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Panten J, Heinen T, Ernst C, Eling N, Wagner RE, Satorius M, Marioni JC, Stegle O, Odom DT. The dynamic genetic determinants of increased transcriptional divergence in spermatids. Nat Commun 2024; 15:1272. [PMID: 38341412 PMCID: PMC10858866 DOI: 10.1038/s41467-024-45133-1] [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: 02/07/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify allele-specific expression during spermatogenic differentiation at single-cell resolution in an F1 hybrid mouse system, allowing for the comprehensive characterisation of cis- and trans-genetic effects, including their dynamics across cellular differentiation. Collectively, almost half of the genes subject to genetic regulation show evidence for dynamic cis-effects that vary during differentiation. Our system also allows us to robustly identify dynamic trans-effects, which are less pervasive than cis-effects. In aggregate, genetic effects were strongest in round spermatids, which parallels their increased transcriptional divergence we identified between species. Our approach provides a comprehensive quantification of the variability of genetic effects in vivo, and demonstrates a widely applicable strategy to dissect the impact of regulatory variants on gene regulation in dynamic systems.
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Affiliation(s)
- Jasper Panten
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - Tobias Heinen
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Mathematics and Computer Science, Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany
| | - Christina Ernst
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Nils Eling
- University of Zurich, Department of Quantitative Biomedicine, Zurich, 8057, Switzerland
- ETH Zurich, Institute for Molecular Health Sciences, Zurich, 8093, Switzerland
| | - Rebecca E Wagner
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
- Division of Mechanisms Regulating Gene Expression, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Maja Satorius
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Oliver Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
| | - Duncan T Odom
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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Fang L, Guo L, Zhang M, Li X, Deng Z. Analysis of Polyadenylation Signal Usage with Full-Length Transcriptome in Spodoptera frugiperda (Lepidoptera: Noctuidae). INSECTS 2022; 13:803. [PMID: 36135504 PMCID: PMC9505298 DOI: 10.3390/insects13090803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
During the messenger RNA (mRNA) maturation process, RNA polyadenylation is a key step, and is coupled to the termination of transcription. Various cis-acting elements near the cleavage site and their binding factors would affect the process of polyadenylation, and AAUAAA, a highly conserved hexamer, was the most important polyadenylation signal (PAS). PAS usage is one of the critical modification determinants targeted at mRNA post-transcription. The full-length transcriptome has recently generated a massive amount of sequencing data, revealing poly(A) variation and alternative polyadenylation (APA) in Spodoptera frugiperda. We identified 50,616 polyadenylation signals in Spodoptera frugiperda via analysis of full-length transcriptome combined with expression Sequence Tags Technology (EST). The polyadenylation signal usage in Spodoptera frugiperda is conserved, and it is similar to that of flies and other animals. AAUAAA and AUUAAA are the most highly conserved polyadenylation signals of all polyadenylation signals we identified. Additionally, we found the U/GU-rich downstream sequence element (DSE) in the cleavage site. These results demonstrate that APA in Spodoptera frugiperda plays a significant role in root growth and development. This is the first polyadenylation signal usage analysis in agricultural pests, which can deepen our understanding of Spodoptera frugiperda and provide a theoretical basis for pest control.
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Affiliation(s)
- Liying Fang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lina Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Min Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xianchun Li
- Department of Entomology, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
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3
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Zou X, Schaefke B, Li Y, Jia F, Sun W, Li G, Liang W, Reif T, Heyd F, Gao Q, Tian S, Li Y, Tang Y, Fang L, Hu Y, Chen W. Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law. Life Sci Alliance 2022; 5:5/4/e202101333. [PMID: 34969779 PMCID: PMC8739531 DOI: 10.26508/lsa.202101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
This study globally investigates the allelic splicing pattern in multiple tissues of an F1 hybrid mouse and reveals the underlying driving forces shaping such tissue-dependent splicing divergence. Alternative splicing is ubiquitous, but the mechanisms underlying its pattern of evolutionary divergence across mammalian tissues are still underexplored. Here, we investigated the cis-regulatory divergences and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid between two mouse species. Large splicing changes between tissues are highly conserved and likely reflect functional tissue-dependent regulation. In particular, micro-exons frequently exhibit this pattern with high inclusion levels in the brain. Cis-divergence of splicing appears to be largely non-adaptive. Although divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform apparently tolerate more mutations, explaining why their exon sequences are highly conserved but their intronic splicing site flanking regions are not. Moreover, we demonstrate that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attribute such buffering effect to trans-regulatory splicing efficiency.
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Affiliation(s)
- Xudong Zou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Bernhard Schaefke
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yisheng Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fujian Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Sun
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Weizheng Liang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Tristan Reif
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Florian Heyd
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Qingsong Gao
- Laboratory for Systems Biology and Functional Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Shuye Tian
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yanping Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yisen Tang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China .,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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4
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Tian S, Zhang B, He Y, Sun Z, Li J, Li Y, Yi H, Zhao Y, Zou X, Li Y, Cui H, Fang L, Gao X, Hu Y, Chen W. OUP accepted manuscript. Nucleic Acids Res 2022; 50:e26. [PMID: 35191504 PMCID: PMC8934656 DOI: 10.1093/nar/gkac108] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/01/2022] [Accepted: 02/19/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Yuhao He
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhiyuan Sun
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jun Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yisheng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongyang Yi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Zhao
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xudong Zou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yunfei Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Huanhuan Cui
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei Chen
- To whom correspondence should be addressed. Tel: +86 755 88018449;
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