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Hou H, Wang X, Yang C, Cai X, Lv W, Tu Y, Bao A, Wu Q, Zhao W, Yao J, Ding W. Comparative Genome and Transcriptome Integration Studies Reveal the Mechanism of Pectoral Muscle Development and Function in Pigeons. Front Genet 2022; 12:735795. [PMID: 34987544 PMCID: PMC8721168 DOI: 10.3389/fgene.2021.735795] [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: 07/03/2021] [Accepted: 11/26/2021] [Indexed: 11/13/2022] Open
Abstract
Pigeon breed resources provide a genetic model for the study of phenomics. The pectoral muscles play a key role for the meat production performance of the meat pigeon and the athletic ability of the High flyers. Euro-pigeons and Silver King pigeons are commercial varieties that exhibit good meat production performance. In contrast to the domestication direction of meat pigeons, the traditional Chinese ornamental pigeon breed, High flyers, has a small and light body. Here, we investigate the molecular mechanism of the pectoral muscle development and function of pigeons using whole-genome and RNA sequencing data. The selective sweep analysis (FST and log2 (θπ ratio)) revealed 293 and 403 positive selection genes in Euro-pigeons and Silver King, respectively, of which 65 genes were shared. With the Silver King and Euro-pigeon as the control group, the High flyers were selected for 427 and 566 genes respectively. There were 673 differentially expressed genes in the breast muscle transcriptome between the commercial meat pigeons and ornamental pigeons. Pigeon genome selection signal combined with the breast muscle transcriptome revealed that six genes (SLC16A10, S100B, SYNE1, HECW2, CASQ2 and LOC110363470) from commercial varieties of pigeons and five genes (INSC, CALCB, ZBTB21, B2M and LOC110356506) from Chinese traditional ornamental pigeons were positively selected which were involved in pathways related to muscle development and function. This study provides new insights into the selection of different directions and the genetic mechanism related to muscle development in pigeons.
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Affiliation(s)
- Haobin Hou
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Xiaoliang Wang
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Changsuo Yang
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Xia Cai
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Wenwei Lv
- National Poultry Engineer Research Center, Shanghai, China
| | - Yingying Tu
- National Poultry Engineer Research Center, Shanghai, China
| | | | - Quanli Wu
- Shanghai Jinhuang Pigeon Company, Shanghai, China
| | - Weimin Zhao
- Shanghai Jinhuang Pigeon Company, Shanghai, China
| | - Junfeng Yao
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Weixing Ding
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
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Rust K, Wodarz A. Transcriptional Control of Apical-Basal Polarity Regulators. Int J Mol Sci 2021; 22:ijms222212340. [PMID: 34830224 PMCID: PMC8624420 DOI: 10.3390/ijms222212340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/06/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022] Open
Abstract
Cell polarity is essential for many functions of cells and tissues including the initial establishment and subsequent maintenance of epithelial tissues, asymmetric cell division, and morphogenetic movements. Cell polarity along the apical-basal axis is controlled by three protein complexes that interact with and co-regulate each other: The Par-, Crumbs-, and Scrib-complexes. The localization and activity of the components of these complexes is predominantly controlled by protein-protein interactions and protein phosphorylation status. Increasing evidence accumulates that, besides the regulation at the protein level, the precise expression control of polarity determinants contributes substantially to cell polarity regulation. Here we review how gene expression regulation influences processes that depend on the induction, maintenance, or abolishment of cell polarity with a special focus on epithelial to mesenchymal transition and asymmetric stem cell division. We conclude that gene expression control is an important and often neglected mechanism in the control of cell polarity.
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Affiliation(s)
- Katja Rust
- Department of Molecular Cell Physiology, Institute of Physiology and Pathophysiology, Philipps-University, 35037 Marburg, Germany
- Correspondence: (K.R.); (A.W.)
| | - Andreas Wodarz
- Department of Molecular Cell Biology, Institute I for Anatomy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cluster of Excellence—Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
- Correspondence: (K.R.); (A.W.)
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Gao L, Wu K, Liu Z, Yao X, Yuan S, Tao W, Yi L, Yu G, Hou Z, Fan D, Tian Y, Liu J, Chen ZJ, Liu J. Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution. Cell 2018. [PMID: 29526463 DOI: 10.1016/j.cell.2018.02.028] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The dynamics of the chromatin regulatory landscape during human early embryogenesis remains unknown. Using DNase I hypersensitive site (DHS) sequencing, we report that the chromatin accessibility landscape is gradually established during human early embryogenesis. Interestingly, the DHSs with OCT4 binding motifs are enriched at the timing of zygotic genome activation (ZGA) in humans, but not in mice. Consistently, OCT4 contributes to ZGA in humans, but not in mice. We further find that lower CpG promoters usually establish DHSs at later stages. Similarly, younger genes tend to establish promoter DHSs and are expressed at later embryonic stages, while older genes exhibit these features at earlier stages. Moreover, our data show that human active transposons SVA and HERV-K harbor DHSs and are highly expressed in early embryos, but not in differentiated tissues. In summary, our data provide an evolutionary developmental view for understanding the regulation of gene and transposon expression.
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Affiliation(s)
- Lei Gao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Keliang Wu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Zhenbo Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xuelong Yao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Shenli Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Wenrong Tao
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Lizhi Yi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Guanling Yu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Zhenzhen Hou
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China
| | - Dongdong Fan
- Key Laboratory of RNA Biology of CAS, University of Chinese Academy of Sciences, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yong Tian
- Key Laboratory of RNA Biology of CAS, University of Chinese Academy of Sciences, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jianqiao Liu
- Center for Reproductive Medicine, Third Affiliated Hospital, Guangzhou Medical University, 510150 Guangzhou, China.
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology, Shandong University, Ministry of Education, Jinan, 250001 Shandong, China.
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, 100049 Beijing, China.
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