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Bylino OV, Ogienko AA, Batin MA, Georgiev PG, Omelina ES. Genetic, Environmental, and Stochastic Components of Lifespan Variability: The Drosophila Paradigm. Int J Mol Sci 2024; 25:4482. [PMID: 38674068 PMCID: PMC11050664 DOI: 10.3390/ijms25084482] [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: 01/04/2024] [Revised: 03/25/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Lifespan is a complex quantitative trait involving genetic and non-genetic factors as well as the peculiarities of ontogenesis. As with all quantitative traits, lifespan shows considerable variation within populations and between individuals. Drosophila, a favourite object of geneticists, has greatly advanced our understanding of how different forms of variability affect lifespan. This review considers the role of heritable genetic variability, phenotypic plasticity and stochastic variability in controlling lifespan in Drosophila melanogaster. We discuss the major historical milestones in the development of the genetic approach to study lifespan, the breeding of long-lived lines, advances in lifespan QTL mapping, the environmental factors that have the greatest influence on lifespan in laboratory maintained flies, and the mechanisms, by which individual development affects longevity. The interplay between approaches to study ageing and lifespan limitation will also be discussed. Particular attention will be paid to the interaction of different types of variability in the control of lifespan.
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Affiliation(s)
- Oleg V. Bylino
- Department of Regulation of Genetic Processes, Laboratory of Molecular Organization of the Genome, Institute of Gene Biology RAS, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anna A. Ogienko
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Mikhail A. Batin
- Open Longevity, 15260 Ventura Blvd., Sherman Oaks, Los Angeles, CA 91403, USA
| | - Pavel G. Georgiev
- Department of Regulation of Genetic Processes, Laboratory of Molecular Organization of the Genome, Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - Evgeniya S. Omelina
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
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Lee SA, Kristjánsdóttir K, Kwak H. eRNA co-expression network uncovers TF dependency and convergent cooperativity. Sci Rep 2023; 13:19085. [PMID: 37925545 PMCID: PMC10625640 DOI: 10.1038/s41598-023-46415-2] [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: 02/15/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023] Open
Abstract
Enhancer RNAs (eRNAs) are non-coding RNAs produced by transcriptional enhancers that are highly correlated with their activity. Using a capped nascent RNA sequencing (PRO-cap) dataset in human lymphoblastoid cell lines across 67 individuals, we identified inter-individual variation in the expression of over 80 thousand transcribed transcriptional regulatory elements (tTREs), in both enhancers and promoters. Co-expression analysis of eRNAs from tTREs across individuals revealed how enhancers are associated with each other and with promoters. Mid- to long-range co-expression showed a distance-dependent decay that was modified by TF occupancy. In particular, we found a class of "bivalent" TFs, including Cohesin, that both facilitate and isolate the interaction between enhancers and/or promoters, depending on their topology. At short distances, we observed strand-specific correlations between nearby eRNAs in both convergent and divergent orientations. Our results support a cooperative model of convergent eRNAs, consistent with eRNAs facilitating adjacent enhancers rather than interfering with each other. Therefore, our approach to infer functional interactions from co-expression analyses provided novel insights into the principles of enhancer interactions as a function of distance, orientation, and binding landscapes of TFs.
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Affiliation(s)
- Seungha Alisa Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Katla Kristjánsdóttir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
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Lee SA, Kristjánsdóttir K, Kwak H. Revealing eRNA interactions: TF dependency and convergent cooperativity. RESEARCH SQUARE 2023:rs.3.rs-2592357. [PMID: 36909657 PMCID: PMC10002804 DOI: 10.21203/rs.3.rs-2592357/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Enhancer RNAs (eRNAs) are non-coding RNAs produced from transcriptional enhancers that are highly correlated with their activities. Using capped nascent RNA sequencing (PRO-cap) dataset in human lymphoblastoid cell lines across individuals, we identified inter-individual variation of expression in over 80 thousand transcribed transcriptional regulatory elements (tTREs), in both enhancers and promoters. Co-expression analysis of eRNAs from tTREs across individuals revealed how enhancers interact with each other and with promoters. Mid-to-long range interactions showed distance-dependent decay, which was modified by TF occupancy. In particular, we found a class of 'bivalent' TFs, including Cohesin, which both facilitates and insulates the interaction between enhancers and/or promoters depending on the topology. In short ranges, we observed strand specific interactions between nearby eRNAs in both convergent or divergent orientations. Our finding supports a cooperative convergent eRNA model, which is compatible with eRNA remodeling neighboring enhancers rather than interfering with each other. Therefore, our approach to infer functional interactions from co-expression analyses provided novel insights into the principles of enhancer interactions depending on the distance, orientation, and the binding landscapes of TFs.
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Gene Set Enrichment Analysis Detected Immune Cell-Related Pathways Associated with Primary Sclerosing Cholangitis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2371347. [PMID: 36060137 PMCID: PMC9439919 DOI: 10.1155/2022/2371347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022]
Abstract
Aim To explore various immune cell-related causal pathways for primary sclerosing cholangitis (PSC). Methods Immune cell-related pathway association study was conducted via integrative analysis of PSC GWAS summary and five immune cell-related eQTL datasets. The GWAS summary data of PSC was driven from 4,796 PSC cases and 19,955 healthy controls. The eQTL datasets of CD4+ T cells, CD8+ T cells, B cells, natural killer cells (NK), monocytes, and peripheral blood cells (PB) were collected from recently eQTL study. The PSC GWAS summary dataset was first aligned with eQTL datasets of six blood cells to obtain the GWAS summary data at overlapped eQTL loci, separately. For each type of cell, the obtained PSC GWAS summary dataset of eQTLs was subjected to pathway enrichment analysis. 853 biological pathways from Kyoto Encyclopedia of Genes and Genomes, BioCarta, and Reactome pathway databases were analyzed. Results We identified 36 pathways for B cells, 33 pathways for CD4+ T cells, 28 pathways for CD8+ T cells, 33 pathways for monocytes (MN), 35 pathways for NK cells, and 33 for PB cells (all empirical P values <5.0 × 10−5). Comparing the pathway analysis results detected 25 pathways shared by five immune cells, such as KEGG_CELL_ADHESION_MOLECULES_CAMS (P value <5.0 × 10−5) and REACTOME_MHC_CLASS_II_ANTIGEN_ PRESENTATION (P value <5.0 × 10−5). Several cell-specific pathways were also identified, including BIOCARTA_INFLAM_PATHWAY (P value <5 × 10−5) for B cell. Conclusion Our study holds potential to identify novel candidate causal pathways and provides clues for revealing the complex genetic mechanism of PSC.
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Zhang T, Wang T, Niu Q, Xu L, Chen Y, Gao X, Gao H, Zhang L, Liu GE, Li J, Xu L. Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. BMC Biol 2022; 20:79. [PMID: 35351103 PMCID: PMC8966188 DOI: 10.1186/s12915-022-01269-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/03/2022] [Indexed: 11/12/2022] Open
Abstract
Background A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. We performed a large-scale gene expression analysis and generated a high-resolution atlas of the transcriptome in beef cattle. Results Our transcriptome atlas was generated from 135 bovine tissues in adult beef cattle, covering 51 tissue types of major organ systems (e.g., muscular system, digestive system, immune system, reproductive system). Approximately 94.76% of sequencing reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We detected a total of 60,488 transcripts, and 32% of them were not reported before. We identified 2654 housekeeping genes (HKGs) and 477 tissue-specific genes (TSGs) across tissues. Using weighted gene co-expression network analysis, we obtained 24 modules with 237 hub genes (HUBGs). Functional enrichment analysis showed that HKGs mainly maintain the basic biological activities of cells, while TSGs were involved in tissue differentiation and specific physiological processes. HKGs in bovine tissues were more conserved in terms of expression pattern as compared to TSGs and HUBGs among multiple species. Finally, we obtained a subset of tissue-specific differentially expressed genes (DEGs) between beef and dairy cattle and several functional pathways, which may be involved in production and health traits. Conclusions We generated a large-scale gene expression atlas across the major tissues in beef cattle, providing valuable information for enhancing genome assembly and annotation. HKGs, TSGs, and HUBGs further contribute to better understanding the biology and evolution of multiple tissues in cattle. DEGs between beef and dairy cattle also fill in the knowledge gaps about differential transcriptome regulation of bovine tissues underlying economically important traits. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01269-4.
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Affiliation(s)
- Tianliu Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Tianzhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Qunhao Niu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Lei Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, 20705, USA
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
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Secchia S, Forneris M, Heinen T, Stegle O, Furlong EEM. Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories. Dev Cell 2022; 57:496-511.e8. [PMID: 35176234 PMCID: PMC8893321 DOI: 10.1016/j.devcel.2022.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/04/2021] [Accepted: 01/26/2022] [Indexed: 11/09/2022]
Abstract
Developmental progression and cellular diversity are largely driven by transcription factors (TFs); yet, characterizing their loss-of-function phenotypes remains challenging and often disconnected from their underlying molecular mechanisms. Here, we combine single-cell regulatory genomics with loss-of-function mutants to jointly assess both cellular and molecular phenotypes. Performing sci-ATAC-seq at eight overlapping time points during Drosophila mesoderm development could reconstruct the developmental trajectories of all major muscle types and reveal the TFs and enhancers involved. To systematically assess mutant phenotypes, we developed a single-nucleus genotyping strategy to process embryo pools of mixed genotypes. Applying this to four TF mutants could identify and quantify their characterized phenotypes de novo and discover new ones, while simultaneously revealing their regulatory input and mode of action. Our approach is a general framework to dissect the functional input of TFs in a systematic, unbiased manner, identifying both cellular and molecular phenotypes at a scale and resolution that has not been feasible before. scATAC time course constructs regulatory trajectories of Drosophila muscle lineages Combining a wild-type trajectory with mutants identifies and quantifies phenotypes de novo Digital nuclear genotyping enables the processing of pooled embryos of mixed genotypes This framework simultaneously uncovers cellular and molecular phenotypes in embryos
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Affiliation(s)
- Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Baden-Württemberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Baden-Württemberg, Germany
| | - Mattia Forneris
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Baden-Württemberg, Germany
| | - Tobias Heinen
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Baden-Württemberg, Germany; Heidelberg University, Faculty of Mathematics and Computer Science, 69120 Heidelberg, Baden-Württemberg, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Baden-Württemberg, Germany; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Baden-Württemberg, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Baden-Württemberg, Germany.
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Heinen T, Secchia S, Reddington JP, Zhao B, Furlong EEM, Stegle O. scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation. Genome Biol 2022; 23:8. [PMID: 34991671 PMCID: PMC8734213 DOI: 10.1186/s13059-021-02593-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/27/2021] [Indexed: 01/04/2023] Open
Abstract
While it is established that the functional impact of genetic variation can vary across cell types and states, capturing this diversity remains challenging. Current studies using bulk sequencing either ignore this heterogeneity or use sorted cell populations, reducing discovery and explanatory power. Here, we develop scDALI, a versatile computational framework that integrates information on cellular states with allelic quantifications of single-cell sequencing data to characterize cell-state-specific genetic effects. We apply scDALI to scATAC-seq profiles from developing F1 Drosophila embryos and scRNA-seq from differentiating human iPSCs, uncovering heterogeneous genetic effects in specific lineages, developmental stages, or cell types.
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Affiliation(s)
- Tobias Heinen
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Mathematics and Computer Science, Heidelberg University, Heidelberg, Germany
| | - Stefano Secchia
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - James P Reddington
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bingqing Zhao
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Oliver Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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8
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Choate LA, Barshad G, McMahon PW, Said I, Rice EJ, Munn PR, Lewis JJ, Danko CG. Multiple stages of evolutionary change in anthrax toxin receptor expression in humans. Nat Commun 2021; 12:6590. [PMID: 34782625 PMCID: PMC8592990 DOI: 10.1038/s41467-021-26854-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/18/2021] [Indexed: 11/09/2022] Open
Abstract
The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease may have influenced human evolution, we study changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 is 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. We also observe multiple genetic signatures consistent with recent positive selection driving a European-specific decrease in ANTXR2 expression in multiple tissues affected by anthrax toxins. Our observations fit a model in which humans adapted to anthrax disease following early ecological changes associated with hunting and scavenging, as well as a second period of adaptation after the rise of modern agriculture.
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Affiliation(s)
- Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Pierce W McMahon
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Iskander Said
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Paul R Munn
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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Buchberger E, Bilen A, Ayaz S, Salamanca D, Matas de las Heras C, Niksic A, Almudi I, Torres-Oliva M, Casares F, Posnien N. Variation in Pleiotropic Hub Gene Expression Is Associated with Interspecific Differences in Head Shape and Eye Size in Drosophila. Mol Biol Evol 2021; 38:1924-1942. [PMID: 33386848 PMCID: PMC8097299 DOI: 10.1093/molbev/msaa335] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Revealing the mechanisms underlying the breathtaking morphological diversity observed in nature is a major challenge in Biology. It has been established that recurrent mutations in hotspot genes cause the repeated evolution of morphological traits, such as body pigmentation or the gain and loss of structures. To date, however, it remains elusive whether hotspot genes contribute to natural variation in the size and shape of organs. As natural variation in head morphology is pervasive in Drosophila, we studied the molecular and developmental basis of differences in compound eye size and head shape in two closely related Drosophila species. We show differences in the progression of retinal differentiation between species and we applied comparative transcriptomics and chromatin accessibility data to identify the GATA transcription factor Pannier (Pnr) as central factor associated with these differences. Although the genetic manipulation of Pnr affected multiple aspects of dorsal head development, the effect of natural variation is restricted to a subset of the phenotypic space. We present data suggesting that this developmental constraint is caused by the coevolution of expression of pnr and its cofactor u-shaped (ush). We propose that natural variation in expression or function of highly connected developmental regulators with pleiotropic functions is a major driver for morphological evolution and we discuss implications on gene regulatory network evolution. In comparison to previous findings, our data strongly suggest that evolutionary hotspots are not the only contributors to the repeated evolution of eye size and head shape in Drosophila.
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Affiliation(s)
- Elisa Buchberger
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Anıl Bilen
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Sanem Ayaz
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - David Salamanca
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Present address: Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | | | - Armin Niksic
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Isabel Almudi
- CABD (CSIC/UPO/JA), DMC2 Unit, Pablo de Olavide University Campus, Seville, Spain
| | - Montserrat Torres-Oliva
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Present address: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Fernando Casares
- CABD (CSIC/UPO/JA), DMC2 Unit, Pablo de Olavide University Campus, Seville, Spain
| | - Nico Posnien
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Corresponding author: E-mail:
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Li S, Shao W, Wang C, Wang L, Xia R, Yao S, Du M, Ji X, Chu H, Zhang Z, Wang M, Wang SL. Identification of common genetic variants associated with serum concentrations of p, p'-DDE in non-occupational populations in eastern China. ENVIRONMENT INTERNATIONAL 2021; 152:106507. [PMID: 33756427 DOI: 10.1016/j.envint.2021.106507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Dichlorodiphenyldichloroethylene (DDE) is the major and most stable toxic metabolite of dichlorodiphenyltrichloroethane (DDT), a well-known organochlorine pesticide banned worldwide in the 1980s. However, it remains easy to detect in humans, and internal levels vary widely among individuals. In the present study, a genome-wide association study (GWAS) (511 subjects) and two replications (812 and 1030 subjects) were performed in non-occupational populations in eastern China. An estimated dietary intake (EDI) of p, p'-DDT and p, p'-DDE was calculated by a food frequency questionnaire (FFQ) and the determination of 195 food and 85 drinking water samples. In addition, functional verifications of susceptible loci were performed by dual-luciferase reporter, immunoblotting and metabolic activity assays in vitro. p, p'-DDT and p, p'-DDE were measured using gas chromatography-tandem mass spectrometry (GC-MS/MS). A common loci rs3181842 (high linkage equilibrium with rs2279345) in CYP2B6 at 19p13.2 were found to be strongly associated with low serum levels of p, p'-DDE in this population in GWAS and were verified by two replications and combined analysis of 2353 subjects (P = 1.00 × 10-22). In addition, p, p'-DDE levels were significantly lower in subjects with the rs3181842 C allele than in those carrying the normal genotype, even in individuals with similar EDIs of p, p'-DDT. Furthermore, the rs3181842 C allele functionally led to low CYP2B6 expression and activity, resulting in a low metabolic capacity for the formation of p, p'-DDE from p, p'-DDT. The study highlighted that CYP2B6 variants were more relevant than environmental exposure to internal p, p'-DDE exposure, which is important information for DDT risk assessments.
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Affiliation(s)
- Shushu Li
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China; Changzhou Center for Disease Control and Prevention, 203 Taishan Road, Changzhou, 213022, PR China
| | - Wei Shao
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China; Sir Run Run Hospital, Nanjing Medical University, 109 Longmian Avenue, Nanjing 211166, PR China
| | - Chao Wang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China; State Key Lab of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Li Wang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Rong Xia
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Shen Yao
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Mulong Du
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Xiaoming Ji
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Haiyan Chu
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Zhengdong Zhang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Meilin Wang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China; State Key Lab of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China.
| | - Shou-Lin Wang
- Key Lab of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China; State Key Lab of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China.
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11
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Li L, Huang KL, Gao Y, Cui Y, Wang G, Elrod ND, Li Y, Chen YE, Ji P, Peng F, Russell WK, Wagner EJ, Li W. An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability. Nat Genet 2021; 53:994-1005. [PMID: 33986536 DOI: 10.1038/s41588-021-00864-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/05/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies have identified thousands of noncoding variants associated with human traits and diseases. However, the functional interpretation of these variants is a major challenge. Here, we constructed a multi-tissue atlas of human 3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs), containing approximately 0.4 million common genetic variants associated with the APA of target genes, identified in 46 tissues isolated from 467 individuals (Genotype-Tissue Expression Project). Mechanistically, 3'aQTLs can alter poly(A) motifs, RNA secondary structure and RNA-binding protein-binding sites, leading to thousands of APA changes. Our CRISPR-based experiments indicate that such 3'aQTLs can alter APA regulation. Furthermore, we demonstrate that mapping 3'aQTLs can identify APA regulators, such as La-related protein 4. Finally, 3'aQTLs are colocalized with approximately 16.1% of trait-associated variants and are largely distinct from other QTLs, such as expression QTLs. Together, our findings show that 3'aQTLs contribute substantially to the molecular mechanisms underlying human complex traits and diseases.
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Affiliation(s)
- Lei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yipeng Gao
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Gao Wang
- The Gertrude H. Sergievsky Center and Department of Neurology, Columbia University, New York, NY, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yumei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yiling Elaine Chen
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Fanglue Peng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA.
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12
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Feregrino C, Tschopp P. Assessing evolutionary and developmental transcriptome dynamics in homologous cell types. Dev Dyn 2021; 251:1472-1489. [PMID: 34114716 PMCID: PMC9545966 DOI: 10.1002/dvdy.384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/19/2021] [Accepted: 06/04/2021] [Indexed: 12/03/2022] Open
Abstract
Background During development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built—largely—by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear. Results Here, we developed a user‐friendly bioinformatics workflow to detect gene co‐expression modules and test for their conservation across developmental stages and species boundaries. Using a paradigm of morphological diversification, the tetrapod limb, and single‐cell RNA‐sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. With mouse limb data as reference, we identified 19 gene co‐expression modules with varying tissue or cell type‐restricted activities. Testing for co‐expression conservation revealed modules with high evolutionary turnover, while others seemed maintained—to different degrees, in module make‐up, density or connectivity—over developmental and evolutionary timescales. Conclusions We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data. We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data.
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Affiliation(s)
- Christian Feregrino
- DUW Zoology, University of Basel, Basel, Switzerland.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany. Hannoversche Str. 28, Berlin, Germany
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13
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Floc'hlay S, Wong ES, Zhao B, Viales RR, Thomas-Chollier M, Thieffry D, Garfield DA, Furlong EEM. Cis-acting variation is common across regulatory layers but is often buffered during embryonic development. Genome Res 2021; 31:211-224. [PMID: 33310749 PMCID: PMC7849415 DOI: 10.1101/gr.266338.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Precise patterns of gene expression are driven by interactions between transcription factors, regulatory DNA sequences, and chromatin. How DNA mutations affecting any one of these regulatory "layers" are buffered or propagated to gene expression remains unclear. To address this, we quantified allele-specific changes in chromatin accessibility, histone modifications, and gene expression in F1 embryos generated from eight Drosophila crosses at three embryonic stages, yielding a comprehensive data set of 240 samples spanning multiple regulatory layers. Genetic variation (allelic imbalance) impacts gene expression more frequently than chromatin features, with metabolic and environmental response genes being most often affected. Allelic imbalance in cis-regulatory elements (enhancers) is common and highly heritable, yet its functional impact does not generally propagate to gene expression. When it does, genetic variation impacts RNA levels through two alternative mechanisms involving either H3K4me3 or chromatin accessibility and H3K27ac. Changes in RNA are more predictive of variation in H3K4me3 than vice versa, suggesting a role for H3K4me3 downstream from transcription. The impact of a substantial proportion of genetic variation is consistent across embryonic stages, with 50% of allelic imbalanced features at one stage being also imbalanced at subsequent developmental stages. Crucially, buffering, as well as the magnitude and evolutionary impact of genetic variants, is influenced by regulatory complexity (i.e., number of enhancers regulating a gene), with transcription factors being most robust to cis-acting, but most influenced by trans-acting, variation.
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Affiliation(s)
- Swann Floc'hlay
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Emily S Wong
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales 2052, Australia
| | - Bingqing Zhao
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Rebecca R Viales
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Morgane Thomas-Chollier
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Denis Thieffry
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
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14
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Population-scale genetic control of alternative polyadenylation and its association with human diseases. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-021-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture. Nat Commun 2020; 11:5963. [PMID: 33235186 PMCID: PMC7687912 DOI: 10.1038/s41467-020-19829-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022] Open
Abstract
Enhancer RNAs (eRNA) are unstable non-coding RNAs, transcribed bidirectionally from active regulatory sequences, whose expression levels correlate with enhancer activity. We use capped-nascent-RNA sequencing to efficiently capture bidirectional transcription initiation across several human lymphoblastoid cell lines (Yoruba population) and detect ~75,000 eRNA transcription sites with high sensitivity and specificity. The use of nascent-RNA sequencing sidesteps the confounding effect of eRNA instability. We identify quantitative trait loci (QTLs) associated with the level and directionality of eRNA expression. High-resolution analyses of these two types of QTLs reveal distinct positions of enrichment at the central transcription factor (TF) binding regions and at the flanking eRNA initiation regions, both of which are associated with mRNA expression QTLs. These two regions-the central TF-binding footprint and the eRNA initiation cores-define a bipartite architecture of enhancers, inform enhancer function, and can be used as an indicator of the significance of non-coding regulatory variants.
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16
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Abstract
Key discoveries in Drosophila have shaped our understanding of cellular "enhancers." With a special focus on the fly, this chapter surveys properties of these adaptable cis-regulatory elements, whose actions are critical for the complex spatial/temporal transcriptional regulation of gene expression in metazoa. The powerful combination of genetics, molecular biology, and genomics available in Drosophila has provided an arena in which the developmental role of enhancers can be explored. Enhancers are characterized by diverse low- or high-throughput assays, which are challenging to interpret, as not all of these methods of identifying enhancers produce concordant results. As a model metazoan, the fly offers important advantages to comprehensive analysis of the central functions that enhancers play in gene expression, and their critical role in mediating the production of phenotypes from genotype and environmental inputs. A major challenge moving forward will be obtaining a quantitative understanding of how these cis-regulatory elements operate in development and disease.
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Affiliation(s)
- Stephen Small
- Department of Biology, Developmental Systems Training Program, New York University, 10003 and
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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17
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Sigalova OM, Shaeiri A, Forneris M, Furlong EEM, Zaugg JB. Predictive features of gene expression variation reveal mechanistic link with differential expression. Mol Syst Biol 2020; 16:e9539. [PMID: 32767663 PMCID: PMC7411568 DOI: 10.15252/msb.20209539] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022] Open
Abstract
For most biological processes, organisms must respond to extrinsic cues, while maintaining essential gene expression programmes. Although studied extensively in single cells, it is still unclear how variation is controlled in multicellular organisms. Here, we used a machine-learning approach to identify genomic features that are predictive of genes with high versus low variation in their expression across individuals, using bulk data to remove stochastic cell-to-cell variation. Using embryonic gene expression across 75 Drosophila isogenic lines, we identify features predictive of expression variation (controlling for expression level), many of which are promoter-related. Genes with low variation fall into two classes reflecting different mechanisms to maintain robust expression, while genes with high variation seem to lack both types of stabilizing mechanisms. Applying this framework to humans revealed similar predictive features, indicating that promoter architecture is an ancient mechanism to control expression variation. Remarkably, expression variation features could also partially predict differential expression after diverse perturbations in both Drosophila and humans. Differential gene expression signatures may therefore be partially explained by genetically encoded gene-specific features, unrelated to the studied treatment.
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Affiliation(s)
- Olga M Sigalova
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Amirreza Shaeiri
- Structures and Computational Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Mattia Forneris
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Eileen EM Furlong
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Judith B Zaugg
- Structures and Computational Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
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18
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Developmental plasticity shapes social traits and selection in a facultatively eusocial bee. Proc Natl Acad Sci U S A 2020; 117:13615-13625. [PMID: 32471944 PMCID: PMC7306772 DOI: 10.1073/pnas.2000344117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Developmental processes are an important source of phenotypic variation, but the extent to which this variation contributes to evolutionary change is unknown. We used integrative genomic analyses to explore the relationship between developmental and social plasticity in a bee species that can adopt either a social or solitary lifestyle. We find genes regulating this social flexibility also regulate development, and positive selection on these genes is influenced by their function during development. This suggests that developmental plasticity may influence the evolution of sociality. Our additional finding of genetic variants linked to differences in social behavior sheds light on how phenotypic variation derived from development may become encoded into the genome, and thus contribute to evolutionary change. Developmental plasticity generates phenotypic variation, but how it contributes to evolutionary change is unclear. Phenotypes of individuals in caste-based (eusocial) societies are particularly sensitive to developmental processes, and the evolutionary origins of eusociality may be rooted in developmental plasticity of ancestral forms. We used an integrative genomics approach to evaluate the relationships among developmental plasticity, molecular evolution, and social behavior in a bee species (Megalopta genalis) that expresses flexible sociality, and thus provides a window into the factors that may have been important at the evolutionary origins of eusociality. We find that differences in social behavior are derived from genes that also regulate sex differentiation and metamorphosis. Positive selection on social traits is influenced by the function of these genes in development. We further identify evidence that social polyphenisms may become encoded in the genome via genetic changes in regulatory regions, specifically in transcription factor binding sites. Taken together, our results provide evidence that developmental plasticity provides the substrate for evolutionary novelty and shapes the selective landscape for molecular evolution in a major evolutionary innovation: Eusociality.
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19
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Guo Y, Xiong Z, Su M, Huang L, Liao J, Xiao H, Huang X, Xiong Z. Positive association of SCD1 genetic variation and metabolic syndrome in dialysis patients in China. Per Med 2020; 17:111-119. [PMID: 32125933 DOI: 10.2217/pme-2019-0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Metabolic syndrome (MetS) diagnosed in the dialysis patients is increasingly reported which worsens the prognosis of the renal diseases. The relationship of SCD1 with MetS is largely unknown. The purpose of this study was to investigate the relationship between SCD1 polymorphism and MetS in dialysis patients. Methods: A cross-sectional study was conducted on 323 Chinese dialysis patients, and the correlation between the seven SNPs of SCD1 gene (rs10883465, rs2060792, rs1502593, rs522951, rs3071, rs3978768 and rs1393492) and MetS was analyzed. Results: One tag-SNP (rs1393492) has significantly associated with the prevalence of MetS. Dialysis patients with rs1393492 AA genotype of SCD1 are more prone to MetS (p = 0.021). Conclusion: This study shows that the rs1393492 variations of SCD1 gene are related with the development of MetS in Chinese dialysis patients.
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Affiliation(s)
- Yanyan Guo
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen, PR China
| | - Zibo Xiong
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen, PR China
| | - Meiling Su
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen, PR China
| | - Limin Huang
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen, PR China
| | - Jinlan Liao
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen, PR China
| | - Hongbo Xiao
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen, PR China
| | - Xiaoyan Huang
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen, PR China
| | - Zuying Xiong
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen, PR China
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20
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Frochaux MV, Bou Sleiman M, Gardeux V, Dainese R, Hollis B, Litovchenko M, Braman VS, Andreani T, Osman D, Deplancke B. cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel. Genome Biol 2020; 21:6. [PMID: 31948474 PMCID: PMC6966807 DOI: 10.1186/s13059-019-1912-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants affect different molecular mechanisms to determine gut immunocompetence is still limited. RESULTS To address this, we perform a systems genetics analysis of the gut transcriptomes from 38 DGRP lines that were orally infected with Pseudomonas entomophila. We identify a large number of condition-specific, expression quantitative trait loci (local-eQTLs) with infection-specific ones located in regions enriched for FOX transcription factor motifs. By assessing the allelic imbalance in the transcriptomes of 19 F1 hybrid lines from a large round robin design, we independently attribute a robust cis-regulatory effect to only 10% of these detected local-eQTLs. However, additional analyses indicate that many local-eQTLs may act in trans instead. Comparison of the transcriptomes of DGRP lines that were either susceptible or resistant to Pseudomonas entomophila infection reveals nutcracker as the only differentially expressed gene. Interestingly, we find that nutcracker is linked to infection-specific eQTLs that correlate with its expression level and to enteric infection susceptibility. Further regulatory analysis reveals one particular eQTL that significantly decreases the binding affinity for the repressor Broad, driving differential allele-specific nutcracker expression. CONCLUSIONS Our collective findings point to a large number of infection-specific cis- and trans-acting eQTLs in the DGRP, including one common non-coding variant that lowers enteric infection susceptibility.
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Affiliation(s)
- Michael V. Frochaux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Current Address: Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Brian Hollis
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Current Address: Department of Biological Sciences, University of South Carolina, Columbia, South Carolina USA
| | - Maria Litovchenko
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Virginie S. Braman
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Tommaso Andreani
- Computational Biology and Data Mining Group, Institute of Molecular Biology, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Dani Osman
- Faculty of Sciences III and Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300 Lebanon
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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21
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Vandiedonck C. Genetic association of molecular traits: A help to identify causative variants in complex diseases. Clin Genet 2019; 93:520-532. [PMID: 29194587 DOI: 10.1111/cge.13187] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022]
Abstract
In the past 15 years, major progresses have been made in the understanding of the genetic basis of regulation of gene expression. These new insights have revolutionized our approach to resolve the genetic variation underlying complex diseases. Gene transcript levels were the first expression phenotypes that were studied. They are heritable and therefore amenable to genome-wide association studies. The genetic variants that modulate them are called expression quantitative trait loci. Their study has been extended to other molecular quantitative trait loci (molQTLs) that regulate gene expression at the various levels, from chromatin state to cellular responses. Altogether, these studies have generated a wealth of basic information on the genome-wide patterns of gene expression and their inter-individual variation. Most importantly, molQTLs have become an invaluable asset in the genetic study of complex diseases. Although the identification of the disease-causing variants on the basis of their overlap with molQTLs requires caution, molQTLs can help to prioritize the relevant candidate gene(s) in the disease-associated regions and bring a functional interpretation of the associated variants, therefore, bridging the gap between genotypes and clinical phenotypes.
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Affiliation(s)
- C Vandiedonck
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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22
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Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system. Nat Immunol 2019; 20:1372-1380. [PMID: 31451789 PMCID: PMC6754753 DOI: 10.1038/s41590-019-0471-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/16/2019] [Indexed: 12/12/2022]
Abstract
In multicellular organisms, duplicated genes can diverge through tissue-specific gene expression patterns, as exemplified by highly regulated expression of Runx transcription factor paralogs with apparent functional redundancy. Here we asked what cell type-specific biologies might be supported by the selective expression of Runx paralogs during Langerhans cell and inducible regulatory T cell differentiation. We uncovered functional non-equivalence between Runx paralogs. Selective expression of native paralogs allowed integration of transcription factor activity with extrinsic signals, while non-native paralogs enforced differentiation even in the absence of exogenous inducers. DNA-binding affinity was controlled by divergent amino acids within the otherwise highly conserved RUNT domain, and evolutionary reconstruction suggested convergence of RUNT domain residues towards sub-maximal strength. Hence, the selective expression of gene duplicates in specialized cell types can synergize with the acquisition of functional differences to enable appropriate gene expression, lineage choice and differentiation in the mammalian immune system.
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23
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Alpern D, Gardeux V, Russeil J, Mangeat B, Meireles-Filho ACA, Breysse R, Hacker D, Deplancke B. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 2019; 20:71. [PMID: 30999927 PMCID: PMC6474054 DOI: 10.1186/s13059-019-1671-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 03/07/2019] [Indexed: 01/10/2023] Open
Abstract
Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3' cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.
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Affiliation(s)
- Daniel Alpern
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Vincent Gardeux
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Julie Russeil
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Bastien Mangeat
- Gene Expression Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Antonio C A Meireles-Filho
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Romane Breysse
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - David Hacker
- Protein Expression Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland.
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24
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Liu S, Li L, Meng J, Song K, Huang B, Wang W, Zhang G. Association and Functional Analyses Revealed That PPP1R3B Plays an Important Role in the Regulation of Glycogen Content in the Pacific Oyster Crassostrea gigas. Front Genet 2019; 10:106. [PMID: 30853975 PMCID: PMC6396720 DOI: 10.3389/fgene.2019.00106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022] Open
Abstract
The Pacific oyster (Crassostrea gigas) is one of the most important aquaculture species worldwide. Glycogen contributes greatly to the special taste and creamy white color of oysters. Previous genome-wide association studies (GWAS) identified several single nucleotide polymorphism (SNP) sites that were strongly related to glycogen content. Genes within 100 kb upstream and downstream of the associated SNPs were screened. One gene annotated as protein phosphatase 1 regulatory subunit 3B (PPP1R3B), which can promote glycogen synthesis together with protein phosphatase 1 catalytic subunit (PPP1C) in mammals, was selected as a candidate gene in this study. First, full-length CgPPP1R3B was cloned and its function was characterized. The gene expression profiles of CgPPP1R3B in different tissues and seasons showed a close relationship to glycogen content. RNA interference (RNAi) experiments of this gene in vivo showed that decreased CgPPP1R3B levels resulted in lower glycogen contents in the experimental group than in the control group. Co-immunoprecipitation (Co-IP) and yeast two-hybrid (Y2H) assays indicated that CgPPP1R3B can interact with CgPPP1C, glycogen synthase (CgGS) and glycogen phosphorylase (CgGP), thus participating in glycogen metabolism. Co-sedimentation analysis in vitro demonstrated that the CgPPP1R3B protein can bind to glycogen molecules directly, and these results indicated the conserved function of the CgPPP1R3B protein compared to that of mammals. In addition, thirteen SNPs were precisely mapped in this gene. Ten of the thirteen SNPs were confirmed to be significantly (p < 0.05) related to glycogen content in an independent wild population (n = 288). The CgPPP1R3B levels in oysters with high glycogen content were significantly higher than those of oysters with low glycogen content, and gene expression levels were significantly associated with various genotypes of four associated SNPs (p < 0.05). The data indicated that the associated SNPs may control glycogen content by regulating CgPPP1R3B expression. These results suggest that CgPPP1R3B is an important gene for glycogen metabolic regulation and that the associated SNPs of this gene are potential markers for oyster molecular breeding for increased glycogen content.
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Affiliation(s)
- Sheng Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Kai Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Baoyu Huang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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25
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Enhancer Trapping and Annotation in Zebrafish Mediated with Sleeping Beauty, piggyBac and Tol2 Transposons. Genes (Basel) 2018; 9:genes9120630. [PMID: 30551672 PMCID: PMC6316676 DOI: 10.3390/genes9120630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 12/18/2022] Open
Abstract
Although transposon-mediated enhancer trapping (ET) is successfully applied in diverse models, the efficiency of various transposon systems varies significantly, and little information is available regarding efficiency of enhancer trapping by various transposons in zebrafish. Most potential enhancers (Ens) still lack evidence of actual En activity. Here, we compared the differences in ET efficiency between sleeping beauty (SB), piggyBac (PB) and Tol2 transposons. Tol2 represented the highest germline transfer efficiencies at 55.56% (NF0 = 165), followed by SB (38.36%, NF0 = 151) and PB (32.65%, NF0 = 149). ET lines generated by the Tol2 transposon tended to produce offspring with a single expression pattern per line, while PB and SB tended to generate embryos with multiple expression patterns. In our tests, 10 putative Ens (En1–10) were identified by splinkerette PCR and comparative genomic analysis. Combining the GFP expression profiles and mRNA expression patterns revealed that En1 and En2 may be involved in regulation of the expression of dlx1a and dlx2a, while En6 may be involved in regulation of the expression of line TK4 transgene and rps26, and En7 may be involved in the regulation of the expression of wnt1 and wnt10b. Most identified Ens were found to be transcribed in zebrafish embryos, and their regulatory function may involve eRNAs.
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26
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Schor IE, Bussotti G, Maleš M, Forneris M, Viales RR, Enright AJ, Furlong EEM. Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis. Curr Biol 2018; 28:3547-3561.e9. [PMID: 30393032 PMCID: PMC6264527 DOI: 10.1016/j.cub.2018.09.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/10/2018] [Accepted: 09/12/2018] [Indexed: 01/02/2023]
Abstract
Long non-coding RNAs (lncRNAs) can often function in the regulation of gene expression during development; however, their generality as essential regulators in developmental processes and organismal phenotypes remains unclear. Here, we performed a tailored investigation of lncRNA expression and function during Drosophila embryogenesis, interrogating multiple stages, tissue specificity, nuclear localization, and genetic backgrounds. Our results almost double the number of annotated lncRNAs expressed at these embryonic stages. lncRNA levels are generally positively correlated with those of their neighboring genes, with little evidence of transcriptional interference. Using fluorescent in situ hybridization, we report the spatiotemporal expression of 15 new lncRNAs, revealing very dynamic tissue-specific patterns. Despite this, deletion of selected lncRNA genes had no obvious developmental defects or effects on viability under standard and stressed conditions. However, two lncRNA deletions resulted in modest expression changes of a small number of genes, suggesting that they fine-tune expression of non-essential genes. Several lncRNAs have strain-specific expression, indicating that they are not fixed within the population. This intra-species variation across genetic backgrounds may thereby be a useful tool to distinguish rapidly evolving lncRNAs with as yet non-essential roles.
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Affiliation(s)
- Ignacio E Schor
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Departamento de Fisiología, Biología Molecular y Celular, FCEyN, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Giovanni Bussotti
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Matilda Maleš
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Mattia Forneris
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Rebecca R Viales
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Anton J Enright
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
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27
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Wang R, Zheng D, Yehia G, Tian B. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res 2018; 28:1427-1441. [PMID: 30143597 PMCID: PMC6169888 DOI: 10.1101/gr.237826.118] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
Abstract
Cleavage and polyadenylation is essential for 3' end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA isoforms with different 3' UTRs and/or coding sequences. Here, we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on approximately 1.2 billion 3' end sequencing reads from more than 360 human, mouse, and rat samples. We show that ∼80% of mammalian mRNA genes contain at least one conserved PAS, and ∼50% have conserved APA events. PAS conservation generally reduces promiscuous 3' end processing, stabilizing gene expression levels across species. Conservation of APA correlates with gene age, gene expression features, and gene functions. Genes with certain functions, such as cell morphology, cell proliferation, and mRNA metabolism, are particularly enriched with conserved APA events. Whereas tissue-specific genes typically have a low APA rate, brain-specific genes tend to evolve APA. In addition, we show enrichment of mRNA destabilizing motifs in alternative 3' UTR sequences, leading to substantial differences in mRNA stability between 3' UTR isoforms. Using conserved PASs, we reveal sequence motifs surrounding APA sites and a preference of adenosine at the cleavage site. Furthermore, we show that mutations of U-rich motifs around the PAS often accompany APA profile differences between species. Analysis of lncRNA PASs indicates a mechanism of PAS fixation through evolution of A-rich motifs. Taken together, our results present a comprehensive view of PAS evolution in mammals, and a phylogenic perspective on APA functions.
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Affiliation(s)
- Ruijia Wang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
| | - Ghassan Yehia
- Genome Editing Core Facility, Rutgers University, New Brunswick, New Jersey 08901, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
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28
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Du Y, Ning Y, Wen Y, Liu L, Liang X, Li P, Ding M, Zhao Y, Cheng B, Ma M, Zhang L, Cheng S, Yu W, Hu S, Guo X, Zhang F. A genome-wide pathway enrichment analysis identifies brain region related biological pathways associated with intelligence. Psychiatry Res 2018; 268:238-242. [PMID: 30071386 DOI: 10.1016/j.psychres.2018.07.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/31/2018] [Accepted: 07/17/2018] [Indexed: 01/15/2023]
Abstract
Intelligence is an important quantitative trait associated with human cognitive ability. The genetic basis of intelligence remains unclear now. Utilizing the latest chromosomal enhancer maps of brain regions, we explored brain region related biological pathways associated with intelligence. Summary data was derived from a large scale genome-wide association study (GWAS) of human, involving 78,308 unrelated individuals from 13 cohorts. The chromosomal enhancer maps of 8 brain regions were then aligned with the GWAS summary data to obtain the association testing results of enhancer regions for intelligence. Gene set enrichment analysis was then conducted to identify the biological pathways associated with intelligence for 8 brain regions, respectively. A total of 178 KEGG pathways was analyzed in this study. We detected multiple biological pathways showing cross brain regions or brain region specific association signals for human intelligence. For instance, KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS pathway presented association signals for intelligence across 8 brain regions (all P value < 0.01). KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES was detected for 5 brain regions. We also identified several brain region specific pathways, such as AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM for Germinal Matrix (P value = 0.009) and FRUCTOSE_AND_MANNOSE_METABOLISM for Anterior Caudate (P value = 0.005). Our study results provided novel clues for understanding the genetic mechanism of intelligence.
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Affiliation(s)
- Yanan Du
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China.
| | - Yujie Ning
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Yan Wen
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Li Liu
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Xiao Liang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Ping Li
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Miao Ding
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Yan Zhao
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Bolun Cheng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Mei Ma
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Lu Zhang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Shiqiang Cheng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Wenxing Yu
- Department of Osteonecrosis and Joint Reconstruction, Xi'an Red Cross Hospital, Xi'an Jiaotong University, Shaanxi Province, PR China
| | - Shouye Hu
- Department of Osteonecrosis and Joint Reconstruction, Xi'an Red Cross Hospital, Xi'an Jiaotong University, Shaanxi Province, PR China
| | - Xiong Guo
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China
| | - Feng Zhang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, No., 76 Yan Ta West Road, Xi'an 710061, PR China.
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29
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Song B, Mott R, Gan X. Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test. PLoS Genet 2018; 14:e1007699. [PMID: 30325920 PMCID: PMC6203403 DOI: 10.1371/journal.pgen.1007699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/26/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
Short insertions, deletions (INDELs) and larger structural variants have been increasingly employed in genetic association studies, but few improvements over SNP-based association have been reported. In order to understand why this might be the case, we analysed two publicly available datasets and observed that 63% of INDELs called in A. thaliana and 64% in D. melanogaster populations are misrepresented as multiple alleles with different functional annotations, i.e. where the same underlying variant is represented by inconsistent alignments leading to different variant calls. To address this issue, we have developed the software Irisas to reclassify and re-annotate these variants, which we then used for single-locus tests of association. We also integrated them to predict the functional impact of SNPs, INDELs, and structural variants for burden testing. Using both approaches, we re-analysed the genetic architecture of complex traits in A. thaliana and D. melanogaster. Heritability analysis using SNPs alone explained on average 27% and 19% of phenotypic variance for A. thaliana and D. melanogaster respectively. Our method explained an additional 11% and 3%, respectively. We also identified novel trait loci that previous SNP-based association studies failed to map, and which contain established candidate genes. Our study shows the value of the association test with INDELs and integrating multiple types of variants in association studies in plants and animals.
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Affiliation(s)
- Baoxing Song
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Richard Mott
- UCL Genetics Institute, University College London, London United Kingdom
| | - Xiangchao Gan
- Max Planck Institute for Plant Breeding Research, Köln, Germany
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30
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Abstract
Developmental enhancers mediate on/off patterns of gene expression in specific cell types at particular stages during metazoan embryogenesis. They typically integrate multiple signals and regulatory determinants to achieve precise spatiotemporal expression. Such enhancers can map quite far-one megabase or more-from the genes they regulate. How remote enhancers relay regulatory information to their target promoters is one of the central mysteries of genome organization and function. A variety of contrasting mechanisms have been proposed over the years, including enhancer tracking, linking, looping, and mobilization to transcription factories. We argue that extreme versions of these mechanisms cannot account for the transcriptional dynamics and precision seen in living cells, tissues, and embryos. We describe emerging evidence for dynamic three-dimensional hubs that combine different elements of the classical models.
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Affiliation(s)
- Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117, Heidelberg, Germany.
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ 08540, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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31
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Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature 2018. [PMID: 29539636 PMCID: PMC5866720 DOI: 10.1038/nature25981] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding how gene regulatory networks control the progressive restriction of cell fates is a long-standing challenge. Recent advances in measuring single cell gene expression are providing new insights into lineage commitment. However, the regulatory events underlying these changes remain elusive. Here we investigate the dynamics of chromatin regulatory landscapes during embryogenesis at single cell resolution. Using single cell combinatorial indexing assay for transposase accessible chromatin (sci-ATAC-seq)1, we profiled chromatin accessibility in over 20,000 single nuclei from fixed Drosophila embryos spanning three landmark embryonic stages: 2-4 hours (hrs) after egg laying (predominantly stage 5 blastoderm nuclei), when each embryo comprises ~6,000 multipotent cells; 6-8hrs (predominantly stage 10-11), to capture a midpoint in embryonic development when major lineages in the mesoderm and ectoderm are specified; and 10-12hrs (predominantly stage 13), when each of the embryo’s >20,000 cells are undergoing terminal differentiation. Our results reveal spatial heterogeneity in the usage of the regulatory genome prior to gastrulation, a feature that aligns with future cell fate, and nuclei can be temporally ordered along developmental trajectories. During mid-embryogenesis, tissue granularity emerges such that individual cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin. The data reveal overlapping usage of regulatory elements between cells of the endoderm and non-myogenic mesoderm, suggesting a common developmental program reminiscent of the mesendoderm lineage in other species2–4. Altogether, we identify over 30,000 distal regulatory elements exhibiting tissue-specific accessibility. We validated the germ layer specificity of a subset of these predicted enhancers in transgenic embryos, achieving 90% accuracy. Overall, our results demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in the chromatin landscape during development, and to uncover the cis-regulatory programs of metazoan germ layers and cell types.
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Affiliation(s)
- Darren A Cusanovich
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James P Reddington
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Delasa Aghamirzaie
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Raquel Marco-Ferreres
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Hannah A Pliner
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Xiaojie Qiu
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
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32
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Mikhaylichenko O, Bondarenko V, Harnett D, Schor IE, Males M, Viales RR, Furlong EEM. The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription. Genes Dev 2018; 32:42-57. [PMID: 29378788 PMCID: PMC5828394 DOI: 10.1101/gad.308619.117] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/21/2017] [Indexed: 12/03/2022]
Abstract
Here, Mikhaylichenko et al. investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. The authors demonstrate that while the timing of enhancer transcription is correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers and conclude that this is likely an inherent sequence property of the elements themselves. Gene expression is regulated by promoters, which initiate transcription, and enhancers, which control their temporal and spatial activity. However, the discovery that mammalian enhancers also initiate transcription questions the inherent differences between enhancers and promoters. Here, we investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. We show that while the timing of enhancer transcription is generally correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers. To assess how this impacts function, we developed a dual transgenic assay to simultaneously measure enhancer and promoter activities from a single element in the same embryo. Extensive transgenic analysis revealed a relationship between the direction of endogenous transcription and the ability to function as an enhancer or promoter in vivo, although enhancer RNA (eRNA) production and activity are not always strictly coupled. Some enhancers (mainly bidirectional) can act as weak promoters, producing overlapping spatio–temporal expression. Conversely, bidirectional promoters often act as strong enhancers, while unidirectional promoters generally cannot. The balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the elements themselves.
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Affiliation(s)
- Olga Mikhaylichenko
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Vladyslav Bondarenko
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Dermot Harnett
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Ignacio E Schor
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Matilda Males
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Rebecca R Viales
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
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33
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.289. [PMID: 28834395 PMCID: PMC5746472 DOI: 10.1002/wdev.289+10.1002/wdev.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 01/20/2024]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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34
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Wang M, Wang P, Liang F, Ye Z, Li J, Shen C, Pei L, Wang F, Hu J, Tu L, Lindsey K, He D, Zhang X. A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation. THE NEW PHYTOLOGIST 2018; 217:163-178. [PMID: 28892169 DOI: 10.1111/nph.14762] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/25/2017] [Indexed: 05/21/2023]
Abstract
Alternative splicing (AS) is a crucial regulatory mechanism in eukaryotes, which acts by greatly increasing transcriptome diversity. The extent and complexity of AS has been revealed in model plants using high-throughput next-generation sequencing. However, this technique is less effective in accurately identifying transcript isoforms in polyploid species because of the high sequence similarity between coexisting subgenomes. Here we characterize AS in the polyploid species cotton. Using Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq), we developed an integrated pipeline for Iso-Seq transcriptome data analysis (https://github.com/Nextomics/pipeline-for-isoseq). We identified 176 849 full-length transcript isoforms from 44 968 gene models and updated gene annotation. These data led us to identify 15 102 fibre-specific AS events and estimate that c. 51.4% of homoeologous genes produce divergent isoforms in each subgenome. We reveal that AS allows differential regulation of the same gene by miRNAs at the isoform level. We also show that nucleosome occupancy and DNA methylation play a role in defining exons at the chromatin level. This study provides new insights into the complexity and regulation of AS, and will enhance our understanding of AS in polyploid species. Our methodology for Iso-Seq data analysis will be a useful reference for the study of AS in other species.
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Affiliation(s)
- Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Fan Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhengxiu Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Feng Wang
- Nextomics Biosciences, Wuhan, 430000, Hubei, China
| | - Jiang Hu
- Nextomics Biosciences, Wuhan, 430000, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Daohua He
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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35
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.289. [PMID: 28834395 PMCID: PMC5746472 DOI: 10.1002/wdev.289 10.1002/wdev.289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2023]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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Sanfilippo P, Wen J, Lai EC. Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species. Genome Biol 2017; 18:229. [PMID: 29191225 PMCID: PMC5707805 DOI: 10.1186/s13059-017-1358-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Drosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3'-sequencing data in this species precludes comprehensive assessment of alternative polyadenylation (APA), which is subject to broad tissue-specific control. RESULTS Here, we generate deep 3'-sequencing data from 23 developmental stages, tissues, and cell lines of D. melanogaster, yielding a comprehensive atlas of ~ 62,000 polyadenylated ends. These data broadly extend the annotated transcriptome, identify ~ 40,000 novel 3' termini, and reveal that two-thirds of Drosophila genes are subject to APA. Furthermore, we dramatically expand the numbers of genes known to be subject to tissue-specific APA, such as 3' untranslated region (UTR) lengthening in head and 3' UTR shortening in testis, and characterize new tissue and developmental 3' UTR patterns. Our thorough 3' UTR annotations permit reassessment of post-transcriptional regulatory networks, via conserved miRNA and RNA binding protein sites. To evaluate the evolutionary conservation and divergence of APA patterns, we generate developmental and tissue-specific 3'-seq libraries from Drosophila yakuba and Drosophila virilis. We document broadly analogous tissue-specific APA trends in these species, but also observe significant alterations in 3' end usage across orthologs. We exploit the population of functionally evolving poly(A) sites to gain clear evidence that evolutionary divergence in core polyadenylation signal (PAS) and downstream sequence element (DSE) motifs drive broad alterations in 3' UTR isoform expression across the Drosophila phylogeny. CONCLUSIONS These data provide a critical resource for the Drosophila community and offer many insights into the complex control of alternative tissue-specific 3' UTR formation and its consequences for post-transcriptional regulatory networks.
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Affiliation(s)
- Piero Sanfilippo
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York, 10065, USA.,Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA
| | - Jiayu Wen
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York, 10065, USA.,Present address: Biochemistry and Biomedical Sciences, Research School of Biology, ANU College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Eric C Lai
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York, 10065, USA. .,Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA.
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Pelechano V. From transcriptional complexity to cellular phenotypes: Lessons from yeast. Yeast 2017; 34:475-482. [PMID: 28866863 DOI: 10.1002/yea.3277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/12/2022] Open
Abstract
Pervasive transcription has been reported in many eukaryotic organisms, revealing a highly interleaved transcriptome organization that involves thousands of coding and non-coding RNAs. However, to date, the biological impact of transcriptome complexity is still poorly understood. Here I will review how subtle variations of the transcriptome can lead to divergent cellular phenotypes by fine-tuning both its coding potential and regulation. I will discuss strategies that can be used to link molecular variations with divergent biological outcomes. Finally, I will explore the implication of transcriptional complexity for our understanding of gene expression in the context of cell-to-cell phenotypic variability. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, P-Box 1031, 171 21, Solna, Sweden
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39
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Ortmann D, Vallier L. Variability of human pluripotent stem cell lines. Curr Opin Genet Dev 2017; 46:179-185. [DOI: 10.1016/j.gde.2017.07.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/07/2017] [Accepted: 07/14/2017] [Indexed: 12/23/2022]
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40
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Zdraljevic S, Andersen EC. Natural diversity facilitates the discovery of conserved chemotherapeutic response mechanisms. Curr Opin Genet Dev 2017; 47:41-47. [PMID: 28892780 DOI: 10.1016/j.gde.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/15/2017] [Accepted: 08/05/2017] [Indexed: 11/15/2022]
Abstract
Organismal fitness depends on adaptation to complex niches where chemical compounds and pathogens are omnipresent. These stresses can lead to the fixation of alleles in both xenobiotic responses and proliferative signaling pathways that promote survival in these niches. However, both xenobiotic responses and proliferative pathways vary within and among species. For example, genetic differences can accumulate within populations because xenobiotic exposures are not constant and selection is variable. Additionally, neutral genetic variation can accumulate in conserved proliferative pathway genes because these systems are robust to genetic perturbations given their essential roles in normal cell-fate specification. For these reasons, sensitizing mutations or chemical perturbations can disrupt pathways and reveal cryptic variation. With this fundamental view of how organisms respond to cytotoxic compounds and cryptic variation in conserved signaling pathways, it is not surprising that human patients have highly variable responses to chemotherapeutic compounds. These different responses result in the low FDA-approval rates for chemotherapeutics and underscore the need for new approaches to understand these diseases and therapeutic interventions. Model organisms, especially the classic invertebrate systems of Caenorhabditis elegans and Drosophila melanogaster, can be used to combine studies of natural variation across populations with responses to both xenobiotic compounds and chemotherapeutics targeted to conserved proliferative signaling pathways.
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Affiliation(s)
- Stefan Zdraljevic
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA.
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 7. [PMID: 28834395 DOI: 10.1002/wdev.289] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 11/08/2022]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 2017; 546:370-375. [PMID: 28489815 PMCID: PMC5524171 DOI: 10.1038/nature22403] [Citation(s) in RCA: 360] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 04/27/2017] [Indexed: 02/07/2023]
Abstract
Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells.
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Affiliation(s)
- Helena Kilpinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Angela Goncalves
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Andreas Leha
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Vackar Afzal
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, DD1 5EH, United Kingdom
| | - Kaur Alasoo
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sofie Ashford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sendu Bala
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Dalila Bensaddek
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, DD1 5EH, United Kingdom
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Oliver J Culley
- Centre for Stem Cells & Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Petr Danecek
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Adam Faulconbridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Annie Kathuria
- Centre for Stem Cells & Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Davis McCarthy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- St Vincent’s Institute of Medical Research, 41 Victoria Parade Fitzroy Victoria 3065, Australia
| | - Shane A McCarthy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Ruta Meleckyte
- Centre for Stem Cells & Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Yasin Memari
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Nathalie Moens
- Centre for Stem Cells & Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Filipa Soares
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Biomedical Research Centre, Anne McLaren Laboratory, Department of Surgery, University of Cambridge, CB2 0SZ, United Kingdom
| | - Alice Mann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Chukwuma A Agu
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Alex Alderton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Rachel Nelson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sarah Harper
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Minal Patel
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Alistair White
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sharad R Patel
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Reena Halai
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Christopher M Kirton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Anja Kolb-Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Philip Beales
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, United Kingdom
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Davide Danovi
- Centre for Stem Cells & Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Angus I Lamond
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, DD1 5EH, United Kingdom
| | - Willem H Ouwehand
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ludovic Vallier
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Biomedical Research Centre, Anne McLaren Laboratory, Department of Surgery, University of Cambridge, CB2 0SZ, United Kingdom
| | - Fiona M Watt
- Centre for Stem Cells & Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Daniel J Gaffney
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
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Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EEM. Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet 2017; 49:550-558. [PMID: 28191888 DOI: 10.1038/ng.3791] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/20/2017] [Indexed: 12/29/2022]
Abstract
Animal promoters initiate transcription either at precise positions (narrow promoters) or dispersed regions (broad promoters), a distinction referred to as promoter shape. Although highly conserved, the functional properties of promoters with different shapes and the genetic basis of their evolution remain unclear. Here we used natural genetic variation across a panel of 81 Drosophila lines to measure changes in transcriptional start site (TSS) usage, identifying thousands of genetic variants affecting transcript levels (strength) or the distribution of TSSs within a promoter (shape). Our results identify promoter shape as a molecular trait that can evolve independently of promoter strength. Broad promoters typically harbor shape-associated variants, with signatures of adaptive selection. Single-cell measurements demonstrate that variants modulating promoter shape often increase expression noise, whereas heteroallelic interactions with other promoter variants alleviate these effects. These results uncover new functional properties of natural promoters and suggest the minimization of expression noise as an important factor in promoter evolution.
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Affiliation(s)
- Ignacio E Schor
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Jacob F Degner
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Dermot Harnett
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Enrico Cannavò
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Francesco P Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Heejung Shim
- Department of Statistics, Purdue University, West Lafayette, Indiana, USA
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany
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