation and analysis of a mouse multi-tissue genome annotation atlas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578267. [PMID: 38352519 PMCID: PMC10862843 DOI: 10.1101/2024.01.31.578267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Generating an accurate and complete genome annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive genome annotation should contain information on what tissues express what transcript isoforms at what level. This tissue-level isoform information can then inform a wide range of research questions as well as experiment designs. Long-read sequencing technology combined with advanced full-length cDNA library preparation methods has now achieved throughput and accuracy where generating these types of annotations is achievable. Here, we show this by generating a genome annotation of the mouse (Mus musculus). We used the nanopore-based R2C2 long-read sequencing method to generate 64 million highly accurate full length cDNA consensus reads - averaging 5.4 million reads per tissue for a dozen tissues. Using the Mandalorion tool we processed these reads to generate the Tissue-level Atlas of Mouse Isoforms (TAMI - available at https://genome.ucsc.edu/s/vollmers/TAMI) which we believe will be a valuable complement to conventional, manually curated reference genome annotations.
Collapse
Affiliation(s)
- Matthew Adams
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz
| | | |
Collapse
|
5
|
Huang Y, Li L, An G, Yang X, Cui M, Song X, Lin J, Zhang X, Yao Z, Wan C, Zhou C, Zhao J, Song K, Ren S, Xia X, Fu X, Lan Y, Hu X, Wang W, Wang M, Zheng Y, Miao K, Bai X, Hutchins AP, Chang G, Gao S, Zhao XY. Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination. Nat Cell Biol 2023; 25:1520-1534. [PMID: 37723297 DOI: 10.1038/s41556-023-01232-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 08/15/2023] [Indexed: 09/20/2023]
Abstract
Human spermatogenesis is a highly ordered process; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes using the modified single-cell chromatin overall omic-scale landscape sequencing approach, we revealed that the transcriptional changes throughout human spermatogenesis were correlated with chromatin accessibility changes. In particular, we identified a set of transcription factors and cis elements with potential functions. A round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. Aberrant DNA hypermethylation could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination and fertility. Our work provides multi-omics landscapes of human spermatogenesis at single-cell resolution and offers insights into the association between DNA demethylation and male meiotic recombination.
Collapse
Affiliation(s)
- Yaping Huang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Lin Li
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Geng An
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xinyan Yang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Manman Cui
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xiuling Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jing Lin
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xiaoling Zhang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Zhaokai Yao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Cong Wan
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Cai Zhou
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jiexiang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Ke Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Shaofang Ren
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xinyu Xia
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xin Fu
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Yu Lan
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xuesong Hu
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Wen Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Mei Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Yi Zheng
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Kai Miao
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, P. R. China
| | - Xiaochun Bai
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P. R. China
| | - Gang Chang
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, P. R. China.
| | - Shuai Gao
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China.
| | - Xiao-Yang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China.
- Guangdong Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, P. R. China.
- Key Laboratory of Mental Health of the Ministry of Education, Guangzhou, P. R. China.
- Department of Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, P. R. China.
- National Clinical Research Center for Kidney Disease, Guangzhou, P. R. China.
| |
Collapse
|
6
|
Wei YL, Fan XJ, Lin XC, Lin AZ, She ZY, Wang XR. Kinesin-14 KIFC1 promotes acrosome formation and chromatin maturation during mouse spermiogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119555. [PMID: 37524262 DOI: 10.1016/j.bbamcr.2023.119555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/11/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023]
Abstract
KIFC1, a member of kinesin-14 subfamily motors, is essential for meiotic cell division and acrosome formation during spermatogenesis. However, the functions of KIFC1 in the formation and maintenance of the acrosome in male germ cells remain to be elucidated. In this study, we report the structural deformities of acrosomes in the in vivo KIFC1 inhibition mouse models. The proacrosomal vesicles diffuse into the cytoplasm and form atypical acrosomal granules. This phenotype is consistent with globozoospermia patients and probably results from the failure of the Golgi-derived vesicle trafficking and actin filament organization. Moreover, the multinucleated and undifferentiated spermatogenic cells in the epidydimal lumen after KIFC1 inhibition reveal the specific roles of KIFC1 in regulating post-meiotic maturation. Overall, our results uncover KIFC1 as an essential regulator in the trafficking, fusion and maturation of acrosomal vesicles during spermiogenesis.
Collapse
Affiliation(s)
- Ya-Lan Wei
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian 350013, China; College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian 350122, China; Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian 350001, China
| | - Xiao-Jing Fan
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian 350013, China; College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian 350122, China; Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian 350001, China
| | - Xin-Chen Lin
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian 350013, China; College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian 350122, China; Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian 350001, China
| | - Ai-Zhu Lin
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian 350013, China; College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian 350122, China; Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian 350001, China
| | - Zhen-Yu She
- Department of Cell Biology and Genetics, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China.
| | - Xin-Rui Wang
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian 350013, China; College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian 350122, China; Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian 350001, China.
| |
Collapse
|
7
|
Cumplido-Laso G, Benitez DA, Mulero-Navarro S, Carvajal-Gonzalez JM. Transcriptional Regulation of Airway Epithelial Cell Differentiation: Insights into the Notch Pathway and Beyond. Int J Mol Sci 2023; 24:14789. [PMID: 37834236 PMCID: PMC10573127 DOI: 10.3390/ijms241914789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The airway epithelium is a critical component of the respiratory system, serving as a barrier against inhaled pathogens and toxins. It is composed of various cell types, each with specific functions essential to proper airway function. Chronic respiratory diseases can disrupt the cellular composition of the airway epithelium, leading to a decrease in multiciliated cells (MCCs) and an increase in secretory cells (SCs). Basal cells (BCs) have been identified as the primary stem cells in the airway epithelium, capable of self-renewal and differentiation into MCCs and SCs. This review emphasizes the role of transcription factors in the differentiation process from BCs to MCCs and SCs. Recent advancements in single-cell RNA sequencing (scRNAseq) techniques have provided insights into the cellular composition of the airway epithelium, revealing specialized and rare cell types, including neuroendocrine cells, tuft cells, and ionocytes. Understanding the cellular composition and differentiation processes within the airway epithelium is crucial for developing targeted therapies for respiratory diseases. Additionally, the maintenance of BC populations and the involvement of Notch signaling in BC self-renewal and differentiation are discussed. Further research in these areas could provide valuable insights into the mechanisms underlying airway epithelial homeostasis and disease pathogenesis.
Collapse
Affiliation(s)
- Guadalupe Cumplido-Laso
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain; (D.A.B.); (S.M.-N.)
| | | | | | - Jose Maria Carvajal-Gonzalez
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain; (D.A.B.); (S.M.-N.)
| |
Collapse
|
8
|
Coyle MC, Tajima AM, Leon F, Choksi SP, Yang A, Espinoza S, Hughes TR, Reiter JF, Booth DS, King N. An RFX transcription factor regulates ciliogenesis in the closest living relatives of animals. Curr Biol 2023; 33:3747-3758.e9. [PMID: 37552984 PMCID: PMC10530576 DOI: 10.1016/j.cub.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/30/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Cilia allowed our protistan ancestors to sense and explore their environment, avoid predation, and capture bacterial prey.1,2,3 Regulated ciliogenesis was likely critical for early animal evolution,2,4,5,6 and in modern animals, deploying cilia in the right cells at the right time is crucial for development and physiology. Two transcription factors, RFX and FoxJ1, coordinate ciliogenesis in animals7,8,9 but are absent from the genomes of many other ciliated eukaryotes, raising the question of how the regulation of ciliogenesis in animals evolved.10,11 By comparing the genomes of animals with those of their closest living relatives, the choanoflagellates, we found that the genome of their last common ancestor encoded at least three RFX paralogs and a FoxJ1 homolog. Disruption of the RFX homolog cRFXa in the model choanoflagellate Salpingoeca rosetta resulted in delayed cell proliferation and aberrant ciliogenesis, marked by the collapse and resorption of nascent cilia. In cRFXa mutants, ciliogenesis genes and foxJ1 were significantly downregulated. Moreover, the promoters of S. rosetta ciliary genes are enriched for DNA motifs matching those bound by the cRFXa protein in vitro. These findings suggest that an ancestral cRFXa homolog coordinated ciliogenesis in the progenitors of animals and choanoflagellates and that the selective deployment of the RFX regulatory module may have been necessary to differentiate ciliated from non-ciliated cell types during early animal evolution.
Collapse
Affiliation(s)
- Maxwell C Coyle
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Adia M Tajima
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Fredrick Leon
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Semil P Choksi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada
| | - Sarah Espinoza
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S 3E1, Canada
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - David S Booth
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
9
|
Derderian C, Canales GI, Reiter JF. Seriously cilia: A tiny organelle illuminates evolution, disease, and intercellular communication. Dev Cell 2023; 58:1333-1349. [PMID: 37490910 PMCID: PMC10880727 DOI: 10.1016/j.devcel.2023.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/18/2023] [Accepted: 06/30/2023] [Indexed: 07/27/2023]
Abstract
The borders between cell and developmental biology, which have always been permeable, have largely dissolved. One manifestation is the blossoming of cilia biology, with cell and developmental approaches (increasingly complemented by human genetics, structural insights, and computational analysis) fruitfully advancing understanding of this fascinating, multifunctional organelle. The last eukaryotic common ancestor probably possessed a motile cilium, providing evolution with ample opportunity to adapt cilia to many jobs. Over the last decades, we have learned how non-motile, primary cilia play important roles in intercellular communication. Reflecting their diverse motility and signaling functions, compromised cilia cause a diverse range of diseases collectively called "ciliopathies." In this review, we highlight how cilia signal, focusing on how second messengers generated in cilia convey distinct information; how cilia are a potential source of signals to other cells; how evolution may have shaped ciliary function; and how cilia research may address thorny outstanding questions.
Collapse
Affiliation(s)
- Camille Derderian
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Gabriela I Canales
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
10
|
Zhang GW, Wang L, Wu J, Ye Y, Zhao J, Du Y, Tu Y, Luo Z, Fu S, Zuo F. Evaluation of MYBL1 as the master regulator for pachytene spermatocyte genes dysregulated in interspecific hybrid dzo. J Dairy Sci 2023; 106:4366-4379. [PMID: 37059660 DOI: 10.3168/jds.2022-22963] [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: 10/29/2022] [Accepted: 12/08/2022] [Indexed: 04/16/2023]
Abstract
Misregulation of spermatogenesis transcription factors (TF) in hybrids can lead to misexpression, which is a mechanism for hybrid male sterility (HMS). We used dzo (male offspring of Bos taurus ♂ × Bos grunniens ♀) in bovines to investigate the relationship of the key TF with HMS via RNA sequencing and assay for transposase-accessible chromatin with high-throughput sequencing analyses. RNA sequencing showed that the widespread misexpression in dzo was associated with spermatogenesis-related genes and somatic or progenitor genes. The transition from leptotene or zygotene spermatocytes to pachytene spermatocytes may be the key stage for meiosis arrest in dzo. The analysis of TF-binding motif enrichment revealed that the male meiosis-specific master TF MYB proto-oncogene like 1 (MYBL1, known as A-MYB) motif was enriched on the promoters of downregulated pachytene spermatocyte genes in dzo. Assay for transposase-accessible chromatin with high-throughput sequencing revealed that TF-binding sites for MYBL1, nuclear transcription factor Y, and regulatory factor X were enriched in the low-chromatin accessibility region of dzo. The target genes of the MYBL1-binding motif were associated with meiosis-specific genes and significantly downregulated in dzo testis. The transcription factor MYBL1 may be the candidate master regulator for pachytene spermatocyte genes dysregulated in interspecific HMS dzo. This study reported that a few upstream TF regulation changes might exert a cascading effect downstream in a regulatory network as a mechanism for HMS.
Collapse
Affiliation(s)
- Gong-Wei Zhang
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, 402460, Chongqing, China.
| | - Ling Wang
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, 402460, Chongqing, China
| | - Jingjing Wu
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Yiru Ye
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Jianjun Zhao
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Yanan Du
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Yun Tu
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Zonggang Luo
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China
| | - Shubing Fu
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, 402460, Chongqing, China
| | - Fuyuan Zuo
- College of Animal Science and Technology, Southwest University, Rongchang, 402460, Chongqing, China; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, 402460, Chongqing, China.
| |
Collapse
|
11
|
Liu Z, Dai H, Huo H, Li W, Jiang Y, Zhang X, Huo J. Molecular characteristics and transcriptional regulatory of spermatogenesis-related gene RFX2 in adult Banna mini-pig inbred line (BMI). Anim Reprod 2023; 20:e20220090. [PMID: 36922987 PMCID: PMC10010159 DOI: 10.1590/1984-3143-ar2022-0090] [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: 09/27/2022] [Accepted: 12/31/2022] [Indexed: 03/08/2023] Open
Abstract
RFX2 plays critical roles in mammalian spermatogenesis and cilium maturation. Here, the testes of 12-month-old adult boars of Banna mini-pig inbred line (BMI) were subjected to whole-transcriptome sequencing. The results indicated that the average expression (raw count) of RFX2 gene in BMI testes was 16138.25, and the average expression value of the corresponding transcript ENSSSCT00000043271.2 was 123.1898. The CDS of RFX2 obtained from BMI testes was 2,817 bp (GenBank accession number: OL362242). Gene structure analysis showed that RFX2 was located on chromosome 2 of the pig genome with 19 exons. Protein structure analysis indicated that RFX2 contains 728 amino acids with two conserved domains. Phylogenetic analysis revealed that RFX2 was highly conserved with evolutionary homologies among mammalian species. Other analyses, including PPI networks, KEGG, and GO, indicated that BMI RFX2 had interactions with 43 proteins involving various functions, such as in cell cycle, spermatid development, spermatid differentiation, cilium assembly, and cilium organization, etc. Correlation analysis between these proteins and the transcriptome data implied that RFX2 was significantly associated with FOXJ1, DNAH9, TMEM138, E2F7, and ATR, and particularly showed the highest correlation with ATR, demonstrating the importance of RFX2 and ART in spermatogenesis. Functional annotation implied that RFX2 was involved in 17 GO terms, including three cellular components (CC), six molecular functions (MF), and eight biological processes (BP). The analysis of miRNA-gene targeting indicated that BMI RFX2 was mainly regulated by two miRNAs, among which four lncRNAs and five lncRNAs competitively bound ssc-miR-365-5p and ssc-miR-744 with RFX2, respectively. Further, the dual-luciferase report assay indicated that the ssc-miR-365-5p and ssc-miR-744 significantly reduced luciferase activity of RFX2 3'UTR in the 293T cells, suggesting that these two miRNAs regulated the expression of RFX2. Our results revealed the important role of RFX2 in BMI spermatogenesis, making it an intriguing candidate for follow-up studies.
Collapse
Affiliation(s)
- Zhipeng Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hongmei Dai
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hailong Huo
- Yunnan Vocational and Technical College of Agriculture, Kunming, Yunnan, China
| | - Weizhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yun Jiang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xia Zhang
- College of Life Science, Lyuliang University, Lvliang, Shanxi, China
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.,Department of Biology, University of Rochester, Rochester, New York, USA
| |
Collapse
|
12
|
Zhang W, Xia S, Zhong X, Gao G, Yang J, Wang S, Cao M, Liang Z, Yang C, Wang J. Characterization of 2,2'4,4'-Tetrabromodiphenyl ether (BDE47)-induced testicular toxicity via single-cell RNA-sequencing. PRECISION CLINICAL MEDICINE 2022; 5:pbac016. [PMID: 35875604 PMCID: PMC9306015 DOI: 10.1093/pcmedi/pbac016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/12/2022] [Indexed: 11/30/2022] Open
Abstract
Background The growing male reproductive diseases have been linked to higher exposure to certain environmental compounds such as 2,2′,4,4′-tetrabromodiphenyl ether (BDE47) that are widely distributed in the food chain. However, the specific underlying molecular mechanisms for BDE47-induced male reproductive toxicity are not completely understood. Methods Here, for the first time, advanced single-cell RNA sequencing (ScRNA-seq) was employed to dissect BDE47-induced prepubertal testicular toxicity in mice from a pool of 76 859 cells. Results Our ScRNA-seq results revealed shared and heterogeneous information of differentially expressed genes, signaling pathways, transcription factors, and ligands-receptors in major testicular cell types in mice upon BDE47 treatment. Apart from disruption of hormone homeostasis, BDE47 was discovered to downregulate multiple previously unappreciated pathways such as double-strand break repair and cytokinesis pathways, indicative of their potential roles involved in BDE47-induced testicular injury. Interestingly, transcription factors analysis of ScRNA-seq results revealed that Kdm5b (lysine-specific demethylase 5B), a key transcription factor required for spermatogenesis, was downregulated in all germ cells as well as in Sertoli and telocyte cells in BDE47-treated testes of mice, suggesting its contribution to BDE47-induced impairment of spermatogenesis. Conclusions Overall, for the first time, we established the molecular cell atlas of mice testes to define BDE47-induced prepubertal testicular toxicity using the ScRNA-seq approach, providing novel insight into our understanding of the underlying mechanisms and pathways involved in BDE47-associated testicular injury at a single-cell resolution. Our results can serve as an important resource to further dissect the potential roles of BDE47, and other relevant endocrine-disrupting chemicals, in inducing male reproductive toxicity.
Collapse
Affiliation(s)
- Wei Zhang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University , Guangzhou 510632 , China
| | - Siyu Xia
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University , Guangzhou 510632 , China
| | - Xiaoru Zhong
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
| | - Guoyong Gao
- Department of Spine Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
| | - Jing Yang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
| | - Shuang Wang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
| | - Min Cao
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
| | - Zhen Liang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
| | - Chuanbin Yang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
| | - Jigang Wang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology) , Shenzhen 518020 , China
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences , Beijing 100700 , China
- Center for Reproductive Medicine, Dongguan Maternal and Child Health Care Hospital, Southern Medical University , Dongguan, 523125, Guangdong , China
| |
Collapse
|
13
|
Duan X, Jia X, Liang K, Huang F, Shan J, Chen H, Ruan X, Li L, Zhao H, Wang Q. Liposome-Encapsulated Rec8 and Dmrt1 Plasmids Induce Red-Spotted Grouper (Epinephelus akaara) Testis Maturation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:345-353. [PMID: 35303207 DOI: 10.1007/s10126-022-10111-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
In fish, the maturity of gonads plays an important role in the development and reproduction of the population, and it also dictates the success of captive breeding. Therefore, finding ways to promote gonadal maturation is an important goal in aquaculture. In this study, we injected recombinant dmrt1 and rec8 overexpression plasmids packaged in liposomes into the immature testis of red-spotted grouper (Epinephelus akaara) and measured the expression of Dmrt1 and Rec8 protein in vivo. Gonadosomatic index (GSI) and gonadal histology analyses showed that the testis developed from the immature to the mature state within 7 days after plasmid injection. Additionally, the spermatozoa concentration and motility in plasmid-injected fish was the same as that of naturally mature fish. These results provided evidence that delivery of dmrt1 and rec8 expression plasmids into the testis via injection induced testis maturation in vivo.
Collapse
Affiliation(s)
- Xuzhuo Duan
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xianze Jia
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Kaishan Liang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Fengqi Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jinhong Shan
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huitao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xinhe Ruan
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lihua Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huihong Zhao
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region On Marine Bioresource Conservation and Exploitation, Guangzhou, 510642, China.
| | - Qing Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region On Marine Bioresource Conservation and Exploitation, Guangzhou, 510642, China.
| |
Collapse
|
14
|
Xu W, Zhang Y, Qin D, Gui Y, Wang S, Du G, Yang F, Li L, Yuan S, Wang M, Wu X. Transcription factor-like 5 is a potential DNA/RNA-binding protein essential for maintaining male fertility in mice. J Cell Sci 2021; 135:273810. [PMID: 34931239 DOI: 10.1242/jcs.259036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022] Open
Abstract
Transcription factor-like 5 (TCFL5) is a testis-specific protein that contains the basic helix-loop-helix domain, but the in vivo functions of TCFL5 remain unknown. Herein, we generated CRISPR/Cas9-mediated knockout mice to dissect the function of TCFL5 in mouse testes. Surprisingly, we found that it was difficult to generate homozygous mice with the Tcfl5 deletion since the heterozygous males (Tcfl5+/-) were infertile. We did; however, observe markedly abnormal phenotypes of spermatids and spermatozoa in the testes and epididymides of Tcfl5+/- mice. Mechanistically, we demonstrated that TCFL5 transcriptionally and post-transcriptionally regulated a set of genes participating in male germ cell development via TCFL5 ChIP-DNA and eCLIP-RNA high-throughput sequencing. We also identified a known RBP, FXR1 as an interacting partner of TCFL5 that may coordinate the transition and localization of TCFL5 in the nucleus. Collectively, we herein report for the first time that Tcfl5 is haploinsufficient in vivo and acts as a dual-function protein that mediates DNA and RNA to regulate spermatogenesis.
Collapse
Affiliation(s)
- Weiya Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yiyun Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Dongdong Qin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shu Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Guihua Du
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Fan Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lufan Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mei Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China.,Centre for Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, China
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| |
Collapse
|
15
|
Novel variations in spermatogenic transcription regulators RFX2 and TAF7 increase risk of azoospermia. J Assist Reprod Genet 2021; 38:3195-3212. [PMID: 34762273 DOI: 10.1007/s10815-021-02352-5] [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: 08/23/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Genetic etiology of idiopathic male infertility is enigmatic owing to involvement of multiple gene regulatory networks in spermatogenesis process. Any change in optimal function of the transcription factors involved in this process owing to polymorphisms/mutations may increase the risk of infertility. We investigated polymorphisms/mutations of spermatogenic transcription regulators TAF7 and RFX2 and analysed their association with incidence of azoospermia among the men from West Bengal, India. METHODS Genotyping was carried by Sanger's dideoxy sequencing of 130 azoospermic men who were detected negative in Y chromosome microdeletion screening and 140 healthy controls. Association study was done by suitable statistical methods. In silico analysis was performed to infer the intuitive damaging effects of detected variants at transcripts and protein level. RESULTS We found significant association of TAF7 C16T (MW827584 G > A), RFX2 562delT (MZ560629delA), rs11547633 A > C, rs17606721 A > G, MW827583 C > T, and MZ379836 C > T variants with the incidence of azoospermia. In silico analysis predicted that the variants either alter the natural splice junctions of the transcript or cause probable damage in the structure of proteins of respective genes. CONCLUSION Polymorphisms/mutations of TAF7 and RFX2 genes increase risk of male infertility in Bengali population. The novel variants may be used as markers for male infertility screening in ART practise.
Collapse
|
16
|
Cunningham AM, Walker DM, Ramakrishnan A, Doyle MA, Bagot RC, Cates HM, Peña CJ, Issler O, Lardner CK, Browne C, Russo SJ, Shen L, Nestler EJ. Sperm Transcriptional State Associated with Paternal Transmission of Stress Phenotypes. J Neurosci 2021; 41:6202-6216. [PMID: 34099514 PMCID: PMC8287983 DOI: 10.1523/jneurosci.3192-20.2021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/25/2021] [Accepted: 04/20/2021] [Indexed: 01/03/2023] Open
Abstract
Paternal stress can induce long-lasting changes in germ cells potentially propagating heritable changes across generations. To date, no studies have investigated differences in transmission patterns between stress-resilient and stress-susceptible mice. We tested the hypothesis that transcriptional alterations in sperm during chronic social defeat stress (CSDS) transmit increased susceptibility to stress phenotypes to the next generation. We demonstrate differences in offspring from stressed fathers that depend on paternal category (resilient vs susceptible) and offspring sex. Importantly, artificial insemination (AI) reveals that sperm mediates some of the behavioral phenotypes seen in offspring. Using RNA-sequencing (RNA-seq), we report substantial and distinct changes in the transcriptomic profiles of sperm following CSDS in susceptible versus resilient fathers, with alterations in long noncoding RNAs (lncRNAs) predominating especially in susceptibility. Correlation analysis revealed that these alterations were accompanied by a loss of regulation of protein-coding genes by lncRNAs in sperm of susceptible males. We also identify several co-expression gene modules that are enriched in differentially expressed genes (DEGs) in sperm from either resilient or susceptible fathers. Taken together, these studies advance our understanding of intergenerational epigenetic transmission of behavioral experience.SIGNIFICANCE STATEMENT This manuscript contributes to the complex factors that influence the paternal transmission of stress phenotypes. By leveraging the segregation of males exposed to chronic social defeat stress (CSDS) into either resilient or susceptible categories we were able to identify the phenotypic differences in the paternal transmission of stress phenotypes across generations between the two lineages. Importantly, this work also alludes to the significance of both long noncoding RNAs (lncRNAs) and protein coding genes (PCGs) mediating the paternal transmission of stress. The knowledge gained from these data are of particular interest in understanding the risk for the development of psychiatric disorders such as anxiety and depression.
Collapse
Affiliation(s)
- Ashley M Cunningham
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Deena M Walker
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Aarthi Ramakrishnan
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Marie A Doyle
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Rosemary C Bagot
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Hannah M Cates
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Catherine J Peña
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Orna Issler
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Casey K Lardner
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Caleb Browne
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Scott J Russo
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Li Shen
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| | - Eric J Nestler
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience and Friedman Brain Institute, New York, New York 10029
| |
Collapse
|
17
|
de Lima AO, Afonso J, Edson J, Marcellin E, Palfreyman R, Porto-Neto LR, Reverter A, Fortes MRS. Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls. Front Genet 2021; 12:610116. [PMID: 33995471 PMCID: PMC8120238 DOI: 10.3389/fgene.2021.610116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
Spermatogenesis relies on complex molecular mechanisms, essential for the genesis and differentiation of the male gamete. Germ cell differentiation starts at the testicular parenchyma and finishes in the epididymis, which has three main regions: head, body, and tail. RNA-sequencing data of the testicular parenchyma (TP), head epididymis (HE), and tail epididymis (TE) from four bulls (three biopsies per bull: 12 samples) were subjected to differential expression analyses, functional enrichment analyses, and co-expression analyses. The aim was to investigate the co-expression and infer possible regulatory roles for transcripts involved in the spermatogenesis of Bos indicus bulls. Across the three pairwise comparisons, 3,826 differentially expressed (DE) transcripts were identified, of which 384 are small RNAs. Functional enrichment analysis pointed to gene ontology (GO) terms related to ion channel activity, detoxification of copper, neuroactive receptors, and spermatogenesis. Using the regulatory impact factor (RIF) algorithm, we detected 70 DE small RNAs likely to regulate the DE transcripts considering all pairwise comparisons among tissues. The pattern of small RNA co-expression suggested that these elements are involved in spermatogenesis regulation. The 3,826 DE transcripts (mRNAs and small RNAs) were further subjected to co-expression analyses using the partial correlation and information theory (PCIT) algorithm for network prediction. Significant correlations underpinned the co-expression network, which had 2,216 transcripts connected by 158,807 predicted interactions. The larger network cluster was enriched for male gamete generation and had 15 miRNAs with significant RIF. The miRNA bta-mir-2886 showed the highest number of connections (601) and was predicted to down-regulate ELOVL3, FEZF2, and HOXA13 (negative co-expression correlations and confirmed with TargetScan). In short, we suggest that bta-mir-2886 and other small RNAs might modulate gene expression in the testis and epididymis, in Bos indicus cattle.
Collapse
Affiliation(s)
- Andressa O de Lima
- Department of Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Juliana Afonso
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Janette Edson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD, Australia
| | - Robin Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD, Australia
| | - Laercio R Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| |
Collapse
|
18
|
Yokota S, Sekine N, Wakayama T, Oshio S. Impact of chronic vitamin A excess on sperm morphogenesis in mice. Andrology 2021; 9:1579-1592. [PMID: 33818007 DOI: 10.1111/andr.13013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/05/2021] [Accepted: 03/31/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND The increasing availability of fortified foods and supplements has caused an overconsumption of vitamin A (VA), above the recommended level. To date, the effects of chronic VA excess (VAE) on spermatogenesis remain unclear. OBJECTIVE This study aims to investigate the long-term excessive intake of VA effects on spermatogenesis in mice. MATERIALS AND METHODS Dams were initially fed a control diet (4 IU/g) or a VAE diet (250 IU/g), 4 weeks prior to mating and during pregnancy. Dams and their male pups continued this diet regimen until the offspring reached 12 weeks of age. At 12 weeks of age, epididymis caudal spermatozoa and testes were collected. For histological analysis, sections were stained with periodic acid-Schiff-hematoxylin, and quantitative PCR was used to detect changes in gene expression in the testes of the VAE mice. Sperm motility and morphology were evaluated to detect the endpoint of VAE toxicity. RESULTS Body weights were not significantly different between the control and VAE groups. Testicular cross-sections from the control and VAE mice contained a normal array of germ cells, and the daily sperm production was similar between the two groups. However, the percentage of seminiferous tubules in stages VII and VIII was significantly lower in the VAE mice than in the control. In addition, significant changes in the expression of genes involved in retinoid metabolism, spermatogenesis, and spermiogenesis were detected in the testes of the VAE mice. Consistently, sperm motility and head morphology were significantly impaired in the VAE mice. DISCUSSION AND CONCLUSION Our findings suggest that long-term dietary intake of VAE was able to influence both pre- and post-meiotic spermatogenesis. As a result of testicular toxicity, we demonstrated, to the best of our knowledge, for the first time that long-term VAE caused sperm-head abnormalities.
Collapse
Affiliation(s)
- Satoshi Yokota
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research, National Institute of Health Sciences, Kawasaki, Japan.,Department of Hygiene Chemistry, School of Pharmaceutical Sciences, Ohu University, Koriyama, Japan
| | - Nao Sekine
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research, National Institute of Health Sciences, Kawasaki, Japan
| | - Tomohiko Wakayama
- Department of Histology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Shigeru Oshio
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research, National Institute of Health Sciences, Kawasaki, Japan
| |
Collapse
|
19
|
Xia M, Xia J, Niu C, Zhong Y, Ge T, Ding Y, Zheng Y. Testis-expressed protein 33 is not essential for spermiogenesis and fertility in mice. Mol Med Rep 2021; 23:317. [PMID: 33760102 PMCID: PMC7974414 DOI: 10.3892/mmr.2021.11956] [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: 05/20/2020] [Accepted: 11/11/2020] [Indexed: 11/06/2022] Open
Abstract
Gene expression analyses have revealed that there are >2,300 testis-enriched genes in mice, and gene knockout models have shown that a number of them are responsible for male fertility. However, the functions of numerous genes have yet to be clarified. The aim of the present study was to identify the expression pattern of testis-expressed protein 33 (TEX33) in mice and explore the role of TEX33 in male reproduction. Reverse transcription-polymerase chain reaction and western blot assays were used to investigate the mRNA and protein levels of TEX33 in mouse testes during the first wave of spermatogenesis. Immunofluorescence analysis was also performed to identify the cellular and structural localization of TEX33 protein in the testes. Tex33 knockout mice were generated by CRISPR/Cas9 gene-editing. Histological analysis with hematoxylin and eosin or periodic acid-Schiff (PAS) staining, computer-assisted sperm analysis (CASA) and fertility testing, were also carried out to evaluate the effect of TEX33 on mouse spermiogenesis and male reproduction. The results showed that Tex33 mRNA and protein were exclusively expressed in mouse testes and were first detected on postnatal days 21–28 (spermiogenesis phase); their expression then remained into adulthood. Immunofluorescence analysis revealed that TEX33 protein was located in the spermatids and sperm within the seminiferous tubules of the mouse testes, and exhibited specific localization to the acrosome, flagellum and manchette during spermiogenesis. These results suggested that TEX33 may play a role in mouse spermiogenesis. However, Tex33 knockout mice presented no detectable difference in testis-to-body weight ratios when compared with wild-type mice. PAS staining and CASA revealed that spermatogenesis and sperm quality were normal in mice lacking Tex33. In addition, fertility testing suggested that the Tex33 knockout mice had normal reproductive functions. In summary, the findings of the present study indicate that TEX33 is associated with spermiogenesis but is not essential for sperm development and male fertility.
Collapse
Affiliation(s)
- Mengmeng Xia
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| | - Jing Xia
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| | - Changmin Niu
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| | - Yanan Zhong
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| | - Tingting Ge
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| | - Yue Ding
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| | - Ying Zheng
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
| |
Collapse
|
20
|
Lewis M, Stracker TH. Transcriptional regulation of multiciliated cell differentiation. Semin Cell Dev Biol 2021; 110:51-60. [DOI: 10.1016/j.semcdb.2020.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/25/2020] [Accepted: 04/13/2020] [Indexed: 01/01/2023]
|
21
|
Androglobin gene expression patterns and FOXJ1-dependent regulation indicate its functional association with ciliogenesis. J Biol Chem 2021; 296:100291. [PMID: 33453283 PMCID: PMC7949040 DOI: 10.1016/j.jbc.2021.100291] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/17/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Androglobin (ADGB) represents the latest addition to the globin superfamily in metazoans. The chimeric protein comprises a calpain domain and a unique circularly permutated globin domain. ADGB expression levels are most abundant in mammalian testis, but its cell-type-specific expression, regulation, and function have remained unexplored. Analyzing bulk and single-cell mRNA-Seq data from mammalian tissues, we found that—in addition to the testes—ADGB is prominently expressed in the female reproductive tract, lungs, and brain, specifically being associated with cell types forming motile cilia. Correlation analysis suggested coregulation of ADGB with FOXJ1, a crucial transcription factor of ciliogenesis. Investigating the transcriptional regulation of the ADGB gene, we characterized its promoter using epigenomic datasets, exogenous promoter-dependent luciferase assays, and CRISPR/dCas9-VPR-mediated activation approaches. Reporter gene assays revealed that FOXJ1 indeed substantially enhanced luciferase activity driven by the ADGB promoter. ChIP assays confirmed binding of FOXJ1 to the endogenous ADGB promoter region. We dissected the minimal sequence required for FOXJ1-dependent regulation and fine mapped the FOXJ1 binding site to two evolutionarily conserved regions within the ADGB promoter. FOXJ1 overexpression significantly increased endogenous ADGB mRNA levels in HEK293 and MCF-7 cells. Similar results were observed upon RFX2 overexpression, another key transcription factor in ciliogenesis. The complex transcriptional regulation of the ADGB locus was illustrated by identifying a distal enhancer, responsible for synergistic regulation by RFX2 and FOXJ1. Finally, cell culture studies indicated an ADGB-dependent increase in the number of ciliated cells upon overexpression of the full-length protein, confirming a ciliogenesis-associated role of ADGB in mammals.
Collapse
|
22
|
Lemeille S, Paschaki M, Baas D, Morlé L, Duteyrat JL, Ait-Lounis A, Barras E, Soulavie F, Jerber J, Thomas J, Zhang Y, Holtzman MJ, Kistler WS, Reith W, Durand B. Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis. Nucleic Acids Res 2020; 48:9019-9036. [PMID: 32725242 PMCID: PMC7498320 DOI: 10.1093/nar/gkaa625] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
Cilia assembly is under strict transcriptional control during animal development. In vertebrates, a hierarchy of transcription factors (TFs) are involved in controlling the specification, differentiation and function of multiciliated epithelia. RFX TFs play key functions in the control of ciliogenesis in animals. Whereas only one RFX factor regulates ciliogenesis in C. elegans, several distinct RFX factors have been implicated in this process in vertebrates. However, a clear understanding of the specific and redundant functions of different RFX factors in ciliated cells remains lacking. Using RNA-seq and ChIP-seq approaches we identified genes regulated directly and indirectly by RFX1, RFX2 and RFX3 in mouse ependymal cells. We show that these three TFs have both redundant and specific functions in ependymal cells. Whereas RFX1, RFX2 and RFX3 occupy many shared genomic loci, only RFX2 and RFX3 play a prominent and redundant function in the control of motile ciliogenesis in mice. Our results provide a valuable list of candidate ciliary genes. They also reveal stunning differences between compensatory processes operating in vivo and ex vivo.
Collapse
Affiliation(s)
- Sylvain Lemeille
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Marie Paschaki
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Dominique Baas
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Laurette Morlé
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Jean-Luc Duteyrat
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Aouatef Ait-Lounis
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Fabien Soulavie
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Julie Jerber
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Joëlle Thomas
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| | - Yong Zhang
- Department of Medicine and Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J Holtzman
- Department of Medicine and Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri
| | - W Stephen Kistler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Bénédicte Durand
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS UMR-5310, INSERM U-1217, Institut NeuroMyoGène, F-69008, Lyon, France
| |
Collapse
|
23
|
Lee L, Ostrowski LE. Motile cilia genetics and cell biology: big results from little mice. Cell Mol Life Sci 2020; 78:769-797. [PMID: 32915243 DOI: 10.1007/s00018-020-03633-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/11/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022]
Abstract
Our understanding of motile cilia and their role in disease has increased tremendously over the last two decades, with critical information and insight coming from the analysis of mouse models. Motile cilia form on specific epithelial cell types and typically beat in a coordinated, whip-like manner to facilitate the flow and clearance of fluids along the cell surface. Defects in formation and function of motile cilia result in primary ciliary dyskinesia (PCD), a genetically heterogeneous disorder with a well-characterized phenotype but no effective treatment. A number of model systems, ranging from unicellular eukaryotes to mammals, have provided information about the genetics, biochemistry, and structure of motile cilia. However, with remarkable resources available for genetic manipulation and developmental, pathological, and physiological analysis of phenotype, the mouse has risen to the forefront of understanding mammalian motile cilia and modeling PCD. This is evidenced by a large number of relevant mouse lines and an extensive body of genetic and phenotypic data. More recently, application of innovative cell biological techniques to these models has enabled substantial advancement in elucidating the molecular and cellular mechanisms underlying the biogenesis and function of mammalian motile cilia. In this article, we will review genetic and cell biological studies of motile cilia in mouse models and their contributions to our understanding of motile cilia and PCD pathogenesis.
Collapse
Affiliation(s)
- Lance Lee
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA. .,Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, USA.
| | - Lawrence E Ostrowski
- Marsico Lung Institute/Cystic Fibrosis Center and Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
24
|
Wang X, Cheng J, Qin W, Chen H, Chen G, Shang X, Zhang M, Balsai N, Chen H. Polymorphisms in 5' proximal regulating region of THRSP gene are associated with fat production in pigs. 3 Biotech 2020; 10:267. [PMID: 32509500 DOI: 10.1007/s13205-020-02266-6] [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: 04/16/2020] [Accepted: 05/18/2020] [Indexed: 01/17/2023] Open
Abstract
Chinese and imported pig breeds differ in fat production potential, which is associated with the polymorphisms in the 5' proximal regulating region (5'PRR) of thyroid hormone responsive gene (THRSP). In three Chinese breeds (Dingyuan, CDY; Wannanhua, CWH; and Jixi, CJX) and one introduced breed (Yorkshire, YKS), three variant sites were located at T/C-400, A/G-376, and G/A-98 in the 5'PRR. Chinese pig breeds had higher C-400 allele frequencies than YKS. The frequencies of A-376 in CDY and G-376 in CWH were about 0.8. G-98 allele frequencies in CWH and YKS were 0.8617 and 0.8149, respectively. TGG was the dominant haplotype in YKS, CGG in CWH and CJX, and CAA in CDY. According to haplotype frequency, four breeds were clustered into three types, which was consistent with the geographical distribution of the breeds. In CDY, the average backfat thickness (BFT) was the highest with the CC-400 genotype, followed by CT-400 and TT-400 genotypes. In YKS, the pigs with CC-400 or CT-400 genotypes had higher BFT and average daily weight gain, whereas those with CC-400 or TT-400 genotypes had larger lion-eye area. No significant difference was observed in carcass traits among different genotypes at the A/G-376 and G/A-98 loci. The mRNA abundance of THRSP expression for the CCAGAG genotype was significantly higher than that for CTAGAG or TTAGAG genotype. These results indicated that the polymorphisms and genotype distribution of THRSP were closely related to the potential for fat production in pig breeds, which were the result of adaptation to artificial selection and natural selection.
Collapse
Affiliation(s)
- Xiaohong Wang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
- Experimental Animal Center of Anhui Medical University, Hefei, 230032 China
| | - Jin Cheng
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Wenjuan Qin
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
- Anhui Agricultural University International Immunization Center, Hefei, 230036 China
| | - Hua Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Gongwei Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Xuanjian Shang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Mengting Zhang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Nyamsuren Balsai
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Hongquan Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 China
- Key Laboratory of Local Livestock and Poultry Genetic Resources Conservation and Biobreeding of Anhui Province, Hefei, 230036 China
- Anhui Agricultural University International Immunization Center, Hefei, 230036 China
| |
Collapse
|
25
|
Jung M, Wells D, Rusch J, Ahmad S, Marchini J, Myers SR, Conrad DF. Unified single-cell analysis of testis gene regulation and pathology in five mouse strains. eLife 2019; 8:e43966. [PMID: 31237565 PMCID: PMC6615865 DOI: 10.7554/elife.43966] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
To fully exploit the potential of single-cell functional genomics in the study of development and disease, robust methods are needed to simplify the analysis of data across samples, time-points and individuals. Here we introduce a model-based factor analysis method, SDA, to analyze a novel 57,600 cell dataset from the testes of wild-type mice and mice with gonadal defects due to disruption of the genes Mlh3, Hormad1, Cul4a or Cnp. By jointly analyzing mutant and wild-type cells we decomposed our data into 46 components that identify novel meiotic gene-regulatory programs, mutant-specific pathological processes, and technical effects, and provide a framework for imputation. We identify, de novo, DNA sequence motifs associated with individual components that define temporally varying modes of gene expression control. Analysis of SDA components also led us to identify a rare population of macrophages within the seminiferous tubules of Mlh3-/- and Hormad1-/- mice, an area typically associated with immune privilege.
Collapse
Affiliation(s)
- Min Jung
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Daniel Wells
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Jannette Rusch
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Suhaira Ahmad
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Jonathan Marchini
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Simon R Myers
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Donald F Conrad
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
- Division of Genetics, Oregon National Primate Research CenterOregon Health & Science UniversityPortlandUnited States
| |
Collapse
|
26
|
Genetic Factors Affecting Sperm Chromatin Structure. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1166:1-28. [PMID: 31301043 DOI: 10.1007/978-3-030-21664-1_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spermatozoa genome has unique features that make it a fascinating field of investigation: first, because, with oocyte genome, it can be transmitted generation after generation; second, because of genetic shuffling during meiosis, each spermatozoon is virtually unique in terms of genetic content, with consequences for species evolution; and finally, because its chromatin organization is very different from that of somatic cells or oocytes, as it is not based on nucleosomes but on nucleoprotamines which confer a higher order of packaging. Histone-to-protamine transition involves many actors, such as regulators of spermatid gene expression, components of the nuclear envelop, histone-modifying enzymes and readers, chaperones, histone variants, transition proteins, protamines, and certainly many more to be discovered.In this book chapter, we will present what is currently known about sperm chromatin structure and how it is established during spermiogenesis, with the aim to list the genetic factors that regulate its organization.
Collapse
|
27
|
Lin Z, Tong MH. m 6A mRNA modification regulates mammalian spermatogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:403-411. [PMID: 30391644 DOI: 10.1016/j.bbagrm.2018.10.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023]
Abstract
Mammalian spermatogenesis is a highly specialized differentiation process involving precise regulatory mechanisms at the transcriptional, posttranscriptional, and translational levels. Emerging evidence has shown that N6-methyladenosine (m6A), an epitranscriptomic regulator of gene expression, can influence pre-mRNA splicing, mRNA export, turnover, and translation, which are controlled in the male germline to ensure coordinated gene expression. In this review, we summarize the typical features of m6A RNA modification on mRNA during male germline development, and highlight the function of writers, erasers, and readers of m6A during mouse spermatogenesis.
Collapse
Affiliation(s)
- Zhen Lin
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Han Tong
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| |
Collapse
|
28
|
Chen Y, Zheng Y, Gao Y, Lin Z, Yang S, Wang T, Wang Q, Xie N, Hua R, Liu M, Sha J, Griswold MD, Li J, Tang F, Tong MH. Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis. Cell Res 2018; 28:879-896. [PMID: 30061742 PMCID: PMC6123400 DOI: 10.1038/s41422-018-0074-y] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 06/25/2018] [Accepted: 07/05/2018] [Indexed: 12/12/2022] Open
Abstract
A systematic interrogation of male germ cells is key to complete understanding of molecular mechanisms governing spermatogenesis and the development of new strategies for infertility therapies and male contraception. Here we develop an approach to purify all types of homogeneous spermatogenic cells by combining transgenic labeling and synchronization of the cycle of the seminiferous epithelium, and subsequent single-cell RNA-sequencing. We reveal extensive and previously uncharacterized dynamic processes and molecular signatures in gene expression, as well as specific patterns of alternative splicing, and novel regulators for specific stages of male germ cell development. Our transcriptomics analyses led us to discover discriminative markers for isolating round spermatids at specific stages, and different embryo developmental potentials between early and late stage spermatids, providing evidence that maturation of round spermatids impacts on embryo development. This work provides valuable insights into mammalian spermatogenesis, and a comprehensive resource for future studies towards the complete elucidation of gametogenesis.
Collapse
Affiliation(s)
- Yao Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuxuan Zheng
- Beijing Advanced Innovation Center for Genomics, Biomedical Institute for Pioneering Investigation via Convergence, College of Life Sciences, Peking University, Beijing, 100871, China.,Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yun Gao
- Beijing Advanced Innovation Center for Genomics, Biomedical Institute for Pioneering Investigation via Convergence, College of Life Sciences, Peking University, Beijing, 100871, China.,Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Zhen Lin
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Suming Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Tongtong Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qiu Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Nannan Xie
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rong Hua
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Michael D Griswold
- School of Molecular Biosciences and the Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Jinsong Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Biomedical Institute for Pioneering Investigation via Convergence, College of Life Sciences, Peking University, Beijing, 100871, China. .,Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Ming-Han Tong
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| |
Collapse
|
29
|
Bai S, Fu K, Yin H, Cui Y, Yue Q, Li W, Cheng L, Tan H, Liu X, Guo Y, Zhang Y, Xie J, He W, Wang Y, Feng H, Xin C, Zhang J, Lin M, Shen B, Sun Z, Guo X, Zheng K, Ye L. Sox30 initiates transcription of haploid genes during late meiosis and spermiogenesis in mouse testes. Development 2018; 145:dev.164855. [PMID: 29866902 DOI: 10.1242/dev.164855] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/23/2018] [Indexed: 12/17/2022]
Abstract
Transcription factors of the Sox protein family contain a DNA-binding HMG box and are key regulators of progenitor cell fate. Here, we report that expression of Sox30 is restricted to meiotic spermatocytes and postmeiotic haploids. Sox30 mutant males are sterile owing to spermiogenic arrest at the early round spermatid stage. Specifically, in the absence of Sox30, proacrosomic vesicles fail to form a single acrosomal organelle, and spermatids arrest at step 2-3. Although most Sox30 mutant spermatocytes progress through meiosis, accumulation of diplotene spermatocytes indicates a delayed or impaired transition from meiotic to postmeiotic stages. Transcriptome analysis of isolated stage-specific spermatogenic cells reveals that Sox30 controls a core postmeiotic gene expression program that initiates as early as the late meiotic cell stage. ChIP-seq analysis shows that Sox30 binds to specific DNA sequences in mouse testes, and its genomic occupancy correlates positively with expression of many postmeiotic genes including Tnp1, Hils1, Ccdc54 and Tsks These results define Sox30 as a crucial transcription factor that controls the transition from a late meiotic to a postmeiotic gene expression program and subsequent round spermatid development.
Collapse
Affiliation(s)
- Shun Bai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Kaiqiang Fu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Huiqi Yin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Qiuling Yue
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Wenbo Li
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Le Cheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Huanhuan Tan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Xiaofei Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yingwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Jie Xie
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Wenxiu He
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Yuanyuan Wang
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Hua Feng
- Omics Core of Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Changpeng Xin
- Omics Core of Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Jinwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Mingyan Lin
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Zheng Sun
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China
| |
Collapse
|
30
|
Castro W, Chelbi ST, Niogret C, Ramon-Barros C, Welten SPM, Osterheld K, Wang H, Rota G, Morgado L, Vivier E, Raeber ME, Boyman O, Delorenzi M, Barras D, Ho PC, Oxenius A, Guarda G. The transcription factor Rfx7 limits metabolism of NK cells and promotes their maintenance and immunity. Nat Immunol 2018; 19:809-820. [PMID: 29967452 DOI: 10.1038/s41590-018-0144-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 04/20/2018] [Indexed: 02/06/2023]
Abstract
Regulatory factor X 7 (Rfx7) is an uncharacterized transcription factor belonging to a family involved in ciliogenesis and immunity. Here, we found that deletion of Rfx7 leads to a decrease in natural killer (NK) cell maintenance and immunity in vivo. Genomic approaches showed that Rfx7 coordinated a transcriptional network controlling cell metabolism. Rfx7-/- NK lymphocytes presented increased size, granularity, proliferation, and energetic state, whereas genetic reduction of mTOR activity mitigated those defects. Notably, Rfx7-deficient NK lymphocytes were rescued by interleukin 15 through engagement of the Janus kinase (Jak) pathway, thus revealing the importance of this signaling for maintenance of such spontaneously activated NK cells. Rfx7 therefore emerges as a novel transcriptional regulator of NK cell homeostasis and metabolic quiescence.
Collapse
Affiliation(s)
- Wilson Castro
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Sonia T Chelbi
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland.,Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Charlène Niogret
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | | | | | - Kevin Osterheld
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Haiping Wang
- Ludwig Center for Cancer Research of the University of Lausanne, Epalinges, Switzerland.,Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland
| | - Giorgia Rota
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Leonor Morgado
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, Marseille, France.,Service d'Immunologie, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France.,Innate Pharma Research Labs., Innate Pharma, Marseille, France
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mauro Delorenzi
- Ludwig Center for Cancer Research of the University of Lausanne, Epalinges, Switzerland.,Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - David Barras
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ping-Chih Ho
- Ludwig Center for Cancer Research of the University of Lausanne, Epalinges, Switzerland.,Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland
| | | | - Greta Guarda
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland. .,Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.
| |
Collapse
|
31
|
Zhang D, Xie D, Lin X, Ma L, Chen J, Zhang D, Wang Y, Duo S, Feng Y, Zheng C, Jiang B, Ning Y, Han C. The transcription factor SOX30 is a key regulator of mouse spermiogenesis. Development 2018; 145:145/11/dev164723. [PMID: 29848638 DOI: 10.1242/dev.164723] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/30/2018] [Indexed: 01/01/2023]
Abstract
The postmeiotic development of male germ cells, also known as spermiogenesis, features the coordinated expression of a large number of spermatid-specific genes. However, only a limited number of key transcription factors have been identified and the underlying regulatory mechanisms remain largely unknown. Here, we report that SOX30, the most-divergent member of the Sry-related high-motility group box (SOX) family of transcription factors, is essential for mouse spermiogenesis. The SOX30 protein was predominantly expressed in spermatids, while its transcription was regulated by retinoic acid and by MYBL1 before and during meiosis. Sox30 knockout mice arrested spermiogenesis at step 3 round spermatids, which underwent apoptosis and abnormal chromocenter formation. We also determined that SOX30 regulated the expression of hundreds of spermatid-specific protein-coding and long non-coding RNA genes. SOX30 bound to the proximal promoter of its own gene and activated its transcription. These results reveal SOX30 as a novel key regulator of spermiogenesis that regulates its own transcription to enforce and activate this meiotic regulatory pathway.
Collapse
Affiliation(s)
- Daoqin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Xie
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiwen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Longfei Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Daoqi Zhang
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yang Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuguang Duo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanmin Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunwei Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Binjie Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Ning
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
32
|
Abstract
Male infertility is a major and growing problem and, in most cases, the specific root cause is unknown. Here we show that the transcription factor SOX30 plays a critical role in mouse spermatogenesis. Sox30-null mice are healthy and females are fertile, but males are sterile. In the absence of Sox30 meiosis initiates normally in both sexes but, in males, germ cell development arrests during the post-meiotic round spermatid period. In the mutant testis, acrosome and axoneme development are aberrant, multinucleated germ cells (symplasts) form and round spermatids unable to process beyond step 3 of spermiogenesis. No elongated spermatids nor spermatozoa are produced. Thus, Sox30 represents a rare example of a gene for which loss of function results in a complete arrest of spermatogenesis at the onset of spermiogenesis. Our results suggest that SOX30 mutations may underlie some instances of unexplained non-obstructive azoospermia in humans.
Collapse
|
33
|
Yu CH, Xie T, Zhang RP, A ZC. Association of the common SNPs in RNF212, STAG3 and RFX2 gene with male infertility with azoospermia in Chinese population. Eur J Obstet Gynecol Reprod Biol 2017; 221:109-112. [PMID: 29277047 DOI: 10.1016/j.ejogrb.2017.12.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/08/2017] [Accepted: 12/14/2017] [Indexed: 11/17/2022]
Abstract
OBJECTIVE The aim of this study was to explore the association between the SNP rs4045481 in RNF212 gene, rs1050482 and rs11531577 in STAG3 gene as well as rs2288846 in RFX2 gene and male infertility with azoospermia in Chinese population. STUDY DESIGN Two hundreds and twenty infertile patients with azoospermia and 248 fertile men were recruited in the present study. The four SNPs investigated were genotyped using polymerase chain reaction and restriction fragment length polymorphism assay. The differences in allelic and genotypic frequencies between patients and controls were evaluated by chi-square test. RESULTS No significant differences in allele and genotype frequencies of SNP rs1050482 and rs11531577 in STAG3 gene as well as rs2288846 in RFX2 gene between patients with azoospermia and controls were observed. However, the frequencies of allele C(43.6% vs. 34.1%, P = 0.003, OR = 1.498, 95% CI 1.150-1.192) and genotype CC (24.6% vs. 12.0%, P = 0.001, OR = 2.346, 95% CI 1.448-3.858) were significantly higher in patients with azoospermia than those in controls at the rs4045481 locus in RNF212 gene. CONCULUSION The polymorphism of SNP rs4045481 in RNF212 gene might be associated with azoospermia and genotype CC of this SNP may be a risk factor of azoospermia.
Collapse
Affiliation(s)
- Cheng-He Yu
- College of Basic Medicine, Dali University, Dali, 671000, China; Department of Reproductive Medicine, Affiliated Hospital of Dali University, Dali, 671000, China
| | - Ting Xie
- College of Basic Medicine, Dali University, Dali, 671000, China
| | - Ruo-Peng Zhang
- Department of Reproductive Medicine, Affiliated Hospital of Dali University, Dali, 671000, China
| | - Zhou-Cun A
- College of Basic Medicine, Dali University, Dali, 671000, China; Department of Genetics, College of Agriculture and Biology, Dali University, Dali, 671003, China.
| |
Collapse
|
34
|
Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. The Gene Ontology of eukaryotic cilia and flagella. Cilia 2017; 6:10. [PMID: 29177046 PMCID: PMC5688719 DOI: 10.1186/s13630-017-0054-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/30/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Recent research into ciliary structure and function provides important insights into inherited diseases termed ciliopathies and other cilia-related disorders. This wealth of knowledge needs to be translated into a computational representation to be fully exploitable by the research community. To this end, members of the Gene Ontology (GO) and SYSCILIA Consortia have worked together to improve representation of ciliary substructures and processes in GO. METHODS Members of the SYSCILIA and Gene Ontology Consortia suggested additions and changes to GO, to reflect new knowledge in the field. The project initially aimed to improve coverage of ciliary parts, and was then broadened to cilia-related biological processes. Discussions were documented in a public tracker. We engaged the broader cilia community via direct consultation and by referring to the literature. Ontology updates were implemented via ontology editing tools. RESULTS So far, we have created or modified 127 GO terms representing parts and processes related to eukaryotic cilia/flagella or prokaryotic flagella. A growing number of biological pathways are known to involve cilia, and we continue to incorporate this knowledge in GO. The resulting expansion in GO allows more precise representation of experimentally derived knowledge, and SYSCILIA and GO biocurators have created 199 annotations to 50 human ciliary proteins. The revised ontology was also used to curate mouse proteins in a collaborative project. The revised GO and annotations, used in comparative 'before and after' analyses of representative ciliary datasets, improve enrichment results significantly. CONCLUSIONS Our work has resulted in a broader and deeper coverage of ciliary composition and function. These improvements in ontology and protein annotation will benefit all users of GO enrichment analysis tools, as well as the ciliary research community, in areas ranging from microscopy image annotation to interpretation of high-throughput studies. We welcome feedback to further enhance the representation of cilia biology in GO.
Collapse
Affiliation(s)
- Paola Roncaglia
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
- The Gene Ontology Consortium, http://geneontology.org
| | - Teunis J. P. van Dam
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Karen R. Christie
- The Gene Ontology Consortium, http://geneontology.org
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Lora Nacheva
- Fakultät Biowissenschaften, Universität Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Grischa Toedt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Rachael P. Huntley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
- Present Address: Centre for Cardiovascular Genetics, University College London, London, WC1E 6JF UK
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Jane Lomax
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
- The Gene Ontology Consortium, http://geneontology.org
- Present Address: SciBite Limited, BioData Innovation Centre, Wellcome Genome Campus, Cambridge, CB10 1DR UK
| |
Collapse
|
35
|
Zhou L, Canagarajah B, Zhao Y, Baibakov B, Tokuhiro K, Maric D, Dean J. BTBD18 Regulates a Subset of piRNA-Generating Loci through Transcription Elongation in Mice. Dev Cell 2017; 40:453-466.e5. [PMID: 28292424 DOI: 10.1016/j.devcel.2017.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/18/2016] [Accepted: 02/09/2017] [Indexed: 11/27/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs essential for animal germ cell development. Despite intense investigation of post-transcriptional processing, chromatin regulators for piRNA biogenesis in mammals remain largely unexplored. Here we document that BTBD18 is a pachytene nuclear protein in mouse testes that occupies a subset of pachytene piRNA-producing loci. Ablation of Btbd18 in mice disrupts piRNA biogenesis, prevents spermiogenesis, and results in male sterility. Transcriptome profiling, chromatin accessibility, and RNA polymerase II occupancy demonstrate that BTBD18 facilitates expression of pachytene piRNA precursors by promoting transcription elongation. Thus, our study identifies BTBD18 as a specific controller for transcription activation through RNA polymerase II elongation at a subset of genomic piRNA loci.
Collapse
Affiliation(s)
- Liquan Zhou
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Bertram Canagarajah
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yangu Zhao
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Boris Baibakov
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keizo Tokuhiro
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dragan Maric
- NINDS Flow Cytometry Core Facility, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
36
|
Cartier-Michaud A, Bailly AL, Betzi S, Shi X, Lissitzky JC, Zarubica A, Sergé A, Roche P, Lugari A, Hamon V, Bardin F, Derviaux C, Lembo F, Audebert S, Marchetto S, Durand B, Borg JP, Shi N, Morelli X, Aurrand-Lions M. Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis. PLoS Genet 2017; 13:e1006803. [PMID: 28617811 PMCID: PMC5472279 DOI: 10.1371/journal.pgen.1006803] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 05/05/2017] [Indexed: 01/01/2023] Open
Abstract
Spermatogenesis is a dynamic process that is regulated by adhesive interactions between germ and Sertoli cells. Germ cells express the Junctional Adhesion Molecule-C (JAM-C, encoded by Jam3), which localizes to germ/Sertoli cell contacts. JAM-C is involved in germ cell polarity and acrosome formation. Using a proteomic approach, we demonstrated that JAM-C interacted with the Golgi reassembly stacking protein of 55 kDa (GRASP55, encoded by Gorasp2) in developing germ cells. Generation and study of Gorasp2-/- mice revealed that knock-out mice suffered from spermatogenesis defects. Acrosome formation and polarized localization of JAM-C in spermatids were altered in Gorasp2-/- mice. In addition, Golgi morphology of spermatocytes was disturbed in Gorasp2-/- mice. Crystal structures of GRASP55 in complex with JAM-C or JAM-B revealed that GRASP55 interacted via PDZ-mediated interactions with JAMs and induced a conformational change in GRASP55 with respect of its free conformation. An in silico pharmacophore approach identified a chemical compound called Graspin that inhibited PDZ-mediated interactions of GRASP55 with JAMs. Treatment of mice with Graspin hampered the polarized localization of JAM-C in spermatids, induced the premature release of spermatids and affected the Golgi morphology of meiotic spermatocytes.
Collapse
Affiliation(s)
| | - Anne-Laure Bailly
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Stéphane Betzi
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Xiaoli Shi
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | | | - Ana Zarubica
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Arnauld Sergé
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Philippe Roche
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Adrien Lugari
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Véronique Hamon
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Florence Bardin
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Carine Derviaux
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Frédérique Lembo
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Stéphane Audebert
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Sylvie Marchetto
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Bénédicte Durand
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, Institut NeuroMyoGène, Lyon, France
| | - Jean-Paul Borg
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Ning Shi
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Xavier Morelli
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Michel Aurrand-Lions
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- * E-mail:
| |
Collapse
|
37
|
Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells. Sci Rep 2017; 7:41279. [PMID: 28145452 PMCID: PMC5286509 DOI: 10.1038/srep41279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/19/2016] [Indexed: 12/14/2022] Open
Abstract
Despite sharing the same sequence specificity in vitro and in vivo, CCCTC-binding factor (CTCF) and its paralog brother of the regulator of imprinted sites (BORIS) are simultaneously expressed in germ cells. Recently, ChIP-seq analysis revealed two classes of CTCF/BORIS-bound regions: single CTCF target sites (1xCTSes) that are bound by CTCF alone (CTCF-only) or double CTCF target sites (2xCTSes) simultaneously bound by CTCF and BORIS (CTCF&BORIS) or BORIS alone (BORIS-only) in germ cells and in BORIS-positive somatic cancer cells. BORIS-bound regions (CTCF&BORIS and BORIS-only sites) are, on average, enriched for RNA polymerase II (RNAPII) binding and histone retention in mature spermatozoa relative to CTCF-only sites, but little else is known about them. We show that subsets of CTCF&BORIS and BORIS-only sites are occupied by several testis-specific transcriptional regulators (TSTRs) and associated with highly expressed germ cell-specific genes and histone retention in mature spermatozoa. We also demonstrate a physical interaction between BORIS and one of the analyzed TSTRs, TATA-binding protein (TBP)-associated factor 7-like (TAF7L). Our data suggest that CTCF and BORIS cooperate with additional TSTRs to regulate gene expression in developing male gametes and histone retention in mature spermatozoa, potentially priming certain regions of the genome for rapid activation following fertilization.
Collapse
|
38
|
The control of male fertility by spermatid-specific factors: searching for contraceptive targets from spermatozoon's head to tail. Cell Death Dis 2016; 7:e2472. [PMID: 27831554 PMCID: PMC5260884 DOI: 10.1038/cddis.2016.344] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 09/18/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023]
Abstract
Male infertility due to abnormal spermatozoa has been reported in both animals and humans, but its pathogenic causes, including genetic abnormalities, remain largely unknown. On the other hand, contraceptive options for men are limited, and a specific, reversible and safe method of male contraception has been a long-standing quest in medicine. Some progress has recently been made in exploring the effects of spermatid-specifical genetic factors in controlling male fertility. A comprehensive search of PubMed for articles and reviews published in English before July 2016 was carried out using the search terms 'spermiogenesis failure', 'globozoospermia', 'spermatid-specific', 'acrosome', 'infertile', 'manchette', 'sperm connecting piece', 'sperm annulus', 'sperm ADAMs', 'flagellar abnormalities', 'sperm motility loss', 'sperm ion exchanger' and 'contraceptive targets'. Importantly, we have opted to focus on articles regarding spermatid-specific factors. Genetic studies to define the structure and physiology of sperm have shown that spermatozoa appear to be one of the most promising contraceptive targets. Here we summarize how these spermatid-specific factors regulate spermiogenesis and categorize them according to their localization and function from spermatid head to tail (e.g., acrosome, manchette, head-tail conjunction, annulus, principal piece of tail). In addition, we emphatically introduce small-molecule contraceptives, such as BRDT and PPP3CC/PPP3R2, which are currently being developed to target spermatogenic-specific proteins. We suggest that blocking the differentiation of haploid germ cells, which rarely affects early spermatogenic cell types and the testicular microenvironment, is a better choice than spermatogenic-specific proteins. The studies described here provide valuable information regarding the genetic and molecular defects causing male mouse infertility to improve our understanding of the importance of spermatid-specific factors in controlling fertility. Although a male contraceptive 'pill' is still many years away, research into the production of new small-molecule contraceptives targeting spermatid-specific proteins is the right avenue.
Collapse
|
39
|
Mutations in DNAJB13, Encoding an HSP40 Family Member, Cause Primary Ciliary Dyskinesia and Male Infertility. Am J Hum Genet 2016; 99:489-500. [PMID: 27486783 DOI: 10.1016/j.ajhg.2016.06.022] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/22/2016] [Indexed: 10/21/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is an autosomal-recessive disease due to functional or ultra-structural defects of motile cilia. Affected individuals display recurrent respiratory-tract infections; most males are infertile as a result of sperm flagellar dysfunction. The great majority of the PCD-associated genes identified so far encode either components of dynein arms (DAs), which are multiprotein-ATPase complexes essential for ciliary motility, or proteins involved in DA assembly. To identify the molecular basis of a PCD phenotype characterized by central complex (CC) defects but normal DA structure, a phenotype found in ∼15% of cases, we performed whole-exome sequencing in a male individual with PCD and unexplained CC defects. This analysis, combined with whole-genome SNP genotyping, identified a homozygous mutation in DNAJB13 (c.833T>G), a gene encoding a HSP40 co-chaperone whose ortholog in the flagellated alga Chlamydomonas localizes to the radial spokes. In vitro studies showed that this missense substitution (p.Met278Arg), which involves a highly conserved residue of several HSP40 family members, leads to protein instability and triggers proteasomal degradation, a result confirmed by the absence of endogenous DNAJB13 in cilia and sperm from this individual. Subsequent DNAJB13 analyses identified another homozygous mutation in a second family; the study of DNAJB13 transcripts obtained from airway cells showed that this mutation (c.68+1G>C) results in a splicing defect consistent with a loss-of-function mutation. Overall, this study, which establishes mutations in DNAJB13 as a cause of PCD, unveils the key role played by DNAJB13 in the proper formation and function of ciliary and flagellar axonemes in humans.
Collapse
|
40
|
Nemajerova A, Kramer D, Siller SS, Herr C, Shomroni O, Pena T, Gallinas Suazo C, Glaser K, Wildung M, Steffen H, Sriraman A, Oberle F, Wienken M, Hennion M, Vidal R, Royen B, Alevra M, Schild D, Bals R, Dönitz J, Riedel D, Bonn S, Takemaru KI, Moll UM, Lizé M. TAp73 is a central transcriptional regulator of airway multiciliogenesis. Genes Dev 2016; 30:1300-12. [PMID: 27257214 PMCID: PMC4911929 DOI: 10.1101/gad.279836.116] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 05/02/2016] [Indexed: 01/25/2023]
Abstract
In this study, Nemajerova et al. identify TP73, a p53 homolog, as a key regulator of airway multiciliogenesis. They show that mice with TP73 deficiency suffer from chronic respiratory tract infections due to profound defects in ciliogenesis and complete loss of mucociliary clearance and identify the downstream components of TP73 during multiciliogenesis. Motile multiciliated cells (MCCs) have critical roles in respiratory health and disease and are essential for cleaning inhaled pollutants and pathogens from airways. Despite their significance for human disease, the transcriptional control that governs multiciliogenesis remains poorly understood. Here we identify TP73, a p53 homolog, as governing the program for airway multiciliogenesis. Mice with TP73 deficiency suffer from chronic respiratory tract infections due to profound defects in ciliogenesis and complete loss of mucociliary clearance. Organotypic airway cultures pinpoint TAp73 as necessary and sufficient for basal body docking, axonemal extension, and motility during the differentiation of MCC progenitors. Mechanistically, cross-species genomic analyses and complete ciliary rescue of knockout MCCs identify TAp73 as the conserved central transcriptional integrator of multiciliogenesis. TAp73 directly activates the key regulators FoxJ1, Rfx2, Rfx3, and miR34bc plus nearly 50 structural and functional ciliary genes, some of which are associated with human ciliopathies. Our results position TAp73 as a novel central regulator of MCC differentiation.
Collapse
Affiliation(s)
- Alice Nemajerova
- Department of Pathology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Daniela Kramer
- Institute of Molecular Oncology, Göttingen University, 37077 Göttingen, Germany
| | - Saul S Siller
- Department of Pharmacology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Christian Herr
- Department of Internal Medicine V, Saarland University, Homburg 66421, Germany
| | - Orr Shomroni
- Computational Systems Biology, German Center for Neurodegenerative Diseases, 37077 Göttingen, Germany
| | - Tonatiuh Pena
- Computational Systems Biology, German Center for Neurodegenerative Diseases, 37077 Göttingen, Germany
| | | | - Katharina Glaser
- Institute of Molecular Oncology, Göttingen University, 37077 Göttingen, Germany
| | - Merit Wildung
- Institute of Molecular Oncology, Göttingen University, 37077 Göttingen, Germany
| | - Henrik Steffen
- Institute of Molecular Oncology, Göttingen University, 37077 Göttingen, Germany
| | - Anusha Sriraman
- Institute of Molecular Oncology, Göttingen University, 37077 Göttingen, Germany
| | - Fabian Oberle
- Institute of Molecular Oncology, Göttingen University, 37077 Göttingen, Germany
| | - Magdalena Wienken
- Institute of Molecular Oncology, Göttingen University, 37077 Göttingen, Germany
| | - Magali Hennion
- Computational Systems Biology, German Center for Neurodegenerative Diseases, 37077 Göttingen, Germany
| | - Ramon Vidal
- Computational Systems Biology, German Center for Neurodegenerative Diseases, 37077 Göttingen, Germany
| | - Bettina Royen
- Department of Neurophysiology and Cellular Biophysics, Göttingen University, 37073 Göttingen, Germany
| | - Mihai Alevra
- Department of Neurophysiology and Cellular Biophysics, Göttingen University, 37073 Göttingen, Germany
| | - Detlev Schild
- Department of Neurophysiology and Cellular Biophysics, Göttingen University, 37073 Göttingen, Germany
| | - Robert Bals
- Department of Internal Medicine V, Saarland University, Homburg 66421, Germany
| | - Jürgen Dönitz
- Department of Evolutionary Developmental Genetics, Göttingen University, 37077 Göttingen, Germany
| | - Dietmar Riedel
- Electron Microscopy, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan Bonn
- Computational Systems Biology, German Center for Neurodegenerative Diseases, 37077 Göttingen, Germany
| | - Ken-Ichi Takemaru
- Department of Pharmacology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Ute M Moll
- Department of Pathology, Stony Brook University, Stony Brook, New York 11794, USA; Institute of Molecular Oncology, Göttingen University, 37077 Göttingen, Germany
| | - Muriel Lizé
- Institute of Molecular Oncology, Göttingen University, 37077 Göttingen, Germany; Clinic for Cardiology and Pneumology, Department of Pneumology, University Medical Center Göttingen, 37099 Göttingen, Germany
| |
Collapse
|
41
|
Al-Maghrebi M, Renno WM, Al-Somali HF, Botras MS, Qadhi IN. Lutein modulates transcription dysregulation of adhesion molecules and spermatogenesis transcription factors induced by testicular ischemia reperfusion injury: it could be SAFE. Naunyn Schmiedebergs Arch Pharmacol 2016; 389:539-51. [DOI: 10.1007/s00210-016-1223-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/15/2016] [Indexed: 12/22/2022]
|
42
|
Ruiz-Orera J, Hernandez-Rodriguez J, Chiva C, Sabidó E, Kondova I, Bontrop R, Marqués-Bonet T, Albà M. Origins of De Novo Genes in Human and Chimpanzee. PLoS Genet 2015; 11:e1005721. [PMID: 26720152 PMCID: PMC4697840 DOI: 10.1371/journal.pgen.1005721] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/11/2015] [Indexed: 11/18/2022] Open
Abstract
The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species--human, chimpanzee, macaque, and mouse--and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins.
Collapse
Affiliation(s)
- Jorge Ruiz-Orera
- Evolutionary Genomics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | | | - Cristina Chiva
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Tomàs Marqués-Bonet
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M.Mar Albà
- Evolutionary Genomics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- * E-mail:
| |
Collapse
|
43
|
Shawlot W, Vazquez-Chantada M, Wallingford JB, Finnell RH. Rfx2 is required for spermatogenesis in the mouse. Genesis 2015; 53:604-611. [PMID: 26248850 DOI: 10.1002/dvg.22880] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
RFX transcription factors are key regulators of ciliogenesis in vertebrates. In Xenopus and zebrafish embryos, knockdown of Rfx2 causes defects in neural tube closure and in left-right axis patterning. To determine the essential role of the Rfx2 gene in mammalian development, we generated Rfx2-deficient mice using an embryonic stem cell clone containing a lacZ gene trap reporter inserted into the first intron of the Rfx2 gene. We found that the Rfx2 lacZ reporter is expressed in ciliated tissues during mouse development including the node, the floor plate and the dorsal neural tube. However, mice homozygous for the Rfx2 gene trap mutation did not have defects in neural tube closure or in organ situs. The gene trap insertion appears to create a null allele as Rfx2 mRNA was not detected in Rfx2gt/gt embryos. Although Rfx2-deficient mice do not have an obvious embryonic phenotype, we found that Rfx2gt/gt males are infertile because of a defect in spermatid maturation at or before the round and elongating spermatid stage. Our results indicate that Rfx2 is not essential for embryonic development in the mouse but is required for spermatogenesis. genesis 53:604-611, 2015. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- William Shawlot
- Department of Nutritional Sciences, The Dell Pediatric Research Institute, The University of Texas at Austin, Texas
| | - Mercedes Vazquez-Chantada
- Department of Nutritional Sciences, The Dell Pediatric Research Institute, The University of Texas at Austin, Texas
| | - John B Wallingford
- Department of Molecular Biosciences, The University of Texas at Austin, Texas.,Howard Hughes Medical Institute, The University of Texas at Austin, Texas
| | - Richard H Finnell
- Department of Nutritional Sciences, The Dell Pediatric Research Institute, The University of Texas at Austin, Texas
| |
Collapse
|