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Abstract
Background The formation of matured and individual sperm involves a series of molecular and spectacular morphological changes of the developing cysts in Drosophila melanogaster testis. Recent advances in RNA Sequencing (RNA-Seq) technology help us to understand the complexity of eukaryotic transcriptomes by dissecting different tissues and developmental stages of organisms. To gain a better understanding of cellular differentiation of spermatogenesis, we applied RNA-Seq to analyse the testis-specific transcriptome, including coding and non-coding genes. Results We isolated three different parts of the wild-type testis by dissecting and cutting the different regions: 1.) the apical region, which contains stem cells and developing spermatocytes 2.) the middle region, with enrichment of meiotic cysts 3.) the basal region, which contains elongated post-meiotic cysts with spermatids. Total RNA was isolated from each region and analysed by next-generation sequencing. We collected data from the annotated 17412 Drosophila genes and identified 5381 genes with significant transcript accumulation differences between the regions, representing the main stages of spermatogenesis. We demonstrated for the first time the presence and region specific distribution of 2061 lncRNAs in testis, with 203 significant differences. Using the available modENCODE RNA-Seq data, we determined the tissue specificity indices of Drosophila genes. Combining the indices with our results, we identified genes with region-specific enrichment in testis. Conclusion By multiple analyses of our results and integrating existing knowledge about Drosophila melanogaster spermatogenesis to our dataset, we were able to describe transcript composition of different regions of Drosophila testis, including several stage-specific transcripts. We present searchable visualizations that can facilitate the identification of new components that play role in the organisation and composition of different stages of spermatogenesis, including the less known, but complex regulation of post-meiotic stages. Electronic supplementary material The online version of this article (10.1186/s12864-018-5085-z) contains supplementary material, which is available to authorized users.
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Gemayel R, Yang Y, Dzialo MC, Kominek J, Vowinckel J, Saels V, Van Huffel L, van der Zande E, Ralser M, Steensels J, Voordeckers K, Verstrepen KJ. Variable repeats in the eukaryotic polyubiquitin gene ubi4 modulate proteostasis and stress survival. Nat Commun 2017; 8:397. [PMID: 28855501 PMCID: PMC5577197 DOI: 10.1038/s41467-017-00533-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 07/05/2017] [Indexed: 01/23/2023] Open
Abstract
Ubiquitin conjugation signals for selective protein degradation by the proteasome. In eukaryotes, ubiquitin is encoded both as a monomeric ubiquitin unit fused to a ribosomal gene and as multiple ubiquitin units in tandem. The polyubiquitin gene is a unique, highly conserved open reading frame composed solely of tandem repeats, yet it is still unclear why cells utilize this unusual gene structure. Using the Saccharomyces cerevisiae UBI4 gene, we show that this multi-unit structure allows cells to rapidly produce large amounts of ubiquitin needed to respond to sudden stress. The number of ubiquitin units encoded by UBI4 influences cellular survival and the rate of ubiquitin-proteasome system (UPS)-mediated proteolysis following heat stress. Interestingly, the optimal number of repeats varies under different types of stress indicating that natural variation in repeat numbers may optimize the chance for survival. Our results demonstrate how a variable polycistronic transcript provides an evolutionary alternative for gene copy number variation. Eukaryotic cells rely on the ubiquitin-proteasome system for selective degradation of proteins, a process vital to organismal fitness. Here the authors show that the number of repeats in the polyubiquitin gene is evolutionarily unstable within and between yeast species, and that this variability may tune the cell’s capacity to respond to sudden environmental perturbations.
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Affiliation(s)
- Rita Gemayel
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Yudi Yang
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Maria C Dzialo
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Jacek Kominek
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Veerle Saels
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Leen Van Huffel
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Elisa van der Zande
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis Court Road, Cambridge, CB2 1GA, UK.,The Francis Crick Institute, 1 Midland Rd, London, NW11AT, UK
| | - Jan Steensels
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Karin Voordeckers
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Kevin J Verstrepen
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium. .,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium.
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Chen L, Tang L, Xiang H, Jin L, Li Q, Dong Y, Wang W, Zhang G. Advances in genome editing technology and its promising application in evolutionary and ecological studies. Gigascience 2014; 3:24. [PMID: 25414792 PMCID: PMC4238018 DOI: 10.1186/2047-217x-3-24] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 10/04/2014] [Indexed: 12/26/2022] Open
Abstract
Genetic modification has long provided an approach for “reverse genetics”, analyzing gene function and linking DNA sequence to phenotype. However, traditional genome editing technologies have not kept pace with the soaring progress of the genome sequencing era, as a result of their inefficiency, time-consuming and labor-intensive methods. Recently, invented genome modification technologies, such as ZFN (Zinc Finger Nuclease), TALEN (Transcription Activator-Like Effector Nuclease), and CRISPR/Cas9 nuclease (Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 nuclease) can initiate genome editing easily, precisely and with no limitations by organism. These new tools have also offered intriguing possibilities for conducting functional large-scale experiments. In this review, we begin with a brief introduction of ZFN, TALEN, and CRISPR/Cas9 technologies, then generate an extensive prediction of effective TALEN and CRISPR/Cas9 target sites in the genomes of a broad range of taxonomic species. Based on the evidence, we highlight the potential and practicalities of TALEN and CRISPR/Cas9 editing in non-model organisms, and also compare the technologies and test interesting issues such as the functions of candidate domesticated, as well as candidate genes in life-environment interactions. When accompanied with a high-throughput sequencing platform, we forecast their potential revolutionary impacts on evolutionary and ecological research, which may offer an exciting prospect for connecting the gap between DNA sequence and phenotype in the near future.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
| | - Linyi Tang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hui Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
| | - Lijun Jin
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiye Li
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Yang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650223, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China ; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
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Li QG, Zhang YM. The origin and functional transition of P34. Heredity (Edinb) 2013; 110:259-66. [PMID: 23211789 PMCID: PMC3668652 DOI: 10.1038/hdy.2012.81] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 09/20/2012] [Accepted: 10/01/2012] [Indexed: 12/19/2022] Open
Abstract
P34, a storage protein and major soybean allergen, has undergone a functional transition from a cysteine peptidase to a syringolide receptor. An exploration of the evolutionary mechanism of this functional transition is made. To identify homologous genes of P34, syntenic network was constructed using syntenic relationships from the Plant Genome Duplication Database. The collected homologous genes, along with SPE31, a highly homologous protein to P34 from the seeds of Pachyrhizus erosus, were used to construct a phylogenetic tree. The results show that multiple gene duplications, exon shuffling and following granulin domain loss and some critical point mutations are associated with the functional transition. Although some tests suggested the existence of positive selection, the possibility that random fixation under relaxation of purifying selection results in the functional transition is also supported. In addition, the genes Glyma08g12340 and Medtr8g086470 may belong to a new group within the papain family.
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Affiliation(s)
- Q-G Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, College of Agriculture, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Y-M Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, College of Agriculture, Nanjing Agricultural University, Nanjing, China
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Roulin A, Auer PL, Libault M, Schlueter J, Farmer A, May G, Stacey G, Doerge RW, Jackson SA. The fate of duplicated genes in a polyploid plant genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:143-53. [PMID: 22974547 DOI: 10.1111/tpj.12026] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/09/2012] [Accepted: 09/10/2012] [Indexed: 05/18/2023]
Abstract
Polyploidy is generally not tolerated in animals, but is widespread in plant genomes and may result in extensive genetic redundancy. The fate of duplicated genes is poorly understood, both functionally and evolutionarily. Soybean (Glycine max L.) has undergone two separate polyploidy events (13 and 59 million years ago) that have resulted in 75% of its genes being present in multiple copies. It therefore constitutes a good model to study the impact of whole-genome duplication on gene expression. Using RNA-seq, we tested the functional fate of a set of approximately 18 000 duplicated genes. Across seven tissues tested, approximately 50% of paralogs were differentially expressed and thus had undergone expression sub-functionalization. Based on gene ontology and expression data, our analysis also revealed that only a small proportion of the duplicated genes have been neo-functionalized or non-functionalized. In addition, duplicated genes were often found in collinear blocks, and several blocks of duplicated genes were co-regulated, suggesting some type of epigenetic or positional regulation. We also found that transcription factors and ribosomal protein genes were differentially expressed in many tissues, suggesting that the main consequence of polyploidy in soybean may be at the regulatory level.
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Affiliation(s)
- Anne Roulin
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA
- Zoologisches Institut, Universität Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Paul L Auer
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marc Libault
- Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK, 73019, USA
| | - Jessica Schlueter
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA
- College of Computing and Informatics, University of North Carolina Charlotte, Charlotte, NC, 28223, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Greg May
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Rebecca W Doerge
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Scott A Jackson
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA
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