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Cao M, Xiong L, Wang X, Guo S, Hu L, Kang Y, Wu X, Bao P, Chu M, Liang C, Pei J, Guo X. Comprehensive analysis of differentially expressed mRNAs, circRNAs, and miRNAs and their ceRNA network in the testis of cattle-yak, yak, and cattle. Genomics 2024; 116:110872. [PMID: 38849017 DOI: 10.1016/j.ygeno.2024.110872] [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: 03/06/2024] [Revised: 05/14/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
Cattle-yak is a hybrid offspring resulting from the crossbreeding of yak and cattle, and it exhibits substantial heterosis in production performance. However, male sterility in cattle-yak remains a concern. Reports suggest that noncoding RNAs are involved in the regulation of spermatogenesis. Therefore, in this study, we comprehensively compared testicular transcription profiles among cattle, yak, and cattle-yak. Numerous differentially expressed genes (DEGs), differentially expressed circRNAs (DECs), and differentially expressed miRNAs (DEMs) were identified in the intersection of two comparison groups, namely cattle versus cattle-yak and yak versus cattle-yak, with the number of DEGs, DECs, and DEMs being 4968, 360, and 59, respectively. The DEGs in cattle-yaks, cattle, and yaks were mainly associated with spermatogenesis, male gamete generation, and sexual reproduction. Concurrently, GO and KEGG analyses indicated that DEC host genes and DEM source genes were involved in the regulation of spermatogenesis. The construction of a potential competing endogenous RNA network revealed that some differentially expressed noncoding RNAs may be involved in regulating the expression of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, and miR-15b, as well as previously unreported miR-6123 and miR-1306, along with various miRNA-circRNA interaction pairs. This study serves as a valuable reference for further investigations into the mechanisms underlying male sterility in cattle-yaks.
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Affiliation(s)
- Mengli Cao
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xingdong Wang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Liyan Hu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yandong Kang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyu Wu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
| | - Xian Guo
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
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Erdmann EA, Forbes M, Becker M, Perez S, Hundley HA. ADR-2 regulates fertility and oocyte fate in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565157. [PMID: 37961348 PMCID: PMC10635048 DOI: 10.1101/2023.11.01.565157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
RNA binding proteins play essential roles in coordinating germline gene expression and development in all organisms. Here, we report that loss of ADR-2, a member of the Adenosine DeAminase acting on RNA (ADAR) family of RNA binding proteins and the sole adenosine-to-inosine RNA editing enzyme in C. elegans, can improve fertility in multiple genetic backgrounds. First, we show that loss of RNA editing by ADR-2 restores normal embryo production to subfertile animals that transgenically express a vitellogenin (yolk protein) fusion to green fluorescent protein. Using this phenotype, a high-throughput screen was designed to identify RNA binding proteins that when depleted yield synthetic phenotypes with loss of adr-2. The screen uncovered a genetic interaction between ADR-2 and SQD-1, a member of the heterogenous nuclear ribonucleoprotein (hnRNP) family of RNA binding proteins. Microscopy, reproductive assays, and high-throughput sequencing reveal that sqd-1 is essential for the onset of oogenesis and oogenic gene expression in young adult animals, and that loss of adr-2 can counteract the effects of loss of sqd-1 on gene expression and rescue the switch from spermatogenesis to oogenesis. Together, these data demonstrate that ADR-2 can contribute to the suppression of fertility and suggest novel roles for both RNA editing-dependent and independent mechanisms in regulating embryogenesis.
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Affiliation(s)
- Emily A Erdmann
- Genome, Cell and Developmental Biology Graduate Program, Indiana University, Bloomington IN, US 47405
| | - Melanie Forbes
- Department of Biology, Indiana University, Bloomington IN, US 47405
| | - Margaret Becker
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington IN, US 47405
| | - Sarina Perez
- Department of Biology, Indiana University, Bloomington IN, US 47405
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Kaneda Y, Miyata H, Xu Z, Shimada K, Kamoshita M, Nakagawa T, Emori C, Ikawa M. FBXO24 deletion causes abnormal accumulation of membraneless electron-dense granules in sperm flagella and male infertility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.10.566635. [PMID: 37986737 PMCID: PMC10659433 DOI: 10.1101/2023.11.10.566635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Ribonucleoprotein (RNP) granules are membraneless electron-dense structures rich in RNAs and proteins, and involved in various cellular processes. Two RNP granules in male germ cells, intermitochondrial cement and the chromatoid body (CB), are associated with PIWI-interacting RNAs (piRNAs) and are required for transposon silencing and spermatogenesis. Other RNP granules in male germ cells, the reticulated body and CB remnants, are also essential for spermiogenesis. In this study, we disrupted FBXO24, a testis-enriched F-box protein, in mice and found numerous membraneless electron-dense granules accumulated in sperm flagella. Fbxo24 knockout (KO) mice exhibited malformed flagellar structures, impaired sperm motility, and male infertility, likely due to the accumulation of abnormal granules. The amount and localization of known RNP granule-related proteins were not disrupted in Fbxo24 KO mice, suggesting that the accumulated granules were distinct from known RNP granules. Further studies revealed that RNAs and two importins, IPO5 and KPNB1, abnormally accumulated in Fbxo24 KO spermatozoa and that FBXO24 could ubiquitinate IPO5. In addition, IPO5 and KPNB1 were recruited to stress granules, RNP complexes, when cells were treated with oxidative stress or a proteasome inhibitor. These results suggest that FBXO24 is involved in the degradation of IPO5, disruption of which may lead to the accumulation of abnormal RNP granules in sperm flagella.
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Affiliation(s)
- Yuki Kaneda
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 5650871 JAPAN
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 5650871 JAPAN
| | - Haruhiko Miyata
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 5650871 JAPAN
| | - Zoulan Xu
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 5650871 JAPAN
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 5650871 JAPAN
| | - Keisuke Shimada
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 5650871 JAPAN
| | - Maki Kamoshita
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 5650871 JAPAN
| | - Tatsuya Nakagawa
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 5650871 JAPAN
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 5650871 JAPAN
| | - Chihiro Emori
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 5650871 JAPAN
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 5650871 JAPAN
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 5650871 JAPAN
- The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 1088639 JAPAN
- Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-8 Yamadaoka, Suita, Osaka 5650871 JAPAN
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, 2-8 Yamadaoka, Suita, Osaka 5650871 JAPAN
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Choi S, Hong SH, Han G, Cho C. Profiling of testis-specific or testis-predominant genes expressed in mouse male germ cell lines GC-1 and GC-2. Genes Genomics 2024; 46:279-287. [PMID: 38291311 DOI: 10.1007/s13258-023-01488-1] [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: 07/08/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND Spermatogenesis is a tightly organized process that utilizes an intrinsic genetic program composed of germ cell-specific genes. Although mouse germ cell-related cell lines are available, few germ cell-specific genes have been comprehensively identified in such cell lines. OBJECTIVE We aimed to profile gene expression in the male mouse germ cell-related cell lines, GC-1 and GC-2, characterize their transcriptomic nature, and identify potential testis- or germ cell-specific or -predominant genes expressed in these cell lines. METHODS We performed profiling analysis of genes transcribed in the mouse germ cell-related cell lines, GC-1 and GC-2, using our previous microarray data together with public transcriptome information. We analyzed the expression of a number of the cell line genes predicted to be preferentially expressed in testis by RT-PCR. RESULTS We found that most testis-specific or -predominant mRNAs are not expressed in GC-1 and GC-2 cells, implying that these cell lines have lost their testis- or germ cell-specific genetic characteristics. RT-PCR analysis of genes predicted to be expressed in the cell lines with preferential testicular expression showed the testis-specific or -predominant expression of nine genes and verified four of them as being expressed in the germ cell lines. Among them, only cyclin-dependent kinase inhibitor 3 genes (Cdkn3) showed testis and germ cell specificity. CONCLUSION Our study provides extensive transcriptomic information to shed light on the limited testicular characteristics of the mouse male germ cell-derived cell lines, GC-1 and GC-2, and offers a list of germ cell line genes with testicular preference.
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Affiliation(s)
- Seungho Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Korea
- R&D Center, KYNOGEN Corp, Suwon, Gyeonggi-do, Korea
| | - Seong Hyeon Hong
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Korea
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Gwidong Han
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Korea
| | - Chunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Korea.
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5
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Davoudi P, Do DN, Rathgeber B, Colombo S, Sargolzaei M, Plastow G, Wang Z, Miar Y. Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data. J Anim Breed Genet 2024. [PMID: 38389405 DOI: 10.1111/jbg.12859] [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: 11/30/2023] [Revised: 01/27/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3-1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR-corrected p-value < 0.05), respectively, among which cGMP-PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Stefanie Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
- Select Sires Inc., Plain City, Ohio, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
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Fang X, Baggett LM, Caylor RC, Percy AK, Neul JL, Lane JB, Glaze DG, Benke TA, Marsh ED, Motil KJ, Barrish JO, Annese FE, Skinner SA. Parental age effects and Rett syndrome. Am J Med Genet A 2024; 194:160-173. [PMID: 37768187 DOI: 10.1002/ajmg.a.63396] [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: 09/13/2022] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
Rett syndrome (RTT) is a progressive neurodevelopmental disorder, and pathogenic Methyl-CpG-binding Protein 2 (MECP2) variants are identified in >95% of individuals with typical RTT. Most of RTT-causing variants in MECP2 are de novo and usually on the paternally inherited X chromosome. While paternal age has been reported to be associated with increased risk of genetic disorders, it is unknown whether parental age contributes to the risk of the development of RTT. Clinical data including parental age, RTT diagnostic status, and clinical severity are collected from 1226 participants with RTT and confirmed MECP2 variants. Statistical analyses are performed using Student t-test, single factor analysis of variance (ANOVA), and multi-factor regression. No significant difference is observed in parental ages of RTT probands compared to that of the general population. A small increase in parental ages is observed in participants with missense variants compared to those with nonsense variants. When we evaluate the association between clinical severity and parental ages by multiple regression analysis, there is no clear association between clinical severity and parental ages. Advanced parental ages do not appear to be a risk factor for RTT, and do not contribute to the clinical severity in individuals with RTT.
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Affiliation(s)
- Xiaolan Fang
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | | | - Alan K Percy
- The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jeffrey L Neul
- Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jane B Lane
- The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Tim A Benke
- University of Colorado School of Medicine, Children's Hospital Colorado-Aurora, Denver, Colorado, USA
| | - Eric D Marsh
- Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathleen J Motil
- Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Fran E Annese
- Greenwood Genetic Center, Greenwood, South Carolina, USA
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Yu T, Ning J, Wang F, Liu G, Wang Q, Xu X, Wang C, Lu X. Whole-Genome Re-sequencing and Transcriptome Reveal Candidate Genes and Pathways Associated with Hybrid Sterility in Hermaphroditic Argopecten Scallops. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:891-906. [PMID: 37632589 DOI: 10.1007/s10126-023-10247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/18/2023] [Indexed: 08/28/2023]
Abstract
The interspecific hybrid scallops generated from the hermaphroditic bay scallops (Argopecten irradians) and Peruvian scallops (Argopecten purpuratus) showed significant heterosis in growth. However, its sterility limits large-scale hybridization and hinders the development of the scallop breeding industry. Hybrid sterility is regulated by plenty of genes and involves a range of biochemical and physiological transformations. In this study, whole-genome re-sequencing and transcriptomic analysis were performed in sterile and fertile hybrid scallops. The potential genetic variations and abnormally expressed genes were detected to explore the mechanism underlying hybrid sterility in hermaphroditic Argopecten scallops. Compared with fertile hybrids, 24 differentially expressed genes (DEGs) with 246 variations were identified to be related to fertility regulation, which were mainly enriched in germarium-derived egg chamber formation, spermatogenesis, spermatid development, mismatch repair, mitotic and meiotic cell cycles, Wnt signaling pathway, MAPK signaling pathway, calcium modulating pathway, and notch signaling pathway. Specifically, variation and abnormal expression of these genes might inhibit the progress of mitosis and meiosis, promote cell apoptosis, and impede the genesis and maturation of gametes in sterile hybrid scallops. Eleven DEGs (XIAP, KAZN, CDC42, MEIS1, SETD1B, NOTCH2, TRPV5, M- EXO1, GGT1, SBDS, and TBCEL) were confirmed by qRT-PCR validation. Our findings may enrich the determination mechanism of hybrid sterility and provide new insights into the use of interspecific hybrids for extensive breeding.
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Affiliation(s)
- Tieying Yu
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junhao Ning
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
| | - Fukai Wang
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Guilong Liu
- Yantai Spring-Sea AquaSeed, Ltd., Yantai, 264006, China
| | - Quanchao Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
| | - Xin Xu
- Yantai Spring-Sea AquaSeed, Ltd., Yantai, 264006, China
| | - Chunde Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xia Lu
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, Shandong, China.
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Keegan LP, Hajji K, O’Connell MA. Adenosine Deaminase Acting on RNA (ADAR) Enzymes: A Journey from Weird to Wondrous. Acc Chem Res 2023; 56:3165-3174. [PMID: 37906879 PMCID: PMC10666284 DOI: 10.1021/acs.accounts.3c00433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 11/02/2023]
Abstract
The adenosine deaminase acting on RNA (ADAR) enzymes that catalyze the conversion of adenosine to inosine in double-stranded (ds)RNA are evolutionarily conserved and are essential for many biological functions including nervous system function, hematopoiesis, and innate immunity. Initially it was assumed that the wide-ranging biological roles of ADARs are due to inosine in mRNA being read as guanosine by the translational machinery, allowing incomplete RNA editing in a target codon to generate two different proteins from the same primary transcript. In humans, there are approximately seventy-six positions that undergo site-specific editing in tissues at greater than 20% efficiency that result in recoding. Many of these transcripts are expressed in the central nervous system (CNS) and edited by ADAR2. Exploiting mouse genetic models revealed that transgenic mice lacking the gene encoding Adar2 die within 3 weeks of birth. Therefore, the role of ADAR2 in generating protein diversity in the nervous system is clear, but why is ADAR RNA editing activity essential in other biological processes, particularly editing mainly involving ADAR1? ADAR1 edits human transcripts having embedded Alu element inverted repeats (AluIRs), but the link from this activity to innate immunity activation was elusive. Mice lacking the gene encoding Adar1 are embryonically lethal, and a major breakthrough was the discovery that the role of Adar1 in innate immunity is due to its ability to edit such repetitive element inverted repeats which have the ability to form dsRNA in transcripts. The presence of inosine prevents activation of the dsRNA sensor melanoma differentiation-associated protein 5 (Mda5). Thus, inosine helps the cell discriminate self from non-self RNA, acting like a barcode on mRNA. As innate immunity is key to many different biological processes, the basis for this widespread biological role of the ADAR1 enzyme became evident.Our group has been studying ADARs from the outset of research on these enzymes. In this Account, we give a historical perspective, moving from the initial purification of ADAR1 and ADAR2 and cloning of their encoding genes up to the current research focus in the field and what questions still remain to be addressed. We discuss the characterizations of the proteins, their localizations, posttranslational modifications, and dimerization, and how all of these affect their biological activities. Another aspect we explore is the use of mouse and Drosophila genetic models to study ADAR functions and how these were crucial in determining the biological functions of the ADAR proteins. Finally, we describe the severe consequences of rare mutations found in the human genes encoding ADAR1 and ADAR2.
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Affiliation(s)
- Liam P. Keegan
- CEITEC, Masaryk
University, Kamenice 735/5, E35, Brno 62500, Czechia
| | - Khadija Hajji
- CEITEC, Masaryk
University, Kamenice 735/5, E35, Brno 62500, Czechia
| | - Mary A. O’Connell
- CEITEC, Masaryk
University, Kamenice 735/5, E35, Brno 62500, Czechia
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9
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Voss G, Rosenthal JJC. High-level RNA editing diversifies the coleoid cephalopod brain proteome. Brief Funct Genomics 2023; 22:525-532. [PMID: 37981860 DOI: 10.1093/bfgp/elad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Coleoid cephalopods (octopus, squid and cuttlefish) have unusually complex nervous systems. The coleoid nervous system is also the only one currently known to recode the majority of expressed proteins through A-to-I RNA editing. The deamination of adenosine by adenosine deaminase acting on RNA (ADAR) enzymes produces inosine, which is interpreted as guanosine during translation. If this occurs in an open reading frame, which is the case for tens of thousands of editing sites in coleoids, it can recode the encoded protein. Here, we describe recent findings aimed at deciphering the mechanisms underlying high-level recoding and its adaptive potential. We describe the complement of ADAR enzymes in cephalopods, including a recently discovered novel domain in sqADAR1. We further summarize current evidence supporting an adaptive role of high-level RNA recoding in coleoids, and review recent studies showing that a large proportion of recoding sites is temperature-sensitive. Despite these new findings, the mechanisms governing the high level of RNA recoding in coleoid cephalopods remain poorly understood. Recent advances using genome editing in squid may provide useful tools to further study A-to-I RNA editing in these animals.
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Affiliation(s)
- Gjendine Voss
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
| | - Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
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Frezza V, Chellini L, Del Verme A, Paronetto MP. RNA Editing in Cancer Progression. Cancers (Basel) 2023; 15:5277. [PMID: 37958449 PMCID: PMC10648226 DOI: 10.3390/cancers15215277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Coding and noncoding RNA molecules play their roles in ensuring cell function and tissue homeostasis in an ordered and systematic fashion. RNA chemical modifications can occur both at bases and ribose sugar, and, similarly to DNA and histone modifications, can be written, erased, and recognized by the corresponding enzymes, thus modulating RNA activities and fine-tuning gene expression programs. RNA editing is one of the most prevalent and abundant forms of post-transcriptional RNA modification in normal physiological processes. By altering the sequences of mRNAs, it makes them different from the corresponding genomic template. Hence, edited mRNAs can produce protein isoforms that are functionally different from the corresponding genome-encoded variants. Abnormalities in regulatory enzymes and changes in RNA-modification patterns are closely associated with the occurrence and development of various human diseases, including cancer. To date, the roles played by RNA modifications in cancer are gathering increasing interest. In this review, we focus on the role of RNA editing in cancer transformation and provide a new perspective on its impact on tumorigenesis, by regulating cell proliferation, differentiation, invasion, migration, stemness, metabolism, and drug resistance.
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Affiliation(s)
- Valentina Frezza
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Arianna Del Verme
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
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Potgieter S, Eddy C, Badrinath A, Chukrallah L, Lo T, Mohanty G, Visconti PE, Snyder EM. ADAD1 is required for normal translation of nuclear pore and transport protein transcripts in spermatids of Mus musculus†. Biol Reprod 2023; 109:340-355. [PMID: 37399121 PMCID: PMC10502568 DOI: 10.1093/biolre/ioad069] [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: 11/28/2022] [Revised: 03/23/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023] Open
Abstract
ADAD1 is a testis-specific RNA-binding protein expressed in post-meiotic spermatids whose loss leads to defective sperm and male infertility. However, the drivers of the Adad1 phenotype remain unclear. Morphological and functional analysis of Adad1 mutant sperm showed defective DNA compaction, abnormal head shaping, and reduced motility. Mutant testes demonstrated minimal transcriptome changes; however, ribosome association of many transcripts was reduced, suggesting ADAD1 may be required for their translational activation. Further, immunofluorescence of proteins encoded by select transcripts showed delayed protein accumulation. Additional analyses demonstrated impaired subcellular localization of multiple proteins, suggesting protein transport is also abnormal in Adad1 mutants. To clarify the mechanism giving rise to this, the manchette, a protein transport microtubule network, and the LINC (linker of nucleoskeleton and cytoskeleton) complex, which connects the manchette to the nuclear lamin, were assessed across spermatid development. Proteins of both displayed delayed translation and/or localization in mutant spermatids implicating ADAD1 in their regulation, even in the absence of altered ribosome association. Finally, ADAD1's impact on the NPC (nuclear pore complex), a regulator of both the manchette and the LINC complex, was examined. Reduced ribosome association of NPC encoding transcripts and reduced NPC protein abundance along with abnormal localization in Adad1 mutants confirmed ADAD1's impact on translation is required for a NPC in post-meiotic germ cells. Together, these studies lead to a model whereby ADAD1's influence on nuclear transport leads to deregulation of the LINC complex and the manchette, ultimately generating the range of physiological defects observed in the Adad1 phenotype.
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Affiliation(s)
- Sarah Potgieter
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Christopher Eddy
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Aditi Badrinath
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Lauren Chukrallah
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Toby Lo
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Gayatri Mohanty
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Pablo E Visconti
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Elizabeth M Snyder
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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12
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Zhang XY, Li J, Chen SL, Li Y, Wang H, He JH. Malakoplakia with aberrant ALK expression by immunohistochemistry: a case report. Diagn Pathol 2023; 18:97. [PMID: 37644531 PMCID: PMC10464214 DOI: 10.1186/s13000-023-01383-z] [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: 03/09/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Malakoplakia is a rare inflammatory disease of the urogenital tract. There have been no reports of malakoplakia expressing anaplastic lymphoma kinase (ALK) to date. Here, we present one case of malakoplakia with aberrant ALK expression by immunohistochemistry and discuss the clinical significance. CASE PRESENTATION A 65-year-old Chinese woman with a history of diabetes presented with solid masses in the liver and kidney and elevated lesions on the mucosal surface of the colon. Right nephrectomy and partial liver resection were performed. Microscopically, sheets of histiocytes with poor intercellular adhesion were seen, with Michaelis-Gutmann bodies present in both the intracellular and extracellular interstitium. CD10-, CD68-, and CD163-positive cells were present, with Michaelis-Gutmann bodies confirmed by staining with Alcian blue, periodic acid-Schiff (PAS), periodic acid-Schiff with diastase, Von Kossa, and Prussian blue. Aberrant ALK1 and ALK (D5F3) expression was observed in the cytoplasm and nucleus of cells. However, ALK gene mutation was not detected by fluorescence in situ hybridization or whole exome next-generation sequencing. NGS revealed nine individual somatic gene mutations: GOT1L1, GLIS2, SPOUT1, TMEM97, MUC3A, NSD2, SFXN5, ADAD1 and RAD50. The significance of the somatic gene mutations detected in this study is not clear, and the relationship between them and malakoplakia cannot be clarified by existing scientific studies. The pathological diagnosis was malakoplakia with aberrant ALK expression by immunohistochemistry. The antibiotics imipenem and vancomycin were started based on the results of drug sensitivity analysis and the patient was subsequently discharged. She experienced no discomfort during 30 months of follow-up. CONCLUSION This is the first reported case of malakoplakia with aberrant ALK expression, it should be differentiated from ALK-positive histiocytosis to avoid misdiagnosis.
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Affiliation(s)
- Xiao-Ying Zhang
- Department of Pathology, Panyu District Central Hospital, Guangzhou, China
| | - Jun Li
- Department of Urology, Panyu District Central Hospital, Guangzhou, China
| | - Shui-Lian Chen
- Department of Pathology, Panyu District Central Hospital, Guangzhou, China
| | - Ying Li
- Department of Pathology, Panyu District Central Hospital, Guangzhou, China
| | - Hao Wang
- Department of Pathology, Panyu District Central Hospital, Guangzhou, China
| | - Jin-Hua He
- Department of Laboratory Medicine, Panyu District Central Hospital, Guangzhou, China.
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13
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Chukrallah LG, Potgieter S, Chueh L, Snyder EM. Two RNA binding proteins, ADAD2 and RNF17, interact to form a heterogeneous population of novel meiotic germ cell granules with developmentally dependent organelle association. PLoS Genet 2023; 19:e1010519. [PMID: 37428816 PMCID: PMC10359003 DOI: 10.1371/journal.pgen.1010519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/20/2023] [Accepted: 06/17/2023] [Indexed: 07/12/2023] Open
Abstract
Mammalian male germ cell differentiation relies on complex RNA biogenesis events, many of which occur in non-membrane bound organelles termed RNA germ cell granules that are rich in RNA binding proteins (RBPs). Though known to be required for male germ cell differentiation, we understand little of the relationships between the numerous granule subtypes. ADAD2, a testis specific RBP, is required for normal male fertility and forms a poorly characterized granule in meiotic germ cells. This work aimed to understand the role of ADAD2 granules in male germ cell differentiation by clearly defining their molecular composition and relationship to other granules. Biochemical analyses identified RNF17, a testis specific RBP that forms meiotic male germ cell granules, as an ADAD2-interacting protein. Phenotypic analysis of Adad2 and Rnf17 mutants identified a rare post-meiotic chromatin defect, suggesting shared biological roles. ADAD2 and RNF17 were found to be dependent on one another for granularization and together form a previously unstudied set of germ cell granules. Based on co-localization studies with well-characterized granule RBPs and organelle-specific markers, a subset of the ADAD2-RNF17 granules are found to be associated with the intermitochondrial cement and piRNA biogenesis. In contrast, a second, morphologically distinct population of ADAD2-RNF17 granules co-localized with the translation regulators NANOS1 and PUM1, along with the molecular chaperone PDI. These large granules form a unique funnel-shaped structure that displays distinct protein subdomains and is tightly associated with the endoplasmic reticulum. Developmental studies suggest the different granule populations represent different phases of a granule maturation process. Lastly, a double Adad2-Rnf17 mutant model suggests the interaction between ADAD2 and RNF17, as opposed to loss of either, is the likely driver of the Adad2 and Rnf17 mutant phenotypes. These findings shed light on the relationship between germ cell granule pools and define new genetic approaches to their study.
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Affiliation(s)
- Lauren G. Chukrallah
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sarah Potgieter
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Lisa Chueh
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Elizabeth M. Snyder
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
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14
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Chukrallah LG, Snyder EM. Modern tools applied to classic structures: Approaches for mammalian male germ cell RNA granule research. Andrology 2023; 11:872-883. [PMID: 36273399 DOI: 10.1111/andr.13320] [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: 07/29/2022] [Revised: 09/20/2022] [Accepted: 10/10/2022] [Indexed: 11/28/2022]
Abstract
First reported in the 1800s, germ cell granules are small nonmembrane bound RNA-rich regions of the cytoplasm. These sites of critical RNA processing and storage in the male germ cell are essential for proper differentiation and development and are present in a wide range of species from Caenorhabditis elegans through mammals. Initially characterized by light and electron microscopy, more modern techniques such as immunofluorescence and genetic models have played a major role in expanding our understanding of the composition of these structures. While these methods have given light to potential granule functions, much work remains to be done. The current expansion of imaging technologies and omics-scale analyses to germ cell granule research will drive the field forward considerably. Many of these methods, both current and upcoming, have considerable caveats and limitations that necessitate a holistic approach to the study of germ granules. By combining and balancing different techniques, the field is poised to elucidate the nature of these critical structures.
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Affiliation(s)
- Lauren G Chukrallah
- Department of Animal Science, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Elizabeth M Snyder
- Department of Animal Science, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
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15
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Zhong Z, Wang Z, Xie X, Tian S, Wang F, Wang Q, Ni S, Pan Y, Xiao Q. Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations. Animals (Basel) 2023; 13:2010. [PMID: 37370521 DOI: 10.3390/ani13122010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Indigenous pig populations in Hainan Province live in tropical climate conditions and a relatively closed geographical environment, which has contributed to the formation of some excellent characteristics, such as heat tolerance, strong disease resistance and excellent meat quality. Over the past few decades, the number of these pig populations has decreased sharply, largely due to a decrease in growth rate and poor lean meat percentage. For effective conservation of these genetic resources (such as heat tolerance, meat quality and disease resistance), the whole-genome sequencing data of 78 individuals from 3 native Chinese pig populations, including Wuzhishan (WZS), Tunchang (TC) and Dingan (DA), were obtained using a 150 bp paired-end platform, and 25 individuals from two foreign breeds, including Landrace (LR) and Large White (LW), were downloaded from a public database. A total of 28,384,282 SNPs were identified, of which 27,134,233 SNPs were identified in native Chinese pig populations. Both genetic diversity statistics and linkage disequilibrium (LD) analysis indicated that indigenous pig populations displayed high genetic diversity. The result of population structure implied the uniqueness of each native Chinese pig population. The selection signatures were detected between indigenous pig populations and foreign breeds by using the population differentiation index (FST) method. A total of 359 candidate genes were identified, and some genes may affect characteristics such as immunity (IL-2, IL-21 and ZFYVE16), adaptability (APBA1), reproduction (FGF2, RNF17, ADAD1 and HIPK4), meat quality (ABCA1, ADIG, TLE4 and IRX5), and heat tolerance (VPS13A, HSPA4). Overall, the findings of this study will provide some valuable insights for the future breeding, conservation and utilization of these three Chinese indigenous pig populations.
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Affiliation(s)
- Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Ziyi Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Xinfeng Xie
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Shuaishuai Tian
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Feifan Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Qishan Wang
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Shiheng Ni
- Animal Husbandry Technology Extending Stations of Hainan Province, Haikou 570203, China
| | - Yuchun Pan
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Qian Xiao
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
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16
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Vallecillo-Viejo IC, Voss G, Albertin CB, Liscovitch-Brauer N, Eisenberg E, Rosenthal JJC. Squid express conserved ADAR orthologs that possess novel features. Front Genome Ed 2023; 5:1181713. [PMID: 37342458 PMCID: PMC10278661 DOI: 10.3389/fgeed.2023.1181713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
The coleoid cephalopods display unusually extensive mRNA recoding by adenosine deamination, yet the underlying mechanisms are not well understood. Because the adenosine deaminases that act on RNA (ADAR) enzymes catalyze this form of RNA editing, the structure and function of the cephalopod orthologs may provide clues. Recent genome sequencing projects have provided blueprints for the full complement of coleoid cephalopod ADARs. Previous results from our laboratory have shown that squid express an ADAR2 homolog, with two splice variants named sqADAR2a and sqADAR2b and that these messages are extensively edited. Based on octopus and squid genomes, transcriptomes, and cDNA cloning, we discovered that two additional ADAR homologs are expressed in coleoids. The first is orthologous to vertebrate ADAR1. Unlike other ADAR1s, however, it contains a novel N-terminal domain of 641 aa that is predicted to be disordered, contains 67 phosphorylation motifs, and has an amino acid composition that is unusually high in serines and basic amino acids. mRNAs encoding sqADAR1 are themselves extensively edited. A third ADAR-like enzyme, sqADAR/D-like, which is not orthologous to any of the vertebrate isoforms, is also present. Messages encoding sqADAR/D-like are not edited. Studies using recombinant sqADARs suggest that only sqADAR1 and sqADAR2 are active adenosine deaminases, both on perfect duplex dsRNA and on a squid potassium channel mRNA substrate known to be edited in vivo. sqADAR/D-like shows no activity on these substrates. Overall, these results reveal some unique features in sqADARs that may contribute to the high-level RNA recoding observed in cephalopods.
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Affiliation(s)
| | - Gjendine Voss
- The Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Caroline B. Albertin
- The Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Noa Liscovitch-Brauer
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
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Shi B, Shah W, Liu L, Gong C, Zhou J, Abbas T, Ma H, Zhang H, Yang M, Zhang Y, Ullah N, Mahammad Z, Khan M, Murtaza G, Ali A, Khan R, Sha J, Yuan Y, Shi Q. Biallelic mutations in RNA-binding protein ADAD2 cause spermiogenic failure and non-obstructive azoospermia in humans. Hum Reprod Open 2023; 2023:hoad022. [PMID: 37325547 PMCID: PMC10266965 DOI: 10.1093/hropen/hoad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 04/19/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023] Open
Abstract
STUDY QUESTION What are some pathogenic mutations for non-obstructive azoospermia (NOA) and their effects on spermatogenesis? SUMMARY ANSWER Biallelic missense and frameshift mutations in ADAD2 disrupt the differentiation of round spermatids to spermatozoa causing azoospermia in humans and mice. WHAT IS KNOWN ALREADY NOA is the most severe cause of male infertility characterized by an absence of sperm in the ejaculate due to impairment of spermatogenesis. In mice, the lack of the RNA-binding protein ADAD2 leads to a complete absence of sperm in epididymides due to failure of spemiogenesis, but the spermatogenic effects of ADAD2 mutations in human NOA-associated infertility require functional verification. STUDY DESIGN SIZE DURATION Six infertile male patients from three unrelated families were diagnosed with NOA at local hospitals in Pakistan based on infertility history, sex hormone levels, two semen analyses and scrotal ultrasound. Testicular biopsies were performed in two of the six patients. Adad2 mutant mice (Adad2Mut/Mut) carrying mutations similar to those found in NOA patients were generated using the CRISPR/Cas9 genome editing tool. Reproductive phenotypes of Adad2Mut/Mut mice were verified at 2 months of age. Round spermatids from the littermates of wild-type (WT) and Adad2Mut/Mut mice were randomly selected and injected into stimulated WT oocytes. This round spermatid injection (ROSI) procedure was conducted with three biological replicates and >400 ROSI-derived zygotes were evaluated. The fertility of the ROSI-derived progeny was evaluated for three months in four Adad2WT/Mut male mice and six Adad2WT/Mut female mice. A total of 120 Adad2Mut/Mut, Adad2WT/Mut, and WT mice were used in this study. The entire study was conducted over 3 years. PARTICIPANTS/MATERIALS SETTING METHODS Whole-exome sequencing was performed to detect potentially pathogenic mutations in the six NOA-affected patients. The pathogenicity of the identified ADAD2 mutations was assessed and validated in human testicular tissues and in mouse models recapitulating the mutations in the NOA patients using quantitative PCR, western blotting, hematoxylin-eosin staining, Periodic acid-Schiff staining, and immunofluorescence. Round spermatids of WT and Adad2Mut/Mut mice were collected by fluorescence-activated cell sorting and injected into stimulated WT oocytes. The development of ROSI-derived offspring was evaluated in the embryonic and postnatal stages. MAIN RESULTS AND THE ROLE OF CHANCE Three recessive mutations were identified in ADAD2 (MT1: c.G829T, p.G277C; MT2: c.G1192A, p.D398N; MT3: c.917_918del, p.Q306Rfs*43) in patients from three unrelated Pakistani families. MT1 and MT2 dramatically reduced the testicular expression of ADAD2, likely causing spermiogenesis failure in the NOA patients. Immunofluorescence analysis of the Adad2Mut/Mut male mice with the corresponding MT3 mutation showed instability and premature degradation of the ADAD2 protein, resulting in the spermiogenesis deficiency phenotype. Through ROSI, the Adad2Mut/Mut mice could produce pups with comparable embryonic development (46.7% in Adad2Mut/Mut versus 50% in WT) and birth rates (21.45 ± 10.43% in Adad2Mut/Mut versus 27.5 ± 3.536% in WT, P = 0.5044) to WT mice. The Adad2WT/Mut progeny from ROSI (17 pups in total via three ROSI replicates) did not show overt developmental defects and had normal fertility. LARGE SCALE DATA N/A. LIMITATIONS REASONS FOR CAUTION This is a preliminary report suggesting that ROSI can be an effective treatment for infertile Adad2Mut/Mut mice. Further assisted reproductive attempts need to be carefully examined in humans during clinical trials. WIDER IMPLICATIONS OF THE FINDINGS Our work provides functional evidence that mutations in the ADAD2 gene are deleterious and cause consistent spermiogenic defects in both humans and mice. In addition, preliminary results show that ROSI can help Adad2Mut/Mut to produce biological progeny. These findings provide valuable clues for genetic counselling on the ADAD2 mutants-associated infertility in human males. STUDY FUNDING/COMPETING INTERESTS This work was supported by the National Natural Science Foundation of China (32000587, U21A20204, and 32061143006), and the National Key Research and Developmental Program of China (2019YFA0802600 and 2021YFC2700202). This work was also supported by Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China. The authors declare no competing interests.
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Affiliation(s)
- Baolu Shi
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Wasim Shah
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Li Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chenjia Gong
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Jianteng Zhou
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Tanveer Abbas
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Hui Ma
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Huan Zhang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Menglei Yang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Yuanwei Zhang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Nadeem Ullah
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Zubair Mahammad
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Mazhar Khan
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Ghulam Murtaza
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Asim Ali
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Ranjha Khan
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yan Yuan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qinghua Shi
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
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18
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Xiong M, Yin L, Gui Y, Lv C, Ma X, Guo S, Wu Y, Feng S, Fan X, Zhou S, Wang L, Wen Y, Wang X, Xie Q, Namekawa SH, Yuan S. ADAD2 interacts with RNF17 in P-bodies to repress the Ping-pong cycle in pachytene piRNA biogenesis. J Cell Biol 2023; 222:e202206067. [PMID: 36930220 PMCID: PMC10040813 DOI: 10.1083/jcb.202206067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/04/2023] [Accepted: 02/21/2023] [Indexed: 03/18/2023] Open
Abstract
Pachytene piRNA biogenesis is a hallmark of the germline, distinct from another wave of pre-pachytene piRNA biogenesis with regard to the lack of a secondary amplification process known as the Ping-pong cycle. However, the underlying molecular mechanism and the venue for the suppression of the Ping-pong cycle remain elusive. Here, we showed that a testis-specific protein, ADAD2, interacts with a TDRD family member protein RNF17 and is associated with P-bodies. Importantly, ADAD2 directs RNF17 to repress Ping-pong activity in pachytene piRNA biogenesis. The P-body localization of RNF17 requires the intrinsically disordered domain of ADAD2. Deletion of Adad2 or Rnf17 causes the mislocalization of each other and subsequent Ping-pong activity derepression, secondary piRNAs overproduced, and disruption of P-body integrity at the meiotic stage, thereby leading to spermatogenesis arrested at the round spermatid stage. Collectively, by identifying the ADAD2-dependent mechanism, our study reveals a novel function of P-bodies in suppressing Ping-pong activity in pachytene piRNA biogenesis.
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Affiliation(s)
- Mengneng Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Reproductive Medicine Center, Wuhan University Renmin Hospital, Wuhan, China
| | - Lisha Yin
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyu Lv
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xixiang Ma
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan, China
| | - Shuangshuang Guo
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanqing Wu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shenglei Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xv Fan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lingjuan Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yujiao Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingzhen Xie
- Reproductive Medicine Center, Wuhan University Renmin Hospital, Wuhan, China
| | - Satoshi H. Namekawa
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan, China
- Shenzhen Huazhong University of Science and Technology, Research Institute, Shenzhen, China
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19
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Ozturk S. Genetic variants underlying spermatogenic arrests in men with non-obstructive azoospermia. Cell Cycle 2023; 22:1021-1061. [PMID: 36740861 PMCID: PMC10081088 DOI: 10.1080/15384101.2023.2171544] [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: 10/17/2022] [Revised: 12/29/2022] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
Spermatogenic arrest is a severe form of non-obstructive azoospermia (NOA), which occurs in 10-15% of infertile men. Interruption in spermatogenic progression at premeiotic, meiotic, or postmeiotic stage can lead to arrest in men with NOA. Recent studies have intensively focused on defining genetic variants underlying these spermatogenic arrests by making genome/exome sequencing. A number of variants were discovered in the genes involving in mitosis, meiosis, germline differentiation and other basic cellular events. Herein, defined variants in NOA cases with spermatogenic arrests and created knockout mouse models for the related genes are comprehensively reviewed. Also, importance of gene panel-based screening for NOA cases was discussed. Screening common variants in these infertile men with spermatogenic arrests may contribute to elucidating the molecular background and designing novel treatment strategies.
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Affiliation(s)
- Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, Antalya, Turkey
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20
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Lu Y, Nagamori I, Kobayashi H, Kojima-Kita K, Shirane K, Chang HY, Nishimura T, Koyano T, Yu Z, Castañeda JM, Matsuyama M, Kuramochi-Miyagawa S, Matzuk MM, Ikawa M. ADAD2 functions in spermiogenesis and piRNA biogenesis in mice. Andrology 2023; 11:698-709. [PMID: 36698249 PMCID: PMC10073342 DOI: 10.1111/andr.13400] [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: 07/29/2022] [Revised: 01/17/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
BACKGROUND Adenosine deaminase domain containing 2 (ADAD2) is a testis-specific protein composed of a double-stranded RNA binding domain and a non-catalytic adenosine deaminase domain. A recent study showed that ADAD2 is indispensable for the male reproduction in mice. However, the detailed functions of ADAD2 remain elusive. OBJECTIVES This study aimed to investigate the cause of male sterility in Adad2 mutant mice and to understand the molecular functions of ADAD2. MATERIALS AND METHODS Adad2 homozygous mutant mouse lines, Adad2-/- and Adad2Δ/Δ , were generated by CRISPR/Cas9. Western blotting and immunohistochemistry were used to reveal the expression and subcellular localization of ADAD2. Co-immunoprecipitation tandem mass spectrometry was employed to determine the ADAD2-interacting proteins in mouse testes. RNA-sequencing analyses were carried out to analyze the transcriptome and PIWI-interacting RNA (piRNA) populations in wildtype and Adad2 mutant testes. RESULTS Adad2-/- and Adad2Δ/Δ mice exhibit male-specific sterility because of abnormal spermiogenesis. ADAD2 interacts with multiple RNA-binding proteins involved in piRNA biogenesis, including MILI, MIWI, RNF17, and YTHDC2. ADAD2 co-localizes and forms novel granules with RNF17 in spermatocytes. Ablation of ADAD2 impairs the formation of RNF17 granules, decreases the number of cluster-derived pachytene piRNAs, and increases expression of ping-pong-derived piRNAs. DISCUSSION AND CONCLUSION In collaboration with RNF17 and other RNA-binding proteins in spermatocytes, ADAD2 directly or indirectly functions in piRNA biogenesis.
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Affiliation(s)
- Yonggang Lu
- Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Ippei Nagamori
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, Nara 634-0813, Japan
| | - Kanako Kojima-Kita
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Kenjiro Shirane
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Hsin-Yi Chang
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Toru Nishimura
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Takayuki Koyano
- Division of Molecular Genetics, Shigei Medical Research Institute, Okayama 701-0202, Japan
| | - Zhifeng Yu
- Center for Drug Discovery and Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Julio M. Castañeda
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Makoto Matsuyama
- Division of Molecular Genetics, Shigei Medical Research Institute, Okayama 701-0202, Japan
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Martin M. Matzuk
- Center for Drug Discovery and Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Masahito Ikawa
- Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Laboratory of Reproductive Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
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21
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Coudert A, Cazin C, Amiri-Yekta A, Ben Mustapha SF, Zouari R, Bessonat J, Zoghmar A, Clergeau A, Metzler-Guillemain C, Triki C, Lejeune H, Sermondade N, Pipiras E, Prisant N, Cedrin I, Koscinski I, Keskes L, Lestrade F, Hesters L, Rives N, Dorphin B, Guichet A, Patrat C, Dulioust E, Feraille A, Robert F, Brouillet S, Morel F, Perrin A, Rougier N, Bieth E, Sorlin A, Siffroi JP, Ben Khelifa M, Boiterelle F, Hennebicq S, Satre V, Arnoult C, Coutton C, Barbotin AL, Thierry-Mieg N, Kherraf ZE, Ray PF. Genetic causes of macrozoospermia and proposal for an optimized genetic diagnosis strategy based on sperm parameters. J Genet Genomics 2023:S1673-8527(23)00094-2. [PMID: 37116580 DOI: 10.1016/j.jgg.2023.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/30/2023]
Affiliation(s)
- Alicia Coudert
- Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble, 38000, France; CHU Grenoble Alpes, UM de Génétique Chromosomique, 38000 Grenoble, France
| | - Caroline Cazin
- Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble, 38000, France
| | - Amir Amiri-Yekta
- Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble, 38000, France; Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | | | - Raoudha Zouari
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, 1003 Tunis, Tunisia
| | - Julien Bessonat
- CHU Grenobles Alpes, UF de Biologie de la Procréation, 38000 Grenoble, France
| | - Abdelali Zoghmar
- Reproduction Sciences and Surgery Clinique, Ibn Rochd, Constantine, Algeria
| | - Antoine Clergeau
- CHU Caen, CECOS de Caen, Département de Biologie, Unité de Biologie de la Reproduction, 14033 Caen, France
| | - Catherine Metzler-Guillemain
- Assistance-Publique des Hôpitaux de Marseille (AP-HM), Pôle Femmes-Parents-Enfants, Centre Clinico-biologique AMP-CECOS, Marseille, France and Aix Marseille Univ, INSERM, MMG, UMR 1251, Marseille, France
| | - Chema Triki
- Clinique Hannibal, Centre d'AMP, les berges du lac, 1053 Tunis, Tunisia
| | - Hervé Lejeune
- Reproductive Medicine Department, Hospices Civil de Lyon, Lyon, France
| | | | - Eva Pipiras
- Hôpital Jean Verdier, Université Sorbonne Paris Nord, Paris, France
| | | | - Isabelle Cedrin
- Service de Médecine de la Reproduction, CHU Jean Verdier, Paris, France
| | | | | | - Florence Lestrade
- CHR Metz-Thionville, Service d'Assistance Médicale à la Procréation, 57530 Ars-Laquenexy, France
| | - Laetitia Hesters
- Laboratoire de Fécondation in vitro, Hôpital Antoine Béclère, France
| | - Nathalie Rives
- Univ Rouen Normandie, Inserm U1239, NorDIC, Adrenal and Gonadal Pathophysiology, Reproductive Biology Laboratory-CECOS, Rouen University Hospital, 76031 Rouen cedex, France
| | - Béatrice Dorphin
- CHAL Centre Hospitalier Alpes Léman, Centre AMP74, 74130 Contamine-sur-Arve
| | - Agnes Guichet
- CHU Angers, Service de Génétique, 49933 Angers, INSERM U1083 France
| | - Catherine Patrat
- Service de Biologie de la Reproduction - CECOS Hopital Cochin, 74014, Paris
| | - Emmanuel Dulioust
- Service de Biologie de la Reproduction - CECOS Hopital Cochin, 74014, Paris
| | - Aurélie Feraille
- Univ Rouen Normandie, Inserm U1239, NorDIC, Adrenal and Gonadal Pathophysiology, Reproductive Biology Laboratory-CECOS, Rouen University Hospital, 76031 Rouen cedex, France
| | - François Robert
- IRH Médicentre, Clinique du Val d'Ouest, 39 chemin de la Vernique, 69 130 Ecully, France
| | - Sophie Brouillet
- CHU Arnaud De Villeneuve, Biologie de la Reproduction, 34000 Montpellier, France
| | - Frédéric Morel
- Faculté de médecine et des sciences de la santé, Université de Brest, EFS, UMR1078, GGB, Brest, France; Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
| | - Aurore Perrin
- Faculté de médecine et des sciences de la santé, Université de Brest, EFS, UMR1078, GGB, Brest, France; Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
| | - Nathalie Rougier
- CHRU Nîmes, Laboratoire d'Assistance Médicale à la Procréation, 30029 Nîmes, France
| | - Eric Bieth
- CHU Toulouse, Service de Génétique, 31059 Toulouse, France
| | - Arthur Sorlin
- Laboratoire national de santé, 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg
| | - Jean-Pierre Siffroi
- Sorbonne Université, INSERM, UMRS_933, AP-HP, Hôpital Armand Trousseau, F-75012 Paris, France
| | | | - Florence Boiterelle
- Service d'assistance médicale à la procréation-Biologie de la reproduction, hôpital de Poissy, 78300 Poissy, France; EA 7404-GIG, UFR des sciences de la santé Simone-Veil, université de Versailles-Saint-Quentin-en-Yvelines, Paris Saclay, 78180 Montigny-le-Bretonneux, France
| | - Sylvianne Hennebicq
- Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU Grenobles Alpes, UF de Biologie de la Procréation, 38000 Grenoble, France
| | - Veronique Satre
- Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU Grenoble Alpes, UM de Génétique Chromosomique, 38000 Grenoble, France
| | - Christophe Arnoult
- Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Charles Coutton
- Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU Grenoble Alpes, UM de Génétique Chromosomique, 38000 Grenoble, France
| | - Anne-Laure Barbotin
- CHU Lille, Hôpital Jeanne De Flandre, Laboratoire de Biologie de la Reproduction-Spermiologie, 59037 Lille, France
| | | | - Zine-Eddine Kherraf
- Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble, 38000, France
| | - Pierre F Ray
- Genetic Epigenetic and Therapies of Infertility team, Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble, 38000, France.
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22
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Rockenbach MK, Fraga LR, Kowalski TW, Sanseverino MTV. Expression profiles of meiotic genes in male vs. female gonads and gametes: Insights into fertility issues. Front Genet 2023; 14:1125097. [PMID: 36999055 PMCID: PMC10045993 DOI: 10.3389/fgene.2023.1125097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
Gametes are specialized cells that, at fertilization, give rise to a totipotent zygote capable of generating an entire organism. Female and male germ cells undergo meiosis to produce mature gametes; however, sex-specific events of oogenesis and spermatogenesis contribute to specific roles of gametes in reproductive issues. We investigate the differential gene expression (DGE) of meiosis-related genes in human female and male gonads and gametes in normal and pathological conditions. The transcriptome data for the DGE analysis was obtained through the Gene Expression Omnibus repository, comprising human ovary and testicle samples of the prenatal period and adulthood, additionally to male (non-obstructive azoospermia (NOA) and teratozoospermia), and female (polycystic ovary syndrome (PCOS) and advanced maternal age) reproductive conditions. Gene ontology terms related to meiosis were associated with 678 genes, of which 17 genes in common were differentially expressed between the testicle and ovary during the prenatal period and adulthood. Except for SERPINA5 and SOX9, the 17 meiosis-related genes were downregulated in the testicle during the prenatal period and upregulated in adulthood compared to the ovary. No differences were observed in the oocytes of PCOS patients; however, meiosis-related genes were differentially expressed according to the patient’s age and maturity of the oocyte. In NOA and teratozoospermia, 145 meiosis-related genes were differentially expressed in comparison to the control, including OOEP; despite no recognized role in male reproduction, OOEP was co-expressed with genes related to male fertility. Taking together, these results shed light on potential genes that might be relevant to comprehend human fertility disorders.
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Affiliation(s)
- Marília Körbes Rockenbach
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
- *Correspondence: Thayne Woycinck Kowalski, ,
| | - Maria Teresa Vieira Sanseverino
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- School of Medicine, Pontifícia Universidade Catolica do Rio Grande do Sul, Porto Alegre, Brazil
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23
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Identification of sex-specific splicing via comparative transcriptome analysis of gonads from sea cucumber Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101031. [PMID: 36371882 DOI: 10.1016/j.cbd.2022.101031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Alternative splicing (AS) is an essential post-transcriptional regulation mechanism for sex differentiation and gonadal development, which has rarely been reported in marine invertebrates. Sea cucumber (Apostichopus japonicus) is an economically important marine benthic echinoderm with a potential XX/XY sex determination mechanism, whose molecular mechanism in the gonadal differentiation has not been clearly understood. In this study, we analyzed available RNA-seq datasets of male and female gonads to explore if AS mechanism exerts an essential function in sex differentiation and gonadal development of A. japonicus. In our results, a total of 20,338 AS events from 7219 alternatively spliced genes, and 189 sexually differential alternative splicing (DAS) events from 156 genes were identified in gonadal transcriptome of sea cucumber. Gene Ontology analysis indicated that these DAS genes were significantly enriched in spermatogenesis-related GO terms. Maximal Clique Centrality (MCC) was then applied for protein-protein interaction (PPI) analysis to search for protein interactions and hub DAS gene. Among all DAS genes, we identified 10 DAS genes closely related to spermatogenesis and (or) sperm motility and a hub gene dnah1. Thus, this study revealed that alternative isoforms were generated from certain genes in female and male gonads through alternative splicing, which may provide direct evidence that alternative splicing mechanisms participate in female and male gonads. These results suggested a novel perspective for explaining the molecular mechanisms underlying gonadal differentiation between male and female sea cucumbers.
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24
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Tian S, Wang Z, Liu L, Zhou Y, Lv Y, Tang D, Wang J, Jiang J, Wu H, Tang S, Wang G, Geng H, Tao F, Liu H, He X, Zhang F, Li J, Jin L, Huang T, Liu C, Cao Y. A homozygous frameshift mutation in ADAD2 causes male infertility with spermatogenic impairments. J Genet Genomics 2023; 50:284-288. [PMID: 36608931 DOI: 10.1016/j.jgg.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023]
Affiliation(s)
- Shixiong Tian
- Institute of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
| | - Ziqi Wang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China
| | - Liting Liu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui 230032, China
| | - Yiling Zhou
- Institute of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Yue Lv
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China
| | - Dongdong Tang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui 230032, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui 230032, China
| | - Jiaxiong Wang
- Center for Reproduction and Genetics, State Key Laboratory of Reproductive Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu 215002, China
| | - Jing Jiang
- Genome Tagging Project (GTP) Center, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huan Wu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui 230032, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui 230032, China
| | - Shuyan Tang
- Institute of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Guanxiong Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui 230032, China
| | - Hao Geng
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui 230032, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui 230032, China
| | - Fangbiao Tao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui 230032, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui 230032, China
| | - Hongbin Liu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China
| | - Xiaojin He
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui 230032, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui 230032, China
| | - Feng Zhang
- Institute of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
| | - Jinsong Li
- Genome Tagging Project (GTP) Center, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Jin
- Institute of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
| | - Tao Huang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.
| | - Chunyu Liu
- Institute of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, Human Phenome Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China.
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui 230032, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui 230032, China.
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25
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Elcombe CS, Monteiro A, Elcombe MR, Ghasemzadeh-Hasankolaei M, Sinclair KD, Lea R, Padmanabhan V, Evans NP, Bellingham M. Developmental exposure to real-life environmental chemical mixture programs a testicular dysgenesis syndrome-like phenotype in prepubertal lambs. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 94:103913. [PMID: 35738462 PMCID: PMC9554787 DOI: 10.1016/j.etap.2022.103913] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 05/30/2023]
Abstract
Current declines in male reproductive health may, in part, be driven by anthropogenic environmental chemical (EC) exposure. Using a biosolids treated pasture (BTP) sheep model, this study examined the effects of gestational exposure to a translationally relevant EC mixture. Testes of 8-week-old ram lambs from mothers exposed to BTP during pregnancy contained fewer germ cells and had a greater proportion of Sertoli-cell-only seminiferous tubules. This concurs with previous published data from fetuses and neonatal lambs from mothers exposed to BTP. Comparison between the testicular transcriptome of biosolids lambs and human testicular dysgenesis syndrome (TDS) patients indicated common changes in genes involved in apoptotic and mTOR signalling. Gene expression data and immunohistochemistry indicated increased HIF1α activation and nuclear localisation in Leydig cells of BTP exposed animals. As HIF1α is reported to disrupt testosterone synthesis, these results provide a potential mechanism for the pathogenesis of this testicular phenotype, and TDS in humans.
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Affiliation(s)
- Chris S Elcombe
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK; School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
| | - Ana Monteiro
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Matthew R Elcombe
- MicroMatrices Associates Ltd, Dundee Technopole, James Lindsay Place, Dundee, UK
| | - Mohammad Ghasemzadeh-Hasankolaei
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Kevin D Sinclair
- University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Richard Lea
- University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | | | - Neil P Evans
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Michelle Bellingham
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
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26
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Omolaoye TS, Hachim MY, du Plessis SS. Using publicly available transcriptomic data to identify mechanistic and diagnostic biomarkers in azoospermia and overall male infertility. Sci Rep 2022; 12:2584. [PMID: 35173218 PMCID: PMC8850557 DOI: 10.1038/s41598-022-06476-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 01/28/2022] [Indexed: 12/23/2022] Open
Abstract
Azoospermia, which is the absence of spermatozoa in an ejaculate occurring due to defects in sperm production, or the obstruction of the reproductive tract, affects about 1% of all men and is prevalent in up to 10–15% of infertile males. Conventional semen analysis remains the gold standard for diagnosing and treating male infertility; however, advances in molecular biology and bioinformatics now highlight the insufficiency thereof. Hence, the need to widen the scope of investigating the aetiology of male infertility stands pertinent. The current study aimed to identify common differentially expressed genes (DEGs) that might serve as potential biomarkers for non-obstructive azoospermia (NOA) and overall male infertility. DEGs across different datasets of transcriptomic profiling of testis from human patients with different causes of infertility/ impaired spermatogenesis and/or azoospermia were explored using the gene expression omnibus (GEO) database. Following the search using the GEOquery, 30 datasets were available, with 5 meeting the inclusion criteria. The DEGs for datasets were identified using limma R packages through the GEO2R tool. The annotated genes of the probes in each dataset were intersected with DEGs from all other datasets. Enriched Ontology Clustering for the identified genes was performed using Metascape to explore the possible connection or interaction between the genes. Twenty-five DEGs were shared between most of the datasets, which might indicate their role in the pathogenesis of male infertility. Of the 25 DEGs, eight genes (THEG, SPATA20, ROPN1L, GSTF1, TSSK1B, CABS1, ADAD1, RIMBP3) are either involved in the overall spermatogenic processes or at specific phases of spermatogenesis. We hypothesize that alteration in the expression of these genes leads to impaired spermatogenesis and, ultimately, male infertility. Thus, these genes can be used as potential biomarkers for the early detection of NOA.
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Affiliation(s)
- Temidayo S Omolaoye
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Mahmood Yaseen Hachim
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.
| | - Stefan S du Plessis
- Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.,Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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27
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Chukrallah LG, Badrinath A, Vittor GG, Snyder EM. ADAD2 regulates heterochromatin in meiotic and post-meiotic male germ cells via translation of MDC1. J Cell Sci 2022; 135:jcs259196. [PMID: 35191498 PMCID: PMC8919335 DOI: 10.1242/jcs.259196] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/09/2022] [Indexed: 11/20/2022] Open
Abstract
Male germ cells establish a unique heterochromatin domain, the XY-body, early in meiosis. How this domain is maintained through the end of meiosis and into post-meiotic germ cell differentiation is poorly understood. ADAD2 is a late meiotic male germ cell-specific RNA-binding protein, loss of which leads to post-meiotic germ cell defects. Analysis of ribosome association in Adad2 mouse mutants revealed defective translation of Mdc1, a key regulator of XY-body formation, late in meiosis. As a result, Adad2 mutants show normal establishment but failed maintenance of the XY-body. Observed XY-body defects are concurrent with abnormal autosomal heterochromatin and ultimately lead to severely perturbed post-meiotic germ cell heterochromatin and cell death. These findings highlight the requirement of ADAD2 for Mdc1 translation, the role of MDC1 in maintaining meiotic male germ cell heterochromatin and the importance of late meiotic heterochromatin for normal post-meiotic germ cell differentiation.
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Affiliation(s)
| | - Aditi Badrinath
- Department of Animal Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Gabrielle G. Vittor
- Department of Animal Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Elizabeth M. Snyder
- Department of Animal Science, Rutgers University, New Brunswick, NJ 08901, USA
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28
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Bendarska-Czerwińska A, Zmarzły N, Morawiec E, Panfil A, Bryś K, Czarniecka J, Ostenda A, Dziobek K, Sagan D, Boroń D, Michalski P, Pallazo-Michalska V, Grabarek BO. Endocrine disorders and fertility and pregnancy: An update. Front Endocrinol (Lausanne) 2022; 13:970439. [PMID: 36733805 PMCID: PMC9887196 DOI: 10.3389/fendo.2022.970439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
It is estimated that more and more couples suffer from fertility and pregnancy maintenance disorders. It is associated with impaired androgen secretion, which is influenced by many factors, ranging from genetic to environmental. It is also important to remember that fertility disorders can also result from abnormal anatomy of the reproductive male and female organ (congenital uterine anomalies - septate, unicornuate, bicornuate uterus; acquired defects of the uterus structure - fibroids, polyps, hypertrophy), disturbed hormonal cycle and obstruction of the fallopian tubes resulting from the presence of adhesions due to inflammation, endometriosis, and surgery, abnormal rhythm of menstrual bleeding, the abnormal concentration of hormones. There are many relationships between the endocrine organs, leading to a chain reaction when one of them fails to function properly. Conditions in which the immune system is involved, including infections and autoimmune diseases, also affect fertility. The form of treatment depends on infertility duration and the patient's age. It includes ovulation stimulation with clomiphene citrate or gonadotropins, metformin use, and weight loss interventions. Since so many different factors affect fertility, it is important to correctly diagnose what is causing the problem and to modify the treatment regimen if necessary. This review describes disturbances in the hormone secretion of individual endocrine organs in the context of fertility and the maintenance of pregnancy.
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Affiliation(s)
- Anna Bendarska-Czerwińska
- Department of Molecular, Biology Gyncentrum Fertility Clinic, Katowice, Poland
- Faculty of Medicine, Academy of Silesia, Zabrze, Poland
- American Medical Clinic, Katowice, Poland
- *Correspondence: Anna Bendarska-Czerwińska, ; Nikola Zmarzły, ; Beniamin Oskar Grabarek,
| | - Nikola Zmarzły
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine, University of Technology, Academy of Silesia in Katowice, Zabrze, Poland
- *Correspondence: Anna Bendarska-Czerwińska, ; Nikola Zmarzły, ; Beniamin Oskar Grabarek,
| | - Emilia Morawiec
- Department of Molecular, Biology Gyncentrum Fertility Clinic, Katowice, Poland
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine, University of Technology, Academy of Silesia in Katowice, Zabrze, Poland
- Department of Microbiology, Faculty of Medicine, University of Technology, Academy of Silesia in Katowice, Zabrze, Poland
| | - Agata Panfil
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine, University of Technology, Academy of Silesia in Katowice, Zabrze, Poland
| | - Kamil Bryś
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine, University of Technology, Academy of Silesia in Katowice, Zabrze, Poland
| | - Justyna Czarniecka
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine, University of Technology, Academy of Silesia in Katowice, Zabrze, Poland
| | | | | | - Dorota Sagan
- Medical Center Dormed Medical SPA, Busko-Zdroj, Poland
| | - Dariusz Boroń
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine, University of Technology, Academy of Silesia in Katowice, Zabrze, Poland
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Academy of Silesia, Zabrze, Poland
- Department of Gynecology and Obstetrics with Gynecologic Oncology, Ludwik Rydygier Memorial Specialized Hospital, Kraków, Poland
- Department of Gynecology and Obstetrics, TOMMED Specjalisci od Zdrowia, Katowice, Poland
| | | | | | - Beniamin Oskar Grabarek
- Department of Molecular, Biology Gyncentrum Fertility Clinic, Katowice, Poland
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine, University of Technology, Academy of Silesia in Katowice, Zabrze, Poland
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Academy of Silesia, Zabrze, Poland
- Department of Gynecology and Obstetrics with Gynecologic Oncology, Ludwik Rydygier Memorial Specialized Hospital, Kraków, Poland
- Department of Gynecology and Obstetrics, TOMMED Specjalisci od Zdrowia, Katowice, Poland
- *Correspondence: Anna Bendarska-Czerwińska, ; Nikola Zmarzły, ; Beniamin Oskar Grabarek,
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Abstract
Epigenetic modifications have gained attention since they can be potentially changed with environmental stimuli and can be associated with adverse health outcomes. Epitranscriptome field has begun to attract attention with several aspects since RNA modifications have been linked with critical biological processes and implicated in diseases. Several RNA modifications have been identified as reversible indicating the dynamic features of modification which can be altered by environmental cues. Currently, we know more than 150 RNA modifications in different organisms and on different bases which are modified by various chemical groups. RNA editing, which is one of the RNA modifications, occurs after transcription, which results in RNA sequence different from its corresponding DNA sequence. Emerging evidence reveals the functions of RNA editing as well as the association between RNA editing and diseases. However, the RNA editing field is beginning to grow up and needs more empirical evidence in regard to disease and toxicology. Thus, this review aims to provide the current evidence-based studies on RNA editing modifying genes for genotoxicity and cancer. The review presented the association between environmental xenobiotics exposure and RNA editing modifying genes and focused on the association between the expression of RNA editing modifying genes and cancer. Furthermore, we discussed the future directions of scientific studies in the area of RNA modifications, especially in the RNA editing field, and provided a knowledge-based framework for further studies.
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Affiliation(s)
- Akin Cayir
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey
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30
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Wang C, Luo X, Qin H, Zhao C, Yang L, Yu T, Zhang Y, Huang X, Xu X, Qin Q, Liu S. Formation of autotriploid Carassius auratus and its fertility-related genes analysis. BMC Genomics 2021; 22:435. [PMID: 34107878 PMCID: PMC8191051 DOI: 10.1186/s12864-021-07753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Background Formation of triploid organism is useful in genetics and breeding. In this study, autotriploid Carassius auratus (3nRR, 3n = 150) was generated from Carassius auratus red var. (RCC, 2n = 100) (♀) and autotetraploid Carassius auratus (4nRR, 4n = 200) (♂). The female 3nRR produced haploid, diploid and triploid eggs, whereas the male 3nRR was infertile. The aim of the present study was to explore fertility of potential candidate genes of 3nRR. Results Gonadal transcriptome profiling of four groups (3 females RCC (FRCC), 3 males 4nRR (M4nRR), 3 males 3nRR (M3nRR) and 3 females 3nRR (F3nRR)) was performed using RNA-SEq. A total of 78.90 Gb of clean short reads and 24,262 differentially expressed transcripts (DETs), including 20,155 in F3nRR vs. FRCC and 4,107 in M3nRR vs. M4nRR were identified. A total of 106 enriched pathways were identified through KEGG enrichment analysis. Out of the enriched pathways, 44 and 62 signalling pathways were identified in F3nRR vs. FRCC and M3nRR vs. M4nRR, respectively. A total of 80 and 25 potential candidate genes for fertility-related in F3nRR and M3nRR were identified, respectively, through GO, KEGG analyses and the published literature. Moreover, protein-protein interaction (PPI) network construction of these fertility-associated genes were performed. Analysis of the PPI networks showed that 6 hub genes (MYC, SOX2, BMP4, GATA4, PTEN and BMP2) were involved in female fertility of F3nRR, and 2 hub genes (TP53 and FGF2) were involved in male sterility of M3nRR. Conclusions Establishment of autotriploid fish offers an ideal model to study reproductive traits of triploid fish. RNA-Seq data revealed 6 genes, namely, MYC, SOX2, BMP4, GATA4, PTEN and BMP2, involved in the female fertility of the F3nRR. Moreover, 2 genes, namely, TP53 and FGF2, were related to the male sterility of the M3nRR. These findings provide information on reproduction and breeding in triploid fish. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07753-5.
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Affiliation(s)
- Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Xiang Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Yuxin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Xidan Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Hunan, 410081, Changsha, People's Republic of China.
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31
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Duan Y, Tang X, Lu J. Evolutionary driving forces of A-to-I editing in metazoans. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1666. [PMID: 33998151 DOI: 10.1002/wrna.1666] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 04/24/2021] [Indexed: 11/05/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is an evolutionarily conserved mechanism that converts adenosines to inosines in metazoans' transcriptomes. However, the landscapes of editomes have considerably changed during evolution. Here, we review some of our current knowledge of A-to-I editing in the metazoan transcriptomes, focusing on the possible evolutionary driving forces underlying the editing events. First, we review the evolution of ADAR gene family in animals. Then, we summarize the recent advances in characterizing the editomes of various metazoan species. Next, we highlight several factors contributing to the interspecies differences in editomes, including variations in copy number and expression patterns of ADAR genes, the differences in genomic architectures and contents, and the differences in the efficacy of natural selection. After that, we review the possible diversifying and restorative effects of the editing (recoding) events that change the protein sequences. Finally, we discuss the possible convergent evolution of RNA editing in distantly related clades. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
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