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Chen J, He Y, Chen L, Wu T, Yang G, Luo H, Hu S, Yin S, Qian Y, Miao H, Li N, Miao C, Feng R. Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals. iScience 2024; 27:109104. [PMID: 38433915 PMCID: PMC10904927 DOI: 10.1016/j.isci.2024.109104] [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: 01/19/2023] [Revised: 11/16/2023] [Accepted: 01/30/2024] [Indexed: 03/05/2024] Open
Abstract
Alternative splicing (AS) as one of the important post-transcriptional regulatory mechanisms has been poorly studied during embryogenesis. In this study, we comprehensively collected and analyzed the transcriptome data of early embryos from human and mouse. We found that AS plays an important role in this process and predicted candidate RNA binding protein (RBP) regulators that are associated with reproductive development. The predicted RBPs such as EIF4A3, MAK16, SRSF2, and UTP23 were found to be associated with reproductive disorders. By Smart-seq2 sequencing analysis, we identified 5445 aberrant alternative splicing events in Eif4a3-knockdown embryos. These events were preferentially associated with RNA processing. In conclusion, our work on the landscape and potential function of alternative splicing events will boost further investigation of detailed mechanisms and key factors regulating mammalian early embryo development and promote the inspiration of pharmaceutical approaches for disorders in this crucial biology process.
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Affiliation(s)
- Jianhua Chen
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yanni He
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Liangliang Chen
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Tian Wu
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Guangping Yang
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Hui Luo
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Saifei Hu
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Siyue Yin
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yun Qian
- Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, China
| | - Hui Miao
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, China
| | - Na Li
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, China
| | - Congxiu Miao
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, China
| | - Ruizhi Feng
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
- Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, China
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Ma S, Liu JY, Zhang JT. eIF3d: A driver of noncanonical cap-dependent translation of specific mRNAs and a trigger of biological/pathological processes. J Biol Chem 2023; 299:104658. [PMID: 36997088 PMCID: PMC10165153 DOI: 10.1016/j.jbc.2023.104658] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Eukaryotic initiation factor 3d (eIF3d), a known RNA-binding subunit of the eIF3 complex, is a 66 to 68-kDa protein with an RNA-binding motif and a cap-binding domain. Compared with other eIF3 subunits, eIF3d is relatively understudied. However, recent progress in studying eIF3d has revealed a number of intriguing findings on its role in maintaining eIF3 complex integrity, global protein synthesis, and in biological and pathological processes. It has also been reported that eIF3d has noncanonical functions in regulating translation of a subset of mRNAs by binding to 5'-UTRs or interacting with other proteins independent of the eIF3 complex and additional functions in regulating protein stability. The noncanonical regulation of mRNA translation or protein stability may contribute to the role of eIF3d in biological processes such as metabolic stress adaptation and in disease onset and progression including severe acute respiratory syndrome coronavirus 2 infection, tumorigenesis, and acquired immune deficiency syndrome. In this review, we critically evaluate the recent studies on these aspects of eIF3d and assess prospects in understanding the function of eIF3d in regulating protein synthesis and in biological and pathological processes.
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Affiliation(s)
- Shijie Ma
- Department of Cell and Cancer Biology, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Jing-Yuan Liu
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, The University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA.
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Xia Y, Zhao YD, Sun GX, Xia SS, Yang ZW. Gene Expression Network Analysis Identifies Potential Targets for Prevention of Preeclampsia. Int J Gen Med 2022; 15:1023-1032. [PMID: 35140505 PMCID: PMC8818964 DOI: 10.2147/ijgm.s348175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/17/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Preeclampsia (PE) is a pregnancy-specific multisystem disease as well as an important cause of maternal and perinatal death. This study aimed to analyze the placental transcriptional data and clinical information of PE patients available in the published database and predict the target genes for prevention of PE. Methods The clinical information and corresponding RNA data of PE patients were downloaded from the GEO database. Cluster analysis was performed to examine the correlation between different genotyping genes and clinical manifestations. Then, bioinformatic approaches including GO, KEGG, WGCNA, and GSEA were employed to functionally characterize candidate target genes involved in pathogenesis of PE. Results Two PE datasets GSE60438 and GSE75010 were obtained and combined, thereby providing the data of 205 samples in total (100 non-PE and 105 PE samples). After eliminating the batch effect, we grouped and analyzed the integrated data, and further performed GSEA analysis. It was found that the genes in group 1 and group 2 were different from those in normal samples. Moreover, WGCNA analysis revealed that genes in group 1 were up-regulated in turquoise module, including SASH1, PIK3CB and FLT-1, while genes in group 2 were up-regulated in the blue and brown modules. We further conducted GO and KEGG pathway enrichment analyses and found that the differential genes in turquoise module were mainly involved in biological processes such as small molecular catabolic process, while being highly enriched in pathways, including MAPK signaling pathway and Rap1 signaling pathway. Conclusion FLT-1 was conventionally used to predict PE risk, and sFLT-1 could also be used as an indicator to evaluate PE treatment effect. As a candidate biomarker for predicting PE, SASH1 may participate in proliferation, migration, invasion and epithelial mesenchymal transformation of human trophoblast cells by regulating MAPK pathway and Rap1 signaling pathway, thus affecting the progression of PE. The mechanism allowing PIK3CB to regulate PE development was not clear, while the gene could be another candidate biomarker for PE risk prediction. This is an exploratory study and our findings were still required verification in further studies.
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Affiliation(s)
- Yu Xia
- Provincial Key Laboratory of TCM Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan Province, 410208, People’s Republic of China
- Institute of Chinese Medicine Diagnosis, Hunan University of Chinese Medicine, Changsha, Hunan Province, 410208, People’s Republic of China
- Department of Obstetrics and Gynecology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan Province, 410007, People’s Republic of China
| | - Yu-Dong Zhao
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, People’s Republic of China
| | - Gui-Xiang Sun
- Provincial Key Laboratory of TCM Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan Province, 410208, People’s Republic of China
- Institute of Chinese Medicine Diagnosis, Hunan University of Chinese Medicine, Changsha, Hunan Province, 410208, People’s Republic of China
- Correspondence: Gui-Xiang Sun, Provincial Key Laboratory of TCM Diagnostics, Hunan University of Chinese Medicine, No. 300, Xueshi Road, Yuelu District, Changsha, Hunan Province, 410208, People’s Republic of China, Tel +86-13787272837, Email
| | - Shuai-Shuai Xia
- Provincial Key Laboratory of TCM Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan Province, 410208, People’s Republic of China
| | - Zheng-Wang Yang
- Department of Obstetrics and Gynecology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan Province, 410007, People’s Republic of China
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