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Hassan NT, Galbraith JD, Adelson DL. Multiple horizontal transfer events of a DNA transposon into turtles, fishes, and a frog. Mob DNA 2024; 15:7. [PMID: 38605364 PMCID: PMC11008031 DOI: 10.1186/s13100-024-00318-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Horizontal transfer of transposable elements (HTT) has been reported across many species and the impact of such events on genome structure and function has been well described. However, few studies have focused on reptilian genomes, especially HTT events in Testudines (turtles). Here, as a consequence of investigating the repetitive content of Malaclemys terrapin terrapin (Diamondback turtle) we found a high similarity DNA transposon, annotated in RepBase as hAT-6_XT, shared between other turtle species, ray-finned fishes, and a frog. hAT-6_XT was notably absent in reptilian taxa closely related to turtles, such as crocodiles and birds. Successful invasion of DNA transposons into new genomes requires the conservation of specific residues in the encoded transposase, and through structural analysis, these residues were identified indicating some retention of functional transposition activity. We document six recent independent HTT events of a DNA transposon in turtles, which are known to have a low genomic evolutionary rate and ancient repeats.
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Affiliation(s)
- Nozhat T Hassan
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - James D Galbraith
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, Australia.
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2
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Baer L, Barthelson K, Postlethwait JH, Adelson DL, Pederson SM, Lardelli M. Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. PLoS Comput Biol 2024; 20:e1011868. [PMID: 38346074 PMCID: PMC10890730 DOI: 10.1371/journal.pcbi.1011868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 02/23/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when the effects of homozygosity for recessive mutations are studied in non-isogenic backgrounds, genes located proximal to the mutation on the same chromosome often appear over-represented among those genes identified as differentially expressed (DE). One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect functional responses to the mutation but, instead, result from an unequal distribution of expression quantitative trait loci (eQTLs) between sample groups of mutant or wild-type genotypes. This is problematic because eQTL expression differences are difficult to distinguish from genes that are DE due to functional responses to a mutation. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) are also observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between those sample groups subjected to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting-based approaches. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. Our method for DAR analysis requires only RNA-sequencing data, facilitating its application across new and existing datasets.
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Affiliation(s)
- Lachlan Baer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Karissa Barthelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - John H. Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen M. Pederson
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael Lardelli
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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3
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Cai J, Zhang Y, He R, Jiang L, Qu Z, Gu J, Yang J, Legascue MF, Wang ZY, Ariel F, Adelson DL, Zhu Y, Wang D. LncRNA DANA1 promotes drought tolerance and histone deacetylation of drought responsive genes in Arabidopsis. EMBO Rep 2024; 25:796-812. [PMID: 38177920 PMCID: PMC10897447 DOI: 10.1038/s44319-023-00030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Although many long noncoding RNAs have been discovered in plants, little is known about their biological function and mode of action. Here we show that the drought-induced long intergenic noncoding RNA DANA1 interacts with the L1p/L10e family member protein DANA1-INTERACTING PROTEIN 1 (DIP1) in the cell nucleus of Arabidopsis, and both DANA1 and DIP1 promote plant drought resistance. DANA1 and DIP1 increase histone deacetylase HDA9 binding to the CYP707A1 and CYP707A2 loci. DIP1 further interacts with PWWP3, a member of the PEAT complex that associates with HDA9 and has histone deacetylase activity. Mutation of DANA1 enhances CYP707A1 and CYP707A2 acetylation and expression resulting in impaired drought tolerance, in agreement with dip1 and pwwp3 mutant phenotypes. Our results demonstrate that DANA1 is a positive regulator of drought response and that DANA1 works jointly with the novel chromatin-related factor DIP1 on epigenetic reprogramming of the plant transcriptome during the response to drought.
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Affiliation(s)
- Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Yongdi Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Liyun Jiang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangdong, China
| | - Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - María Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, 510316, Guangdong, China
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, 330031, Jiangxi, China.
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Hassan NT, Adelson DL. Fake IDs? Widespread misannotation of DNA transposons as a general transcription factor. Genome Biol 2023; 24:260. [PMID: 37957683 PMCID: PMC10641963 DOI: 10.1186/s13059-023-03102-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Accurate annotation of genes and transposable elements (TEs) is vital for understanding genomes, but current annotation pipelines often misannotate TEs as genes. This study reveals how the general transcription factor II-I repeat domain-containing protein 2 (GTF2IRD2) erroneously annotated DNA transposons in non-mammalian species, as it contains a 3' fused hAT transposase domain. We also demonstrate the generality of this problem by identifying misannotated TEs as genes in other vertebrate genomes. Such misannotations can lead to errors in phylogenetic analyses and wasted time for investigators. The study proposes adding a final TE-check to gene annotation pipelines to mitigate this problem.
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Affiliation(s)
- Nozhat T Hassan
- School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia.
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5
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Qu Z, Wang W, Adelson DL. Chromosomal level genome assembly of medicinal plant Sophora flavescens. Sci Data 2023; 10:572. [PMID: 37644152 PMCID: PMC10465603 DOI: 10.1038/s41597-023-02490-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
Sophora flavescens is a medicinal plant in the genus Sophora of the Fabaceae family. The root of S. flavescens is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). In this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to de novo assemble the S. flavescens genome. We obtained a chromosomal level high-quality S. flavescens draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs), which have recently and rapidly proliferated. This genome size is ~5x larger than its closest sequenced relative Lupinus albus L. . We annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues, and also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome highlights the very different evolutionary trajectories that have occurred in recently diverged Fabaceae, leading to smaller duplicated genomes.
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Affiliation(s)
- Zhipeng Qu
- Zhendong Center, Department of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, 5005, Australia.
| | - Wei Wang
- Beijing Zhendong Research Institute, Shanxi Zhendong Pharmaceutical Co Ltd, Beijing, 10587, China
- Shanxi Provincial Key Laboratory of Functional Food with Homology of Medicine and Food, Department of Pharmacy, Changzhi Medical College, Changzhi, 046012, China
| | - David L Adelson
- Zhendong Center, Department of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, 5005, Australia.
- South Australian Museum, Adelaide, 5000, Australia.
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Zhang P, He R, Yang J, Cai J, Qu Z, Yang R, Gu J, Wang ZY, Adelson DL, Zhu Y, Cao X, Wang D. The long non-coding RNA DANA2 positively regulates drought tolerance by recruiting ERF84 to promote JMJ29-mediated histone demethylation. Mol Plant 2023; 16:1339-1353. [PMID: 37553833 DOI: 10.1016/j.molp.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 06/15/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023]
Abstract
Tens of thousands of long non-coding RNAs have been uncovered in plants, but few of them have been comprehensively studied for their biological function and molecular mechanism of their mode of action. Here, we show that the Arabidopsis long non-coding RNA DANA2 interacts with an AP2/ERF transcription factor ERF84 in the cell nucleus and then affects the transcription of JMJ29 that encodes a Jumonji C domain-containing histone H3K9 demethylase. Both RNA sequencing (RNA-seq) and genetic analyses demonstrate that DANA2 positively regulates drought stress responses through JMJ29. JMJ29 positively regulates the expression of ERF15 and GOLS2 by modulation of H3K9me2 demethylation. Accordingly, mutation of JMJ29 causes decreased ERF15 and GOLS2 expression, resulting in impaired drought tolerance, in agreement with drought-sensitive phenotypes of dana2 and erf84 mutants. Taken together, these results demonstrate that DANA2 is a positive regulator of drought response and works jointly with the transcriptional activator ERF84 to modulate JMJ29 expression in plant response to drought.
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Affiliation(s)
- Pengxiang Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Rongxin Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangdong 510316, China
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China.
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Yang J, He R, Qu Z, Gu J, Jiang L, Zhan X, Gao Y, Adelson DL, Li S, Wang ZY, Zhu Y, Wang D. Long noncoding RNA ARTA controls ABA response through MYB7 nuclear trafficking in Arabidopsis. Dev Cell 2023:S1534-5807(23)00236-8. [PMID: 37290444 DOI: 10.1016/j.devcel.2023.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/27/2023] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
In eukaryotes, transcription factors are a crucial element in the regulation of gene expression, and nuclear translocation is the key to the function of transcription factors. Here, we show that the long intergenic noncoding RNA ARTA interacts with an importin β-like protein, SAD2, through a long noncoding RNA-binding region embedded in the carboxyl terminal, and then it blocks the import of the transcription factor MYB7 into the nucleus. Abscisic acid (ABA)-induced ARTA expression can positively regulate ABI5 expression by fine-tuning MYB7 nuclear trafficking. Therefore, the mutation of arta represses ABI5 expression, resulting in desensitization to ABA, thereby reducing Arabidopsis drought tolerance. Our results demonstrate that lncRNA can hijack a nuclear trafficking receptor to modulate the nuclear import of a transcription factor during plant responses to environmental stimuli.
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Affiliation(s)
- Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, the University of Adelaide, South Australia 5005, Australia
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences 510316, Guangdong, China
| | - Liyun Jiang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Ying Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, the University of Adelaide, South Australia 5005, Australia
| | - Sisi Li
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences 510316, Guangdong, China
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China.
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Galbraith JD, Ivancevic AM, Qu Z, Adelson DL. Detecting Horizontal Transfer of Transposons. Methods Mol Biol 2023; 2607:45-62. [PMID: 36449157 DOI: 10.1007/978-1-0716-2883-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Transposable elements (TEs) are prevalent genomic components which can replicate as a function of mobilization in eukaryotes. Not only do they alter genome structure, they also play regulatory functions or organize chromatin structure. In addition to vertical parent-to-offspring inheritance, TEs can also horizontally "jump" between species, known as horizontal transposon transfer (HTT). This can rapidly alter the course of genome evolution. In this chapter, we provide a practical framework to detect HTT events. Our HTT detection framework is based on the use of sequence alignment to determine the divergence/conservation profiles of TE families to determine the history of expansion events. In summary, it includes (a) workflow of HTT detection from Ab initio identified TEs; (b) workflow for detecting HTT for specific, curated TEs; and (c) workflow for validating detected HTT candidates. Our framework covers two common scenarios of HTT detection in the modern omics era, and we believe it will serve as a valuable toolbox for the TE and genomics research community.
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Affiliation(s)
- James D Galbraith
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall, UK
| | - Atma M Ivancevic
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Zhipeng Qu
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - David L Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
- South Australian Museum, Adelaide, SA, Australia.
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Jarred EG, Qu Z, Tsai T, Oberin R, Petautschnig S, Bildsoe H, Pederson S, Zhang QH, Stringer JM, Carroll J, Gardner DK, Van den Buuse M, Sims NA, Gibson WT, Adelson DL, Western PS. Transient Polycomb activity represses developmental genes in growing oocytes. Clin Epigenetics 2022; 14:183. [PMID: 36544159 PMCID: PMC9769065 DOI: 10.1186/s13148-022-01400-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Non-genetic disease inheritance and offspring phenotype are substantially influenced by germline epigenetic programming, including genomic imprinting. Loss of Polycomb Repressive Complex 2 (PRC2) function in oocytes causes non-genetically inherited effects on offspring, including embryonic growth restriction followed by post-natal offspring overgrowth. While PRC2-dependent non-canonical imprinting is likely to contribute, less is known about germline epigenetic programming of non-imprinted genes during oocyte growth. In addition, de novo germline mutations in genes encoding PRC2 lead to overgrowth syndromes in human patients, but the extent to which PRC2 activity is conserved in human oocytes is poorly understood. RESULTS In this study, we identify a discrete period of early oocyte growth during which PRC2 is expressed in mouse growing oocytes. Deletion of Eed during this window led to the de-repression of 343 genes. A high proportion of these were developmental regulators, and the vast majority were not imprinted genes. Many of the de-repressed genes were also marked by the PRC2-dependent epigenetic modification histone 3 lysine 27 trimethylation (H3K27me3) in primary-secondary mouse oocytes, at a time concurrent with PRC2 expression. In addition, we found H3K27me3 was also enriched on many of these genes by the germinal vesicle (GV) stage in human oocytes, strongly indicating that this PRC2 function is conserved in the human germline. However, while the 343 genes were de-repressed in mouse oocytes lacking EED, they were not de-repressed in pre-implantation embryos and lost H3K27me3 during pre-implantation development. This implies that H3K27me3 is a transient feature that represses a wide range of genes in oocytes. CONCLUSIONS Together, these data indicate that EED has spatially and temporally distinct functions in the female germline to repress a wide range of developmentally important genes and that this activity is conserved in the mouse and human germlines.
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Affiliation(s)
- Ellen G. Jarred
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Zhipeng Qu
- grid.1010.00000 0004 1936 7304Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA Australia
| | - Tesha Tsai
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Ruby Oberin
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Sigrid Petautschnig
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Heidi Bildsoe
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
| | - Stephen Pederson
- grid.1010.00000 0004 1936 7304Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA Australia
| | - Qing-hua Zhang
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Monash University, Clayton, VIC Australia
| | - Jessica M. Stringer
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Monash University, Clayton, VIC Australia
| | - John Carroll
- grid.1002.30000 0004 1936 7857Biomedicine Discovery Institute, Monash University, Clayton, VIC Australia
| | - David K. Gardner
- grid.1008.90000 0001 2179 088XSchool of BioSciences, University of Melbourne, Parkville, VIC Australia
| | - Maarten Van den Buuse
- grid.1018.80000 0001 2342 0938School of Psychology and Public Health, La Trobe University, Melbourne, VIC Australia
| | - Natalie A. Sims
- grid.1073.50000 0004 0626 201XBone Cell Biology and Disease Unit, St. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia ,grid.413105.20000 0000 8606 2560Department of Medicine at St, Vincent’s Hospital, Fitzroy, VIC Australia
| | - William T. Gibson
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia and British Columbia Children’s Hospital Research Institute, Vancouver, BC Canada
| | - David L. Adelson
- grid.1010.00000 0004 1936 7304Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA Australia ,grid.437963.c0000 0001 1349 5098South Australian Museum, SA Adelaide, Australia
| | - Patrick S. Western
- grid.452824.dCentre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Molecular and Translational Science, Monash University, Clayton, VIC Australia
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Harata-Lee Y, Qu Z, Bateman E, Xiao X, Keller MD, Bowen J, Wang W, Adelson DL. Compound Kushen injection reduces severity of radiation-induced gastrointestinal mucositis in rats. Front Oncol 2022; 12:929735. [PMID: 36033515 PMCID: PMC9403047 DOI: 10.3389/fonc.2022.929735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022] Open
Abstract
Mucositis, or damage/injury to mucous membranes of the alimentary, respiratory, or genitourinary tract, is the major side effect associated with anticancer radiotherapies. Because there is no effective treatment for mucositis at present, this is a particular issue as it limits the dose of therapy in cancer patients and significantly affects their quality of life. Gastrointestinal mucositis (GIM) occurs in patients receiving radiotherapies to treat cancers of the stomach, abdomen, and pelvis. It involves inflammation and ulceration of the gastrointestinal (GI) tract causing diarrhea, nausea and vomiting, abdominal pain, and bloating. However, there is currently no effective treatment for this debilitating condition. In this study, we investigated the potential of a type of traditional Chinese medicine (TCM), compound Kushen injection (CKI), as a treatment for GIM. It has previously been shown that major groups of chemical compounds found in CKI have anti-inflammatory effects and are capable of inhibiting the expression of pro-inflammatory cytokines. Intraperitoneal administration of CKI to Sprague Dawley (SD) rats that concurrently received abdominal irradiation over five fractions resulted in reduced severity of GIM symptoms compared to rats administered a vehicle control. Histological examination of the intestinal tissues revealed significantly less damaged villus epithelium in CKI-administered rats that had reduced numbers of apoptotic cells in the crypts. Furthermore, it was also found that CKI treatment led to decreased levels of inflammatory factors including lower levels of interleukin (IL)-1β and IL-6 as well as myeloperoxidase (MPO)-producing cells in the intestinal mucosa. Together, our data indicate a novel effect of CKI to reduce the symptoms of radiation-induced GIM by inhibiting inflammation in the mucosa and apoptosis of epithelial cells.
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Affiliation(s)
- Yuka Harata-Lee
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Zhipeng Qu
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Emma Bateman
- School of Biomedicine, University of Adelaide, Adelaide, SA, Australia
| | - Xi Xiao
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Marianne D. Keller
- Preclinical, Imaging and Research Laboratories (PIRL), South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Joanne Bowen
- School of Biomedicine, University of Adelaide, Adelaide, SA, Australia
| | - Wei Wang
- Zhendong Research Institute, Zhendong Pharmaceutical, Beijing, China
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: David L. Adelson,
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11
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Wainwright CL, Teixeira MM, Adelson DL, Buenz EJ, David B, Glaser KB, Harata-Lee Y, Howes MJR, Izzo AA, Maffia P, Mayer AM, Mazars C, Newman DJ, Lughadha EN, Pimenta AM, Parra JA, Qu Z, Shen H, Spedding M, Wolfender JL. Corrigendum to “Future directions for the discovery of natural product-derived immunomodulating drugs: An IUPHAR positional review” [Pharmacol. Res. 177 (2022) 106076]. Pharmacol Res 2022; 180:106207. [DOI: 10.1016/j.phrs.2022.106207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Galbraith JD, Ludington AJ, Sanders KL, Amos TG, Thomson VA, Enosi Tuipulotu D, Dunstan N, Edwards RJ, Suh A, Adelson DL. Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes. Genes (Basel) 2022; 13:genes13020217. [PMID: 35205262 PMCID: PMC8872380 DOI: 10.3390/genes13020217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/23/2022] [Accepted: 01/23/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~30 Mya and have since rapidly diversified into six amphibious, ~60 marine and ~100 terrestrial species that fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.
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Affiliation(s)
- James D. Galbraith
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Alastair J. Ludington
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Kate L. Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Timothy G. Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Vicki A. Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Division of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | | | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology-Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
- South Australian Museum, Adelaide, SA 5000, Australia
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
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13
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Wainwright CL, Teixeira MM, Adelson DL, Buenz EJ, David B, Glaser KB, Harata-Lee Y, Howes MJR, Izzo AA, Maffia P, Mayer AM, Mazars C, Newman DJ, Nic Lughadha E, Pimenta AM, Parra JA, Qu Z, Shen H, Spedding M, Wolfender JL. Future Directions for the Discovery of Natural Product-Derived Immunomodulating Drugs. Pharmacol Res 2022; 177:106076. [PMID: 35074524 DOI: 10.1016/j.phrs.2022.106076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 02/06/2023]
Abstract
Drug discovery from natural sources is going through a renaissance, having spent many decades in the shadow of synthetic molecule drug discovery, despite the fact that natural product-derived compounds occupy a much greater chemical space than those created through synthetic chemistry methods. With this new era comes new possibilities, not least the novel targets that have emerged in recent times and the development of state-of-the-art technologies that can be applied to drug discovery from natural sources. Although progress has been made with some immunomodulating drugs, there remains a pressing need for new agents that can be used to treat the wide variety of conditions that arise from disruption, or over-activation, of the immune system; natural products may therefore be key in filling this gap. Recognising that, at present, there is no authoritative article that details the current state-of-the-art of the immunomodulatory activity of natural products, this in-depth review has arisen from a joint effort between the International Union of Basic and Clinical Pharmacology (IUPHAR) Natural Products and Immunopharmacology, with contributions from a Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation number of world-leading researchers in the field of natural product drug discovery, to provide a "position statement" on what natural products has to offer in the search for new immunomodulatory argents. To this end, we provide a historical look at previous discoveries of naturally occurring immunomodulators, present a picture of the current status of the field and provide insight into the future opportunities and challenges for the discovery of new drugs to treat immune-related diseases.
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Affiliation(s)
- Cherry L Wainwright
- Centre for Natural Products in Health, Robert Gordon University, Aberdeen, UK.
| | - Mauro M Teixeira
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Brazil.
| | - David L Adelson
- Molecular & Biomedical Science, University of Adelaide, Australia.
| | - Eric J Buenz
- Nelson Marlborough Institute of Technology, New Zealand.
| | - Bruno David
- Green Mission Pierre Fabre, Pierre Fabre Laboratories, Toulouse, France.
| | - Keith B Glaser
- AbbVie Inc., Integrated Discovery Operations, North Chicago, USA.
| | - Yuka Harata-Lee
- Molecular & Biomedical Science, University of Adelaide, Australia
| | - Melanie-Jayne R Howes
- Royal Botanic Gardens Kew, Richmond, Surrey, UK; Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, UK.
| | - Angelo A Izzo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Italy.
| | - Pasquale Maffia
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Italy; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK.
| | - Alejandro Ms Mayer
- Department of Pharmacology, College of Graduate Studies, Midwestern University, IL, USA.
| | - Claire Mazars
- Green Mission Pierre Fabre, Pierre Fabre Laboratories, Toulouse, France.
| | | | | | - Adriano Mc Pimenta
- Laboratory of Animal Venoms and Toxins, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - John Aa Parra
- Laboratory of Animal Venoms and Toxins, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Zhipeng Qu
- Molecular & Biomedical Science, University of Adelaide, Australia
| | - Hanyuan Shen
- Molecular & Biomedical Science, University of Adelaide, Australia
| | | | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.
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14
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Galbraith JD, Kortschak RD, Suh A, Adelson DL. Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity. Genome Biol Evol 2021; 13:6433158. [PMID: 34894225 PMCID: PMC8665684 DOI: 10.1093/gbe/evab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/20/2022] Open
Abstract
Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.
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Affiliation(s)
- James D Galbraith
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.,Department of Organismal Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Sweden
| | - David L Adelson
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
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15
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Galbraith JD, Ludington AJ, Sanders KL, Suh A, Adelson DL. Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits ( Laticauda). Biol Lett 2021; 17:20210342. [PMID: 34464541 PMCID: PMC8437027 DOI: 10.1098/rsbl.2021.0342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are self-replicating genetic sequences and are often described as important ‘drivers of evolution’. This driving force is because TEs promote genomic novelty by enabling rearrangement, and through exaptation as coding and regulatory elements. However, most TE insertions potentially lead to neutral or harmful outcomes, therefore host genomes have evolved machinery to suppress TE expansion. Through horizontal transposon transfer (HTT) TEs can colonize new genomes, and since new hosts may not be able to regulate subsequent replication, these TEs may proliferate rapidly. Here, we describe HTT of the Harbinger-Snek DNA transposon into sea kraits (Laticauda), and its subsequent explosive expansion within Laticauda genomes. This HTT occurred following the divergence of Laticauda from terrestrial Australian elapids approximately 15–25 Mya. This has resulted in numerous insertions into introns and regulatory regions, with some insertions into exons which appear to have altered UTRs or added sequence to coding exons. Harbinger-Snek has rapidly expanded to make up 8–12% of Laticauda spp. genomes; this is the fastest known expansion of TEs in amniotes following HTT. Genomic changes caused by this rapid expansion may have contributed to adaptation to the amphibious-marine habitat.
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Affiliation(s)
- James D Galbraith
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alastair J Ludington
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kate L Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala SE-752 36, Sweden
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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16
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Tang Y, Qu Z, Lei J, He R, Adelson DL, Zhu Y, Yang Z, Wang D. The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic. PLoS Genet 2021; 17:e1009461. [PMID: 33739974 PMCID: PMC8011760 DOI: 10.1371/journal.pgen.1009461] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/31/2021] [Accepted: 03/03/2021] [Indexed: 11/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as important regulators in plant development, but few of them have been functionally characterized in fruit ripening. Here, we have identified 25,613 lncRNAs from strawberry ripening fruits based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries, most of which exhibited distinct temporal expression patterns. A novel lncRNA, FRILAIR harbours the miR397 binding site that is highly conserved in diverse strawberry species. FRILAIR overexpression promoted fruit maturation in the Falandi strawberry, which was consistent with the finding from knocking down miR397, which can guide the mRNA cleavage of both FRILAIR and LAC11a (encoding a putative laccase-11-like protein). Moreover, LAC11a mRNA levels were increased in both FRILAIR overexpressing and miR397 knockdown fruits, and accelerated fruit maturation was also found in LAC11a overexpressing fruits. Overall, our study demonstrates that FRILAIR can act as a noncanonical target mimic of miR397 to modulate the expression of LAC11a in the strawberry fruit ripening process.
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Affiliation(s)
- Yajun Tang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, China
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Jiajun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, China
| | - David L. Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, China
| | - Zhenbiao Yang
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, China
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17
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Galbraith JD, Ludington AJ, Suh A, Sanders KL, Adelson DL. New Environment, New Invaders-Repeated Horizontal Transfer of LINEs to Sea Snakes. Genome Biol Evol 2020; 12:2370-2383. [PMID: 33022046 PMCID: PMC7846101 DOI: 10.1093/gbe/evaa208] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Although numerous studies have found horizontal transposon transfer (HTT) to be widespread across metazoans, few have focused on HTT in marine ecosystems. To investigate potential recent HTTs into marine species, we searched for novel repetitive elements in sea snakes, a group of elapids which transitioned to a marine habitat at most 18 Ma. Our analysis uncovered repeated HTTs into sea snakes following their marine transition. The seven subfamilies of horizontally transferred LINE retrotransposons we identified in the olive sea snake (Aipysurus laevis) are transcribed, and hence are likely still active and expanding across the genome. A search of 600 metazoan genomes found all seven were absent from other amniotes, including terrestrial elapids, with the most similar LINEs present in fish and marine invertebrates. The one exception was a similar LINE found in sea kraits, a lineage of amphibious elapids which independently transitioned to a marine environment 25 Ma. Our finding of repeated horizontal transfer events into marine snakes greatly expands past findings that the marine environment promotes the transfer of transposons. Transposons are drivers of evolution as sources of genomic sequence and hence genomic novelty. We identified 13 candidate genes for HTT-induced adaptive change based on internal or neighboring HTT LINE insertions. One of these, ADCY4, is of particular interest as a part of the KEGG adaptation pathway “Circadian Entrainment.” This provides evidence of the ecological interactions between species influencing evolution of metazoans not only through specific selection pressures, but also by contributing novel genomic material.
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Affiliation(s)
| | | | - Alexander Suh
- Department of Ecology and Genetics-Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden.,Department of Organismal Biology-Systematic Biology, Evolutionary Biology Centre, Uppsala University, Sweden.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Kate L Sanders
- School of Biological Sciences, University of Adelaide, Australia
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Australia
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18
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Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan MD, Newcomb RD, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigó R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C. The tuatara genome reveals ancient features of amniote evolution. Nature 2020; 584:403-409. [PMID: 32760000 PMCID: PMC7116210 DOI: 10.1038/s41586-020-2561-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/26/2020] [Indexed: 12/21/2022]
Abstract
The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2-is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
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Affiliation(s)
- Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand.
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Marc Tollis
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - David L Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Alexander Suh
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Terry Bertozzi
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - José H Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen, Berlin, Germany
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chris Organ
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - Paul P Gardner
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Thomas R Buckley
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Melissa Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Ryan K Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Melissa D Jordan
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - Richard D Newcomb
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - José Ignacio Arroyo
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Tim A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Jaime Renart
- Instituto de Investigaciones Biomédicas 'Alberto Sols' CSIC-UAM, Madrid, Spain
| | - Valentina Peona
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Claire R Peart
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Vera M Warmuth
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Lu Zeng
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - R Daniel Kortschak
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Joy M Raison
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Zhiqiang Wu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marco Mariotti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shawn M Rupp
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Victoria G Twort
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Helen Taylor
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hideaki Abe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Donna M Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - James M Paterson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Vanessa L Gonzalez
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | | | - Stephan Pabinger
- Austrian Institute of Technology (AIT), Center for Health and Bioresources, Molecular Diagnostics, Vienna, Austria
| | | | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Oliver Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay Anderson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Nicola Nelson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Clive Stone
- Ngatiwai Trust Board, Whangarei, New Zealand
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19
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Cui J, Qu Z, Harata-Lee Y, Shen H, Aung TN, Wang W, Kortschak RD, Adelson DL. The effect of compound kushen injection on cancer cells: Integrated identification of candidate molecular mechanisms. PLoS One 2020; 15:e0236395. [PMID: 32730293 PMCID: PMC7392229 DOI: 10.1371/journal.pone.0236395] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/05/2020] [Indexed: 12/22/2022] Open
Abstract
Traditional Chinese Medicine (TCM) preparations are often extracts of single or multiple herbs containing hundreds of compounds, and hence it has been difficult to study their mechanisms of action. Compound Kushen Injection (CKI) is a complex mixture of compounds extracted from two medicinal plants and has been used in Chinese hospitals to treat cancer for over twenty years. To demonstrate that a systematic analysis of molecular changes resulting from complex mixtures of bioactives from TCM can identify a core set of differentially expressed (DE) genes and a reproducible set of candidate pathways. We used in vitro cancer models to measure the effect of CKI on cell cycle phases and apoptosis, and correlated those phenotypes with CKI induced changes in gene expression. We treated two cancer cell lines with or without CKI and assessed the resulting phenotypes by employing cell viability and proliferation assays. Based on these results, we carried out high-throughput transcriptome data analysis to identify genes and candidate pathways perturbed by CKI. We integrated these differential gene expression results with previously reported results and carried out validation of selected differentially expressed genes. CKI induced cell-cycle arrest and apoptosis in the cancer cell lines tested. In these cells CKI also altered the expression of 363 core candidate genes associated with cell cycle, apoptosis, DNA replication/repair, and various cancer pathways. Of these, 7 are clinically relevant to cancer diagnosis or therapy, 14 are cell cycle regulators, and most of these 21 candidates are downregulated by CKI. Comparison of our core candidate genes to a database of plant medicinal compounds and their effects on gene expression identified one-to-one, one-to-many and many-to-many regulatory relationships between compounds in CKI and DE genes. By identifying genes and promising candidate pathways associated with CKI treatment based on our transcriptome-based analysis, we have shown that this approach is useful for the systematic analysis of molecular changes resulting from complex mixtures of bioactives.
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Affiliation(s)
- Jian Cui
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Yuka Harata-Lee
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Hanyuan Shen
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Thazin Nwe Aung
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Wei Wang
- Zhendong Research Institute, Shanxi-Zhendong Pharmaceutical Co Ltd, Beijing, China
| | - R. Daniel Kortschak
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - David L. Adelson
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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20
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Shen H, Qu Z, Harata-Lee Y, Cui J, Aung TN, Wang W, Kortschak RD, Adelson DL. A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis: Compound Kushen Injection as a Proof of Principle. Sci Rep 2019; 9:15889. [PMID: 31685921 PMCID: PMC6828681 DOI: 10.1038/s41598-019-52375-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/24/2019] [Indexed: 01/08/2023] Open
Abstract
Drug-drug interactions (DDIs), especially with herbal medicines, are complex, making it difficult to identify potential molecular mechanisms and targets. We introduce a workflow to carry out DDI research using transcriptome analysis and interactions of a complex herbal mixture, Compound Kushen Injection (CKI), with cancer chemotherapy drugs, as a proof of principle. Using CKI combined with doxorubicin or 5-Fu on cancer cells as a model, we found that CKI enhanced the cytotoxic effects of doxorubicin on A431 cells while protecting MDA-MB-231 cells treated with 5-Fu. We generated and analysed transcriptome data from cells treated with single treatments or combined treatments and our analysis showed that opposite directions of regulation for pathways related to DNA synthesis and metabolism which appeared to be the main reason for different effects of CKI when used in combination with chemotherapy drugs. We also found that pathways related to organic biosynthetic and metabolic processes might be potential targets for CKI when interacting with doxorubicin and 5-Fu. Through co-expression analysis correlated with phenotype results, we selected the MYD88 gene as a candidate major regulator for validation as a proof of concept for our approach. Inhibition of MYD88 reduced antagonistic cytotoxic effects between CKI and 5-Fu, indicating that MYD88 is an important gene in the DDI mechanism between CKI and chemotherapy drugs. These findings demonstrate that our pipeline is effective for the application of transcriptome analysis to the study of DDIs in order to identify candidate mechanisms and potential targets.
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Affiliation(s)
- Hanyuan Shen
- Zhendong Australia - China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Zhipeng Qu
- Zhendong Australia - China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Yuka Harata-Lee
- Zhendong Australia - China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Jian Cui
- Zhendong Australia - China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Thazin Nwe Aung
- Zhendong Australia - China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Wei Wang
- Zhendong Research Institute, Shanxi-Zhendong Pharmaceutical Co Ltd, Beijing, China
| | - R Daniel Kortschak
- Zhendong Australia - China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - David L Adelson
- Zhendong Australia - China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia.
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21
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Aung TN, Nourmohammadi S, Qu Z, Harata-Lee Y, Cui J, Shen HY, Yool AJ, Pukala T, Du H, Kortschak RD, Wei W, Adelson DL. Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle. Sci Rep 2019; 9:14200. [PMID: 31578346 PMCID: PMC6775143 DOI: 10.1038/s41598-019-50271-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
We used computational and experimental biology approaches to identify candidate mechanisms of action of aTraditional Chinese Medicine, Compound Kushen Injection (CKI), in a breast cancer cell line (MDA-MB-231). Because CKI is a complex mixture of plant secondary metabolites, we used a high-performance liquid chromatography (HPLC) fractionation and reconstitution approach to define chemical fractions required for CKI to induce apoptosis. The initial fractionation separated major from minor compounds, and it showed that major compounds accounted for little of the activity of CKI. Furthermore, removal of no single major compound altered the effect of CKI on cell viability and apoptosis. However, simultaneous removal of two major compounds identified oxymatrine and oxysophocarpine as critical with respect to CKI activity. Transcriptome analysis was used to correlate compound removal with gene expression and phenotype data. Many compounds in CKI are required to trigger apoptosis but significant modulation of its activity is conferred by a small number of compounds. In conclusion, CKI may be typical of many plant based extracts that contain many compounds in that no single compound is responsible for all of the bioactivity of the mixture and that many compounds interact in a complex fashion to influence a network containing many targets.
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Affiliation(s)
- T N Aung
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - S Nourmohammadi
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Z Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Y Harata-Lee
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - J Cui
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - H Y Shen
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - A J Yool
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - T Pukala
- School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Hong Du
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China
| | - R D Kortschak
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - W Wei
- Beijing Zhendong Guangming Pharmaceutical Research Institute, Shanxi - Zhendong Pharmaceutical Co Ltd, Beijing, P.R. China
| | - D L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia.
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22
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Zhang J, Sun L, Cui J, Wang J, Liu X, Aung TN, Qu Z, Chen Z, Adelson DL, Lin L. Yiqi Chutan Tang Reduces Gefitinib-Induced Drug Resistance in Non-Small-Cell Lung Cancer by Targeting Apoptosis and Autophagy. Cytometry A 2019; 97:70-77. [PMID: 31411813 PMCID: PMC7004076 DOI: 10.1002/cyto.a.23869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/21/2019] [Accepted: 07/01/2019] [Indexed: 12/27/2022]
Abstract
High incidence and mortality rates for non-small-cell lung cancer (NSCLC) lead to low survival rates. Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI) are commonly first prescribed for NSCLC patients with EGFR mutations. However, most patients with sensitizing EGFR mutations become resistant to EGFR-TKI after 9-13 months treatment. Yiqi Chutan Tang (YQCT) has been prescribed as a treatment to this issue for over 20 years. In this report, high-performance liquid chromatography (HPLC) analysis, flow cytometry, western blot analysis, and functional annotation analysis were applied to uncover the molecular mechanisms of YQCT. Our results show the application of YQCT reduces gefitinib-induced drug resistance, induces slight cell cycle arrest, enhances gefitinib-induced apoptosis, and activates the autophagy. These results indicate that at the molecular level YQCT can reduce drug resistance and improve anti-cancer effects when associated with gefitinib, which could be a result of enhancement of apoptosis and autophagy in the EGFR-TKI resistant cells of NSCLC. This research provides a new treatment strategy for patients with EGFR-TKI resistance in NSCLC. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Jue Zhang
- First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510000, Guangdong Province, China
| | - Lingling Sun
- First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510000, Guangdong Province, China
| | - Jian Cui
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Jing Wang
- First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510000, Guangdong Province, China
| | - Xiaomin Liu
- Guangzhou University of Chinese Medicine, Guangzhou, 510000, Guangdong Province, China
| | - Thazin Nwe Aung
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Zhuangzhong Chen
- First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510000, Guangdong Province, China
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Lizhu Lin
- First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, 510000, Guangdong Province, China
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23
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Zhang J, Qu Z, Yao H, Sun L, Harata-Lee Y, Cui J, Aung TN, Liu X, You R, Wang W, Hai L, Adelson DL, Lin L. An effective drug sensitizing agent increases gefitinib treatment by down regulating PI3K/Akt/mTOR pathway and up regulating autophagy in non-small cell lung cancer. Biomed Pharmacother 2019; 118:109169. [PMID: 31310954 DOI: 10.1016/j.biopha.2019.109169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023] Open
Abstract
Gefitinib is one of commonly used first-line treatment options for patients with positive EGFR mutation in non-small cell lung cancer (NSCLC). However, most patients with gefitinib treatment relapse over time due to the loss of drug sensitivity. Compound Kushen injection (CKI) has been used to treat lung cancer, including EGFR-mutated NSCLC. In this report, we examined the anti-cancer and drug sensitivity increased activities of CKI in gefitinib less sensitive NSCLC cell lines H1650 and H1975. Bioinformatics analysis was applied to uncover gene regulation and molecular mechanisms of CKI. Our results indicated that when associating with gefitinib in a dose-dependent fashion, CKI demonstrated the ability to inhibit the proliferation and to increase the sensitivity to gefitinib treatment in gefitinib less sensitive cell lines. This could be the results of down regulation of the PI3K/Akt/mTOR pathway and up regulation of autophagy, which were identified as the potential primary targets of CKI to increase gefitinib treatment effect.
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Affiliation(s)
- Jue Zhang
- First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, PR China
| | - Zhipeng Qu
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Hong Yao
- Foshan hospital of TCM, Guangzhou University of Chinese Medicine, Foshan, Guangdong Province, PR China
| | - Lingling Sun
- First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, PR China
| | - Yuka Harata-Lee
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jian Cui
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Thazin Nwe Aung
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xiaomin Liu
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, PR China
| | - Rongli You
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, PR China
| | - Wei Wang
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lina Hai
- Zhendong Pharmaceutical Research Institute Co., Ltd., Beijing, PR China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, PR China
| | - David L Adelson
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Lizhu Lin
- First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, PR China.
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24
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Shen H, Qu Z, Harata-Lee Y, Aung TN, Cui J, Wang W, Kortschak RD, Adelson DL. Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection With Transcriptome Analysis. Front Oncol 2019; 9:632. [PMID: 31380274 PMCID: PMC6660286 DOI: 10.3389/fonc.2019.00632] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/26/2019] [Indexed: 01/12/2023] Open
Abstract
Herbal compatibility is the knowledge of which herbs to combine in traditional Chinese medicine (TCM) formulations. The lack of understanding of herbal compatibility is one of the key problems for the application and popularization of TCM in western society. Because of the chemical complexity of herbal medicines, it is simpler to begin to conduct compatibility research based on herbs rather than component plant secondary metabolites. We have used transcriptome analysis to explore the effects and interactions of two plant extracts (Kushen and Baituling) combined in Compound Kushen Injection (CKI). Based on shared chemical compounds and in vitro cytotoxicity comparisons, we found that both the major compounds in CKI, and the cytotoxicity effects of CKI were mainly derived from the extract of Kushen (Sophorae flavescentis). We generated and analyzed transcriptome data from MDA-MB-231 cells treated with single-herb extracts or CKI and results showed that Kushen contributed to the perturbation of the majority of cytotoxicity/cancer related pathways in CKI such as cell cycle and DNA replication. We also found that Baituling (Heterosmilax yunnanensis Gagnep) could not only enhance the cytotoxic effects of Kushen in CKI, but also activate immune-related pathways. Our analyses predicted that IL-1β gene expression was upregulated by Baituling in CKI and we confirmed that IL-1β protein expression was increased using an ELISA assay. Altogether, these findings help to explain the rationale for combining Kushen and Baituling in CKI, and show that transcriptome analysis using single herb extracts is an effective method for understanding herbal compatibility in TCM.
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Affiliation(s)
- Hanyuan Shen
- Zhendong Australia-China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Zhipeng Qu
- Zhendong Australia-China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Yuka Harata-Lee
- Zhendong Australia-China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Thazin Nwe Aung
- Zhendong Australia-China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Jian Cui
- Zhendong Australia-China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Wei Wang
- Zhendong Research Institute, Shanxi-Zhendong Pharmaceutical Co., Ltd, Beijing, China
| | - R. Daniel Kortschak
- Zhendong Australia-China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - David L. Adelson
- Zhendong Australia-China Centre for Molecular Chinese Medicine, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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25
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Nourmohammadi S, Aung TN, Cui J, Pei JV, De Ieso ML, Harata-Lee Y, Qu Z, Adelson DL, Yool AJ. Effect of Compound Kushen Injection, a Natural Compound Mixture, and Its Identified Chemical Components on Migration and Invasion of Colon, Brain, and Breast Cancer Cell Lines. Front Oncol 2019; 9:314. [PMID: 31106149 PMCID: PMC6498862 DOI: 10.3389/fonc.2019.00314] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/08/2019] [Indexed: 01/03/2023] Open
Abstract
Traditional Chinese Medicines are promising sources of new agents for controlling cancer metastasis. Compound Kushen Injection (CKI), prepared from medicinal plants Sophora flavescens and Heterosmilax chinensis, disrupts cell cycle and induces apoptosis in breast cancer; however, effects on migration and invasion remained unknown. CKI, fractionated mixtures, and isolated components were tested in migration assays with colon (HT-29, SW-480, DLD-1), brain (U87-MG, U251-MG), and breast (MDA-MB-231) cancer cell lines. Human embryonic kidney (HEK-293) and human foreskin fibroblast (HFF) served as non-cancerous controls. Wound closure, transwell invasion, and live cell imaging showed CKI reduced motility in all eight lines. Fractionation and reconstitution of CKI demonstrated combinations of compounds were required for activity. Live cell imaging confirmed CKI strongly reduced migration of HT-29 and MDA-MB-231 cells, moderately slowed brain cancer cells, and had a small effect on HEK-293. CKI uniformly blocked invasiveness through extracellular matrix. Apoptosis was increased by CKI in breast cancer but not in non-cancerous lines. Cell viability was unaffected by CKI in all cell lines. Transcriptomic analyses of MDA-MB-231indicated down-regulation of actin cytoskeletal and focal adhesion genes with CKI treatment, consistent with observed impairment of cell migration. The pharmacological complexity of CKI is important for effective blockade of cancer migration and invasion.
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Affiliation(s)
- Saeed Nourmohammadi
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Thazin Nwe Aung
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jian Cui
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jinxin V. Pei
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | | | - Yuka Harata-Lee
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - David L. Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Andrea J. Yool
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
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26
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Cui J, Qu Z, Harata-Lee Y, Nwe Aung T, Shen H, Wang W, Adelson DL. Cell cycle, energy metabolism and DNA repair pathways in cancer cells are suppressed by Compound Kushen Injection. BMC Cancer 2019; 19:103. [PMID: 30678652 PMCID: PMC6345000 DOI: 10.1186/s12885-018-5230-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/17/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In this report we examine candidate pathways perturbed by Compound Kushen Injection (CKI), a Traditional Chinese Medicine (TCM) that we have previously shown to alter the gene expression patterns of multiple pathways and induce apoptosis in cancer cells. METHODS We have measured protein levels in Hep G2 and MDA-MB-231 cells for genes in the cell cycle pathway, DNA repair pathway and DNA double strand breaks (DSBs) previously shown to have altered expression by CKI. We have also examined energy metabolism by measuring [ADP]/[ATP] ratio (cell energy charge), lactate production and glucose consumption. Our results demonstrate that CKI can suppress protein levels for cell cycle regulatory proteins and DNA repair while increasing the level of DSBs. We also show that energy metabolism is reduced based on reduced glucose consumption and reduced cellular energy charge. RESULTS Our results validate these pathways as important targets for CKI. We also examined the effect of the major alkaloid component of CKI, oxymatrine and determined that it had no effect on DSBs, a small effect on the cell cycle and increased the cell energy charge. CONCLUSIONS Our results indicate that CKI likely acts through the effect of multiple compounds on multiple targets where the observed phenotype is the integration of these effects and synergistic interactions.
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Affiliation(s)
- Jian Cui
- Department of Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
- Zhendong Australia - China Centre for Molecular Chinese Medicine, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
| | - Zhipeng Qu
- Department of Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
- Zhendong Australia - China Centre for Molecular Chinese Medicine, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
| | - Yuka Harata-Lee
- Department of Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
- Zhendong Australia - China Centre for Molecular Chinese Medicine, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
| | - Thazin Nwe Aung
- Department of Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
- Zhendong Australia - China Centre for Molecular Chinese Medicine, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
| | - Hanyuan Shen
- Department of Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
- Zhendong Australia - China Centre for Molecular Chinese Medicine, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
| | - Wei Wang
- Zhendong Australia - China Centre for Molecular Chinese Medicine, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
- Zhendong Research Institute, Shanxi-Zhendong Pharmaceutical Co Ltd, Beijing, China
| | - David L. Adelson
- Department of Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
- Zhendong Australia - China Centre for Molecular Chinese Medicine, The University of Adelaide, North Terrace, Adelaide, 5005 South Australia Australia
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27
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Abstract
BACKGROUND Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events. RESULTS Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonised more than half of the genome sequence in today's mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms. CONCLUSIONS We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.
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Affiliation(s)
- Atma M Ivancevic
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Neurogenetics Research Program, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - R Daniel Kortschak
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Terry Bertozzi
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - David L Adelson
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
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Zeng L, Pederson SM, Kortschak RD, Adelson DL. Transposable elements and gene expression during the evolution of amniotes. Mob DNA 2018; 9:17. [PMID: 29942365 PMCID: PMC5998507 DOI: 10.1186/s13100-018-0124-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/01/2018] [Indexed: 01/24/2023] Open
Abstract
Background Transposable elements (TEs) are primarily responsible for the DNA losses and gains in genome sequences that occur over time within and between species. TEs themselves evolve, with clade specific LTR/ERV, LINEs and SINEs responsible for the bulk of species-specific genomic features. Because TEs can contain regulatory motifs, they can be exapted as regulators of gene expression. While TE insertions can provide evolutionary novelty for the regulation of gene expression, their overall impact on the evolution of gene expression is unclear. Previous investigators have shown that tissue specific gene expression in amniotes is more similar across species than within species, supporting the existence of conserved developmental gene regulation. In order to understand how species-specific TE insertions might affect the evolution/conservation of gene expression, we have looked at the association of gene expression in six tissues with TE insertions in six representative amniote genomes. Results A novel bootstrapping approach has been used to minimise the conflation of effects of repeat types on gene expression. We compared the expression of orthologs containing recent TE insertions to orthologs that contained older TE insertions, and the expression of non-orthologs containing recent TE insertions to non-orthologs with older TE insertions. Both orthologs and non-orthologs showed significant differences in gene expression associated with TE insertions. TEs were found associated with species-specific changes in gene expression, and the magnitude and direction of expression changes were noteworthy. Overall, orthologs containing species-specific TEs were associated with lower gene expression, while in non-orthologs, non-species specific TEs were associated with higher gene expression. Exceptions were SINE elements in human and chicken, which had an opposite association with gene expression compared to other species. Conclusions Our observed species-specific associations of TEs with gene expression support a role for TEs in speciation/response to selection by species. TEs do not exhibit consistent associations with gene expression and observed associations can vary depending on the age of TE insertions. Based on these observations, it would be prudent to refrain from extrapolating these and previously reported associations to distantly related species.
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Affiliation(s)
- Lu Zeng
- 1School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, 5005 Australia
| | - Stephen M Pederson
- 2Bioinformatics Hub, The University of Adelaide, North Terrace, Adelaide, 5005 Australia
| | - R Daniel Kortschak
- 1School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, 5005 Australia
| | - David L Adelson
- 1School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, 5005 Australia
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Zeng L, Pederson SM, Cao D, Qu Z, Hu Z, Adelson DL, Wei C. Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that Alu Elements Have the Largest Overall Regulatory Impact. J Comput Biol 2018; 25:551-562. [DOI: 10.1089/cmb.2017.0228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Lu Zeng
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Stephen M. Pederson
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Danfeng Cao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhipeng Qu
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Zhiqiang Hu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - David L. Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Chaochun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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30
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Buckley RM, Kortschak RD, Adelson DL. Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse. PLoS Comput Biol 2018; 14:e1006091. [PMID: 29677183 PMCID: PMC5931693 DOI: 10.1371/journal.pcbi.1006091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 05/02/2018] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
The forces driving the accumulation and removal of non-coding DNA and ultimately the evolution of genome size in complex organisms are intimately linked to genome structure and organisation. Our analysis provides a novel method for capturing the regional variation of lineage-specific DNA gain and loss events in their respective genomic contexts. To further understand this connection we used comparative genomics to identify genome-wide individual DNA gain and loss events in the human and mouse genomes. Focusing on the distribution of DNA gains and losses, relationships to important structural features and potential impact on biological processes, we found that in autosomes, DNA gains and losses both followed separate lineage-specific accumulation patterns. However, in both species chromosome X was particularly enriched for DNA gain, consistent with its high L1 retrotransposon content required for X inactivation. We found that DNA loss was associated with gene-rich open chromatin regions and DNA gain events with gene-poor closed chromatin regions. Additionally, we found that DNA loss events tended to be smaller than DNA gain events suggesting that they were able to accumulate in gene-rich open chromatin regions due to their reduced capacity to interrupt gene regulatory architecture. GO term enrichment showed that mouse loss hotspots were strongly enriched for terms related to developmental processes. However, these genes were also located in regions with a high density of conserved elements, suggesting that despite high levels of DNA loss, gene regulatory architecture remained conserved. This is consistent with a model in which DNA gain and loss results in turnover or "churning" in regulatory element dense regions of open chromatin, where interruption of regulatory elements is selected against.
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Affiliation(s)
- Reuben M. Buckley
- Department of Genetics and Evolution, The University of Adelaide, North Tce, Adelaide, Australia
| | - R. Daniel Kortschak
- Department of Genetics and Evolution, The University of Adelaide, North Tce, Adelaide, Australia
| | - David L. Adelson
- Department of Genetics and Evolution, The University of Adelaide, North Tce, Adelaide, Australia
- * E-mail:
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31
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Zeng L, Kortschak RD, Raison JM, Bertozzi T, Adelson DL. Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies. PLoS One 2018; 13:e0193588. [PMID: 29538441 PMCID: PMC5851578 DOI: 10.1371/journal.pone.0193588] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/14/2018] [Indexed: 11/21/2022] Open
Abstract
Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.
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Affiliation(s)
- Lu Zeng
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - R. Daniel Kortschak
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Joy M. Raison
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Terry Bertozzi
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA 5005, Australia
| | - David L. Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
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32
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Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To TH, Kortschak RD, Raison JM, Qu Z, Chin TJ, Alt KW, Claesson S, Dalén L, MacPhee RDE, Meller H, Roca AL, Ryder OA, Heiman D, Young S, Breen M, Williams C, Aken BL, Ruffier M, Karlsson E, Johnson J, Di Palma F, Alfoldi J, Adelson DL, Mailund T, Munch K, Lindblad-Toh K, Hofreiter M, Poinar H, Reich D. A comprehensive genomic history of extinct and living elephants. Proc Natl Acad Sci U S A 2018; 115:E2566-E2574. [PMID: 29483247 PMCID: PMC5856550 DOI: 10.1073/pnas.1720554115] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Elephantids are the world's most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ∼120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant's ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for ∼500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.
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Affiliation(s)
- Eleftheria Palkopoulou
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Svend Nielsen
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus, Denmark
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Sina Baleka
- Unit of General Zoology-Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Life Sciences, University of Potsdam, 14476 Potsdam, Germany
| | - Emil Karpinski
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry, McMaster University, Hamilton, ON L8S 4L8, Canada
- The Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Atma M Ivancevic
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Thu-Hien To
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - R Daniel Kortschak
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Joy M Raison
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Zhipeng Qu
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Tat-Jun Chin
- School of Computer Science, The University of Adelaide, 5005 SA, Australia
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, A-3500 Krems, Austria
- Department of Biomedical Engineering, University Hospital Basel, University of Basel, CH-4123 Basel, Switzerland
- Integrative Prehistory and Archaeological Science, University of Basel, CH-4055 Basel, Switzerland
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, NY 10024
| | - Harald Meller
- State Office for Heritage Management and Archaeology, 06114 Halle (Saale), Germany
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo, Escondido, CA 92027
| | - David Heiman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Christina Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, CB10 1SD Cambridge, United Kingdom
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, CB10 1SD Cambridge, United Kingdom
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | | | | | | | - David L Adelson
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Michael Hofreiter
- Unit of General Zoology-Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Life Sciences, University of Potsdam, 14476 Potsdam, Germany
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Biochemistry, McMaster University, Hamilton, ON L8S 4L8, Canada
- The Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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33
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Buckley RM, Kortschak RD, Raison JM, Adelson DL. Similar Evolutionary Trajectories for Retrotransposon Accumulation in Mammals. Genome Biol Evol 2018; 9:2336-2353. [PMID: 28945883 PMCID: PMC5610350 DOI: 10.1093/gbe/evx179] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2017] [Indexed: 12/19/2022] Open
Abstract
The factors guiding retrotransposon insertion site preference are not well understood. Different types of retrotransposons share common replication machinery and yet occupy distinct genomic domains. Autonomous long interspersed elements accumulate in gene-poor domains and their nonautonomous short interspersed elements accumulate in gene-rich domains. To determine genomic factors that contribute to this discrepancy we analyzed the distribution of retrotransposons within the framework of chromosomal domains and regulatory elements. Using comparative genomics, we identified large-scale conserved patterns of retrotransposon accumulation across several mammalian genomes. Importantly, retrotransposons that were active after our sample-species diverged accumulated in orthologous regions. This suggested a similar evolutionary interaction between retrotransposon activity and conserved genome architecture across our species. In addition, we found that retrotransposons accumulated at regulatory element boundaries in open chromatin, where accumulation of particular retrotransposon types depended on insertion size and local regulatory element density. From our results, we propose a model where density and distribution of genes and regulatory elements canalize retrotransposon accumulation. Through conservation of synteny, gene regulation and nuclear organization, mammalian genomes with dissimilar retrotransposons follow similar evolutionary trajectories.
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Affiliation(s)
- Reuben M Buckley
- Department of Genetics and Evolution, The University of Adelaide, South Australia, Australia
| | - R Daniel Kortschak
- Department of Genetics and Evolution, The University of Adelaide, South Australia, Australia
| | - Joy M Raison
- Department of Genetics and Evolution, The University of Adelaide, South Australia, Australia
| | - David L Adelson
- Department of Genetics and Evolution, The University of Adelaide, South Australia, Australia
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34
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Yu C, Qu Z, Zhang Y, Zhang X, Lan T, Adelson DL, Wang D, Zhu Y. Seed weight differences between wild and domesticated soybeans are associated with specific changes in gene expression. Plant Cell Rep 2017; 36:1417-1426. [PMID: 28653111 DOI: 10.1007/s00299-017-2165-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/08/2017] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Our study systematically explored potential genes and molecular pathways as candidates for differences in seed weight resulting from soybean domestication. In addition, potential contributions of lncRNAs to seed weight were also investigated. Soybeans have a long history of domestication in China, and there are several significant phenotypic differences between cultivated and wild soybeans, for example, seeds of cultivars are generally larger and heavier than those from wild accessions. We analyzed seed transcriptomes from thirteen soybean samples, including six landraces and seven wild accessions using strand-specific RNA sequencing. Differentially expressed genes related to seed weight were identified, and some of their homologs were associated with seed development in Arabidopsis. We also identified 1251 long intergenic noncoding RNAs (lincRNAs), 243 intronic RNAs and 81 antisense lncRNAs de novo from these soybean transcriptomes. We then profiled the expression patterns of lncRNAs in cultivated and wild soybean seeds, and found that transcript levels of a number of lncRNAs were sample-specific. Moreover, gene transcript and lincRNA co-expression network analysis showed that some soybean lincRNAs might have functional roles as they were hubs of co-expression modules. In conclusion, this study systematically explored potential genes and molecular pathways as candidates for differences in seed weight resulting from soybean domestication, and will provide a useful future resource for molecular breeding of soybeans.
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Affiliation(s)
- Chao Yu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330031, Jiangxi, China
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Zhipeng Qu
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Yueting Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xifeng Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - Tingting Lan
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China
| | - David L Adelson
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China.
| | - Youlin Zhu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330031, Jiangxi, China.
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, 330031, China.
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35
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Hempfling AL, Lim SL, Adelson DL, Evans J, O'Connor AE, Qu ZP, Kliesch S, Weidner W, O'Bryan MK, Bergmann M. Expression patterns of HENMT1 and PIWIL1 in human testis: implications for transposon expression. Reproduction 2017; 154:363-374. [PMID: 28676534 DOI: 10.1530/rep-16-0586] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/08/2017] [Accepted: 07/04/2017] [Indexed: 12/20/2022]
Abstract
This study aimed to define the expression patterns of HENMT1 and PIWI proteins in human testis and investigate their association with transposon expression, infertility sub-type or development of testicular germ cell tumours (TGCTs). Testis biopsies showing normal spermatogenesis were used to identify normal localisation patterns of HENMT1 and PIWIL1 by immunolocalisation and RT-PCR after laser microdissection. 222 testis biopsies representing normal spermatogenesis, hypospermatogenesis, spermatogenic arrests, Sertoli cell-only (SCO) tumours and TGCTs were analysed by RT-qPCR for expression of HENMT1/PIWIL1/PIWIL2/PIWIL3/PIWIL4 and LINE-1 Additionally, HENMT1-overexpressing TCam2 seminoma cell lines were analysed for the same parameters by RT-qPCR. We found that HENMT1 and PIWIL1 are coexpressed in pachytene spermatocytes and spermatids. Expression of HENMT1, PIWIL1 and PIWIL2 was mainly dependent on germ cell content but low levels of expression were also detected in some SCO samples. Levels of HENMT1, PIWIL1 and PIWIL2 expression were low in TGCT. Samples with HENMT1, PIWIL2 and PIWIL4 expression showed significantly (P < 0.05) lower transposon expression compared to samples without expression in the same histological group. HENMT1-overexpressing TCam2 cells showed lower LINE-1 expression than empty vector-transfected control lines. Our findings support that the transposon-regulating function of the piRNA pathway found in the mouse is conserved in adult human testis. HENMT1 and PIWI proteins are expressed in a germ-cell-specific manner and required for transposon control.
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Affiliation(s)
- A L Hempfling
- The Development and Stem Cells Program of the Monash Biomedicine Discovery Institute and The Department of Anatomy and Developmental BiologyMonash University Clayton, Clayton, Australia .,Institute for Veterinary AnatomyHistology and Embryology, Justus Liebig University, Giessen, Germany
| | - S L Lim
- The Development and Stem Cells Program of the Monash Biomedicine Discovery Institute and The Department of Anatomy and Developmental BiologyMonash University Clayton, Clayton, Australia
| | - D L Adelson
- School of Biological SciencesThe University of Adelaide, Adelaide, Australia
| | - J Evans
- Centre for Reproductive HealthHudson Institute of Medical Research, Clayton, Australia
| | - A E O'Connor
- The Development and Stem Cells Program of the Monash Biomedicine Discovery Institute and The Department of Anatomy and Developmental BiologyMonash University Clayton, Clayton, Australia
| | - Z P Qu
- School of Biological SciencesThe University of Adelaide, Adelaide, Australia
| | - S Kliesch
- Centre of Reproductive Medicine and AndrologyMuenster, Germany
| | - W Weidner
- Clinic for UrologyPediatric Urology and Andrology, Justus-Liebig-University, Giessen, Germany
| | - M K O'Bryan
- The Development and Stem Cells Program of the Monash Biomedicine Discovery Institute and The Department of Anatomy and Developmental BiologyMonash University Clayton, Clayton, Australia.,The School of Biological SciencesMonash University, Clayton, Australia
| | - M Bergmann
- Institute for Veterinary AnatomyHistology and Embryology, Justus Liebig University, Giessen, Germany
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36
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Wang D, Qu Z, Yang L, Zhang Q, Liu ZH, Do T, Adelson DL, Wang ZY, Searle I, Zhu JK. Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants. Plant J 2017; 90:133-146. [PMID: 28106309 PMCID: PMC5514416 DOI: 10.1111/tpj.13481] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/01/2017] [Accepted: 01/05/2017] [Indexed: 05/20/2023]
Abstract
Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these noncoding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown. By using strand-specific RNA-sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified 47 611 and 398 TE-associated lincRNAs (TE-lincRNAs), respectively. TE-lincRNAs were more often derived from retrotransposons than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE-lincRNAs. We validated the expression of these TE-lincRNAs by strand-specific RT-PCR and also demonstrated tissue-specific transcription and stress-induced TE-lincRNAs either after salt, abscisic acid (ABA) or cold treatments. For Arabidopsis TE-lincRNA11195, mutants had reduced sensitivity to ABA as demonstrated by longer roots and higher shoot biomass when compared to wild-type. Finally, by altering the chromatin state in the Arabidopsis chromatin remodelling mutant ddm1, unique lincRNAs including TE-lincRNAs were generated from the preceding untranscribed regions and interestingly inherited in a wild-type background in subsequent generations. Our findings not only demonstrate that TE-associated lincRNAs play important roles in plant abiotic stress responses but lincRNAs and TE-lincRNAs might act as an adaptive reservoir in eukaryotes.
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Affiliation(s)
- Dong Wang
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhipeng Qu
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Lan Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingzhu Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhi-Hong Liu
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Trung Do
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - David L. Adelson
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Zhen-Yu Wang
- Hainan Key laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, China
| | - Iain Searle
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- For correspondence: or
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- For correspondence: or
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Fruzangohar M, Ebrahimie E, Adelson DL. A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data. PLoS One 2017; 12:e0170486. [PMID: 28199395 PMCID: PMC5310883 DOI: 10.1371/journal.pone.0170486] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 01/05/2017] [Indexed: 11/23/2022] Open
Abstract
Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribute equally to the final GO classification regardless of their actual expression levels. Gene expression levels can significantly affect protein production and hence should be reflected in GO term enrichment. Genes with low expression levels can also participate in GO term enrichment through cumulative effects. In this report, we have introduced a new GO enrichment method that is suitable for multiple samples and time series experiments that uses a statistical outlier test to detect GO categories with special patterns of variation that can potentially identify candidate biological mechanisms. To demonstrate the value of our approach, we have performed two case studies. Whole transcriptome expression profiles of Salmonella enteritidis and Alzheimer's disease (AD) were analysed in order to determine GO term enrichment across the entire transcriptome instead of a subset of differentially expressed genes used in traditional GO analysis. Our result highlights the key role of inflammation related functional groups in AD pathology as granulocyte colony-stimulating factor receptor binding, neuromedin U binding, and interleukin were remarkably upregulated in AD brain when all using all of the gene expression data in the transcriptome. Mitochondrial components and the molybdopterin synthase complex were identified as potential key cellular components involved in AD pathology.
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Affiliation(s)
- Mario Fruzangohar
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Esmaeil Ebrahimie
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- School of Medicine, Faculty of Health Sciences, The University of Adelaide, Adelaide, Australia
- School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, University of South Australia, Adelaide, Australia
- School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
| | - David L. Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Zhendong Australia – China Centre for Molecular Chinese Medicine, The University of Adelaide, Adelaide, South Australia, Australia
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Ivancevic AM, Kortschak RD, Bertozzi T, Adelson DL. LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. Genome Biol Evol 2016; 8:3301-3322. [PMID: 27702814 PMCID: PMC5203782 DOI: 10.1093/gbe/evw243] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to ‘jump’ around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active L1, in particular, are often thought of as tightly constrained, homologous and ubiquitous elements with well-characterized domain organization. For the past 30 years, model organisms have been used to define L1s as 6–8 kb sequences containing a 5′-UTR, two open reading frames working harmoniously in cis, and a 3′-UTR with a polyA tail. In this study, we demonstrate the remarkable and overlooked diversity of L1s via a comprehensive phylogenetic analysis of elements from over 500 species from widely divergent branches of the tree of life. The rapid and recent growth of L1 elements in mammalian species is juxtaposed against the diverse lineages found in other metazoans and plants. In fact, some of these previously unexplored mammalian species (e.g. snub-nosed monkey, minke whale) exhibit L1 retrotranspositional ‘hyperactivity’ far surpassing that of human or mouse. In contrast, non-mammalian L1s have become so varied that the current classification system seems to inadequately capture their structural characteristics. Our findings illustrate how both long-term inherited evolutionary patterns and random bursts of activity in individual species can significantly alter genomes, highlighting the importance of L1 dynamics in eukaryotes.
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Affiliation(s)
- Atma M Ivancevic
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - R Daniel Kortschak
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Terry Bertozzi
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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Ling KH, Brautigan PJ, Moore S, Fraser R, Cheah PS, Raison JM, Babic M, Lee YK, Daish T, Mattiske DM, Mann JR, Adelson DL, Thomas PQ, Hahn CN, Scott HS. Derivation of an endogenous small RNA from double-stranded Sox4 sense and natural antisense transcripts in the mouse brain. Genomics 2016; 107:88-99. [DOI: 10.1016/j.ygeno.2016.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 11/28/2022]
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Ling KH, Brautigan PJ, Moore S, Fraser R, Leong MPY, Leong JW, Zainal Abidin S, Lee HC, Cheah PS, Raison JM, Babic M, Lee YK, Daish T, Mattiske DM, Mann JR, Adelson DL, Thomas PQ, Hahn CN, Scott HS. In depth analysis of the Sox4 gene locus that consists of sense and natural antisense transcripts. Data Brief 2016; 7:282-90. [PMID: 26958646 PMCID: PMC4773576 DOI: 10.1016/j.dib.2016.01.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 10/25/2022] Open
Abstract
SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene expression during post-mitotic cell differentiation within the mammalian brain. Sox4 gene locus has been previously characterized with multiple sense and overlapping natural antisense transcripts [1], [2]. Here we provide accompanying data on various analyses performed and described in Ling et al. [2]. The data include a detail description of various features found at Sox4 gene locus, additional experimental data derived from RNA-Fluorescence in situ Hybridization (RNA-FISH), Western blotting, strand-specific reverse-transcription quantitative polymerase chain reaction (RT-qPCR), gain-of-function and in situ hybridization (ISH) experiments. All the additional data provided here support the existence of an endogenous small interfering- or PIWI interacting-like small RNA known as Sox4_sir3, which origin was found within the overlapping region consisting of a sense and a natural antisense transcript known as Sox4ot1.
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Affiliation(s)
- King-Hwa Ling
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, P.O. Box 14 Rundle Mall Post Office, Adelaide, SA 5000, Australia; School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, SA 5005, Australia; NeuroBiology & Genetics Group, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Peter J Brautigan
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, P.O. Box 14 Rundle Mall Post Office, Adelaide, SA 5000, Australia
| | - Sarah Moore
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, P.O. Box 14 Rundle Mall Post Office, Adelaide, SA 5000, Australia
| | - Rachel Fraser
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, P.O. Box 14 Rundle Mall Post Office, Adelaide, SA 5000, Australia
| | - Melody Pui-Yee Leong
- NeuroBiology & Genetics Group, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Jia-Wen Leong
- NeuroBiology & Genetics Group, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Shahidee Zainal Abidin
- NeuroBiology & Genetics Group, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Han-Chung Lee
- NeuroBiology & Genetics Group, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Pike-See Cheah
- NeuroBiology & Genetics Group, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia; School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia; Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor DE, Malaysia
| | - Joy M Raison
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Milena Babic
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, P.O. Box 14 Rundle Mall Post Office, Adelaide, SA 5000, Australia
| | - Young Kyung Lee
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, P.O. Box 14 Rundle Mall Post Office, Adelaide, SA 5000, Australia
| | - Tasman Daish
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Deidre M Mattiske
- Theme of Laboratory and Community Genetics, Murdoch Childrens Research Institute, Royal Children׳s Hospital, Flemington Road, Parkville, VIC 3052, Australia
| | - Jeffrey R Mann
- Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
| | - David L Adelson
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Paul Q Thomas
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Christopher N Hahn
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, P.O. Box 14 Rundle Mall Post Office, Adelaide, SA 5000, Australia
| | - Hamish S Scott
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, P.O. Box 14 Rundle Mall Post Office, Adelaide, SA 5000, Australia; School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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Lim SL, Qu ZP, Kortschak RD, Lawrence DM, Geoghegan J, Hempfling AL, Bergmann M, Goodnow CC, Ormandy CJ, Wong L, Mann J, Scott HS, Jamsai D, Adelson DL, O'Bryan MK. Correction: HENMT1 and piRNA Stability Are Required for Adult Male Germ Cell Transposon Repression and to Define the Spermatogenic Program in the Mouse. PLoS Genet 2015; 11:e1005782. [PMID: 26714033 PMCID: PMC4695089 DOI: 10.1371/journal.pgen.1005782] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Lim SL, Qu ZP, Kortschak RD, Lawrence DM, Geoghegan J, Hempfling AL, Bergmann M, Goodnow CC, Ormandy CJ, Wong L, Mann J, Scott HS, Jamsai D, Adelson DL, O’Bryan MK. HENMT1 and piRNA Stability Are Required for Adult Male Germ Cell Transposon Repression and to Define the Spermatogenic Program in the Mouse. PLoS Genet 2015; 11:e1005620. [PMID: 26496356 PMCID: PMC4619860 DOI: 10.1371/journal.pgen.1005620] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/30/2015] [Indexed: 02/04/2023] Open
Abstract
piRNAs are critical for transposable element (TE) repression and germ cell survival during the early phases of spermatogenesis, however, their role in adult germ cells and the relative importance of piRNA methylation is poorly defined in mammals. Using a mouse model of HEN methyltransferase 1 (HENMT1) loss-of-function, RNA-Seq and a range of RNA assays we show that HENMT1 is required for the 2’ O-methylation of mammalian piRNAs. HENMT1 loss leads to piRNA instability, reduced piRNA bulk and length, and ultimately male sterility characterized by a germ cell arrest at the elongating germ cell phase of spermatogenesis. HENMT1 loss-of-function, and the concomitant loss of piRNAs, resulted in TE de-repression in adult meiotic and haploid germ cells, and the precocious, and selective, expression of many haploid-transcripts in meiotic cells. Precocious expression was associated with a more active chromatin state in meiotic cells, elevated levels of DNA damage and a catastrophic deregulation of the haploid germ cell gene expression. Collectively these results define a critical role for HENMT1 and piRNAs in the maintenance of TE repression in adult germ cells and setting the spermatogenic program. Piwi-interacting RNAs (piRNAs) are small non-coding RNAs found in great abundance within both embryonic and adult male germ cells. Within embryonic germ cells, piRNAs have a well-recognized role in transposable element (TE) silencing, however, their role in adult cells remains poorly defined. Here we demonstrate that HENMT1 dysfunction and the resultant piRNA instability dramatically impacts multiple aspects of adult germ cell biology. Specifically, pachytene piRNAs are required to maintain TE silencing in adult germ cells and to set the spermatogenic gene expression program. piRNA loss leads to a more active chromatin state in the regulatory regions of numerous normally haploid germ cell genes and their precocious expression during meiosis, followed by a catastrophic deregulation of gene expression in haploid cells and male sterility.
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Affiliation(s)
- Shu Ly Lim
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Zhi Peng Qu
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - R. Daniel Kortschak
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - David M. Lawrence
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Joel Geoghegan
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Anna-Lena Hempfling
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Institute of Veterinary Anatomy, Histology and Embryology, Justus Liebig University Giessen, Giessen, Germany
| | - Martin Bergmann
- Institute of Veterinary Anatomy, Histology and Embryology, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher C. Goodnow
- Australian Phenomics Facility, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Christopher J. Ormandy
- The Garvan Institute of Medical Research, Sydney, Darlinghurst, New South Wales, Australia
| | - Lee Wong
- The Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Jeff Mann
- Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Hamish S. Scott
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
- Australian Cancer Research Foundation Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
- Department of Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Duangporn Jamsai
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - David L. Adelson
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Moira K. O’Bryan
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- * E-mail:
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43
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Buckley RM, Adelson DL. Mammalian genome evolution as a result of epigenetic regulation of transposable elements. Biomol Concepts 2015; 5:183-94. [PMID: 25372752 DOI: 10.1515/bmc-2014-0013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/27/2014] [Indexed: 12/29/2022] Open
Abstract
Transposable elements (TEs) make up a large proportion of mammalian genomes and are a strong evolutionary force capable of rewiring regulatory networks and causing genome rearrangements. Additionally, there are many eukaryotic epigenetic defense mechanisms able to transcriptionally silence TEs. Furthermore, small RNA molecules that target TE DNA sequences often mediate these epigenetic defense mechanisms. As a result, epigenetic marks associated with TE silencing can be reestablished after epigenetic reprogramming - an event during the mammalian life cycle that results in widespread loss of parental epigenetic marks. Furthermore, targeted epigenetic marks associated with TE silencing may have an impact on nearby gene expression. Therefore, TEs may have driven species evolution via their ability to heritably alter the epigenetic regulation of gene expression in mammals.
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Hu Z, Scott HS, Qin G, Zheng G, Chu X, Xie L, Adelson DL, Oftedal BE, Venugopal P, Babic M, Hahn CN, Zhang B, Wang X, Li N, Wei C. Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics. Sci Rep 2015; 5:10940. [PMID: 26156868 PMCID: PMC4496727 DOI: 10.1038/srep10940] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/05/2015] [Indexed: 01/02/2023] Open
Abstract
Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.
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Affiliation(s)
- Zhiqiang Hu
- 1] School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China [2] Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China
| | - Hamish S Scott
- 1] Department of Genetics and Molecular Pathology, Centre for Cancer Biology, Frome Road, Adelaide, SA 5000 Australia [2] School of Biological Sciences, University of Adelaide, SA 5005, Australia [3] School of Medicine, University of Adelaide, North Terrace, Adelaide, SA 5000, Australia [4] School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, SA, Australia [5] ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Frome Road, Adelaide, SA 5000, Australia
| | - Guangrong Qin
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China
| | - Guangyong Zheng
- 1] Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China [2] CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Xixia Chu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Bergithe E Oftedal
- 1] Department of Genetics and Molecular Pathology, Centre for Cancer Biology, Frome Road, Adelaide, SA 5000 Australia [2] Department of Biomedical Informatics (DBMI), Vanderbilt University Medical Center (VUMC), 2525 West End Ave, Suite 800, Nashville, TN 37203, USA
| | - Parvathy Venugopal
- 1] Department of Genetics and Molecular Pathology, Centre for Cancer Biology, Frome Road, Adelaide, SA 5000 Australia [2] School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Milena Babic
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, Frome Road, Adelaide, SA 5000 Australia
| | - Christopher N Hahn
- 1] Department of Genetics and Molecular Pathology, Centre for Cancer Biology, Frome Road, Adelaide, SA 5000 Australia [2] School of Biological Sciences, University of Adelaide, SA 5005, Australia [3] School of Medicine, University of Adelaide, North Terrace, Adelaide, SA 5000, Australia
| | - Bing Zhang
- Department of Biomedical Informatics (DBMI), Vanderbilt University Medical Center (VUMC), 2525 West End Ave, Suite 800, Nashville, TN 37203, USA
| | - Xiaojing Wang
- Department of Biomedical Informatics (DBMI), Vanderbilt University Medical Center (VUMC), 2525 West End Ave, Suite 800, Nashville, TN 37203, USA
| | - Nan Li
- Institute of Immunology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Chaochun Wei
- 1] School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China [2] Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China
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Fruzangohar M, Ebrahimie E, Ogunniyi AD, Mahdi LK, Paton JC, Adelson DL. Correction: Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria. PLoS One 2015; 10:e0125537. [PMID: 25884626 PMCID: PMC4401681 DOI: 10.1371/journal.pone.0125537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Adelson DL, Raison JM, Garber M, Edgar RC. Interspersed repeats in the horse (Equus caballus); spatial correlations highlight conserved chromosomal domains. Anim Genet 2015; 41 Suppl 2:91-9. [PMID: 21070282 DOI: 10.1111/j.1365-2052.2010.02115.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The interspersed repeat content of mammalian genomes has been best characterized in human, mouse and cow. In this study, we carried out de novo identification of repeated elements in the equine genome and identified previously unknown elements present at low copy number. The equine genome contains typical eutherian mammal repeats, but also has a significant number of hybrid repeats in addition to clade-specific Long Interspersed Nuclear Elements (LINE). Equus caballus clade specific LINE 1 (L1) repeats can be classified into approximately five subfamilies, three of which have undergone significant expansion. There are 1115 full-length copies of these equine L1, but of the 103 presumptive active copies, 93 fall within a single subfamily, indicating a rapid recent expansion of this subfamily. We also analysed both interspersed and simple sequence repeats (SSR) genome-wide, finding that some repeat classes are spatially correlated with each other as well as with G+C content and gene density. Based on these spatial correlations, we have confirmed that recently-described ancestral vs. clade-specific genome territories can be defined by their repeat content. The clade-specific Short Interspersed Nuclear Element correlations were scattered over the genome and appear to have been extensively remodelled. In contrast, territories enriched for ancestral repeats tended to be contiguous domains. To determine if the latter territories were evolutionarily conserved, we compared these results with a similar analysis of the human genome, and observed similar ancestral repeat enriched domains. These results indicate that ancestral, evolutionarily conserved mammalian genome territories can be identified on the basis of repeat content alone. Interspersed repeats of different ages appear to be analogous to geologic strata, allowing identification of ancient vs. newly remodelled regions of mammalian genomes.
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Affiliation(s)
- D L Adelson
- School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia, Australia.
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47
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Alanazi I, Hoffmann P, Adelson DL. MicroRNAs are part of the regulatory network that controls EGF induced apoptosis, including elements of the JAK/STAT pathway, in A431 cells. PLoS One 2015; 10:e0120337. [PMID: 25781916 PMCID: PMC4364457 DOI: 10.1371/journal.pone.0120337] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 02/05/2015] [Indexed: 12/20/2022] Open
Abstract
MiRNAs are known to regulate gene expression and in the context of cancer have been shown to regulate metastasis, cell proliferation and cell death. In this report we describe potential miRNA regulatory roles with respect to induction of cell death by pharmacologic dose of Epidermal Growth Factor (EGF). Our previous work suggested that multiple pathways are involved in the induction of apoptosis, including interferon induced genes, cytokines, cytoskeleton and cell adhesion and TP53 regulated genes. Using miRNA time course expression profiling of EGF treated A431 cells and coupling this to our previous gene expression and proteomic data, we have been able to implicate a number of additional miRNAs in the regulation of apoptosis. Specifically we have linked miR-134, miR-145, miR-146b-5p, miR-432 and miR-494 to the regulation of both apoptotic and anti-apoptotic genes expressed as a function of EGF treatment. Whilst additional miRNAs were differentially expressed, these had the largest number of apoptotic and anti-apoptotic targets. We found 5 miRNAs previously implicated in the regulation of apoptosis and our results indicate that an additional 20 miRNAs are likely to be involved based on their correlated expression with targets. Certain targets were linked to multiple miRNAs, including PEG10, BTG1, ID1, IL32 and NCF2. Some miRNAs that target the interferon pathway were found to be down regulated, consistent with a novel layer of regulation of interferon pathway components downstream of JAK/STAT. We have significantly expanded the repertoire of miRNAs that may regulate apoptosis in cancer cells as a result of this work.
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Affiliation(s)
- Ibrahim Alanazi
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Peter Hoffmann
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - David L. Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Zhendong Australia—China Centre for Molecular Chinese Medicine, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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McMichael G, Bainbridge MN, Haan E, Corbett M, Gardner A, Thompson S, van Bon BWM, van Eyk CL, Broadbent J, Reynolds C, O'Callaghan ME, Nguyen LS, Adelson DL, Russo R, Jhangiani S, Doddapaneni H, Muzny DM, Gibbs RA, Gecz J, MacLennan AH. Whole-exome sequencing points to considerable genetic heterogeneity of cerebral palsy. Mol Psychiatry 2015; 20:176-82. [PMID: 25666757 DOI: 10.1038/mp.2014.189] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/12/2014] [Accepted: 11/24/2014] [Indexed: 12/22/2022]
Abstract
Cerebral palsy (CP) is a common, clinically heterogeneous group of disorders affecting movement and posture. Its prevalence has changed little in 50 years and the causes remain largely unknown. The genetic contribution to CP causation has been predicted to be ~2%. We performed whole-exome sequencing of 183 cases with CP including both parents (98 cases) or one parent (67 cases) and 18 singleton cases (no parental DNA). We identified and validated 61 de novo protein-altering variants in 43 out of 98 (44%) case-parent trios. Initial prioritization of variants for causality was by mutation type, whether they were known or predicted to be deleterious and whether they occurred in known disease genes whose clinical spectrum overlaps CP. Further, prioritization used two multidimensional frameworks-the Residual Variation Intolerance Score and the Combined Annotation-dependent Depletion score. Ten de novo mutations in three previously identified disease genes (TUBA1A (n=2), SCN8A (n=1) and KDM5C (n=1)) and in six novel candidate CP genes (AGAP1, JHDM1D, MAST1, NAA35, RFX2 and WIPI2) were predicted to be potentially pathogenic for CP. In addition, we identified four predicted pathogenic, hemizygous variants on chromosome X in two known disease genes, L1CAM and PAK3, and in two novel candidate CP genes, CD99L2 and TENM1. In total, 14% of CP cases, by strict criteria, had a potentially disease-causing gene variant. Half were in novel genes. The genetic heterogeneity highlights the complexity of the genetic contribution to CP. Function and pathway studies are required to establish the causative role of these putative pathogenic CP genes.
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Affiliation(s)
- G McMichael
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - M N Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - E Haan
- 1] South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, Australia [2] School of Pediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia
| | - M Corbett
- 1] Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia [2] School of Pediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia
| | - A Gardner
- 1] Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia [2] School of Pediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia
| | - S Thompson
- 1] School of Pediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia [2] Department of Pediatric Neurology, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - B W M van Bon
- 1] South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, Australia [2] Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - C L van Eyk
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - J Broadbent
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - C Reynolds
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - M E O'Callaghan
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - L S Nguyen
- School of Pediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia
| | - D L Adelson
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, Australia
| | - R Russo
- Department of Pediatric Rehabilitation, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - S Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - H Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - D M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - R A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - J Gecz
- 1] Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia [2] School of Pediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia
| | - A H MacLennan
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
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Mahdi LK, Deihimi T, Zamansani F, Fruzangohar M, Adelson DL, Paton JC, Ogunniyi AD, Ebrahimie E. A functional genomics catalogue of activated transcription factors during pathogenesis of pneumococcal disease. BMC Genomics 2014; 15:769. [PMID: 25196724 PMCID: PMC4171566 DOI: 10.1186/1471-2164-15-769] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/03/2014] [Indexed: 11/11/2022] Open
Abstract
Background Streptococcus pneumoniae (the pneumococcus) is the world’s foremost microbial pathogen, killing more people each year than HIV, TB or malaria. The capacity to penetrate deeper host tissues contributes substantially to the ability of this organism to cause disease. Here we investigated, for the first time, functional genomics modulation of 3 pneumococcal strains (serotype 2 [D39], serotype 4 [WCH43] and serotype 6A [WCH16]) during transition from the nasopharynx to lungs to blood and to brain of mice at both promoter and domain activation levels. Results We found 7 highly activated transcription factors (TFs) [argR, codY, hup, rpoD, rr02, scrR and smrC] capable of binding to a large number of up-regulated genes, potentially constituting the regulatory backbone of pneumococcal pathogenesis. Strain D39 showed a distinct profile in employing a large number of TFs during blood infection. Interestingly, the same highly activated TFs used by D39 in blood are also used by WCH16 and WCH43 during brain infection. This indicates that different pneumococcal strains might activate a similar set of TFs and regulatory elements depending on the final site of infection. Hierarchical clustering analysis showed that all the highly activated TFs, except rpoD, clustered together with a high level of similarity in all 3 strains, which might suggest redundancy in the regulatory roles of these TFs during infection. Discriminant function analysis of the TFs in various niches highlights differential regulatory backgrounds of the 3 strains, and pathogenesis data confirms codY as the most significant predictor discriminating between these strains in various niches, particularly in the blood. Moreover, the predicted TF and domain activation profiles of the 3 strains correspond with their distinct pathogenicity characteristics. Conclusions Our findings suggest that the pneumococcus changes the short binding sites in the promoter regions of genes in a niche-specific manner to enhance its ability to disseminate from one host niche to another. This study provides a framework for an improved understanding of the dynamics of pneumococcal pathogenesis, and opens a new avenue into similar investigations in other pathogenic bacteria. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-769) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Abiodun D Ogunniyi
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia.
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Gagliardi L, Schreiber AW, Hahn CN, Feng J, Cranston T, Boon H, Hotu C, Oftedal BE, Cutfield R, Adelson DL, Braund WJ, Gordon RD, Rees DA, Grossman AB, Torpy DJ, Scott HS. ARMC5 mutations are common in familial bilateral macronodular adrenal hyperplasia. J Clin Endocrinol Metab 2014; 99:E1784-92. [PMID: 24905064 DOI: 10.1210/jc.2014-1265] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
CONTEXT Bilateral macronodular adrenal hyperplasia (BMAH) is a rare form of adrenal Cushing's syndrome. Familial cases have been reported, but at the time we conducted this study, the genetic basis of BMAH was unknown. Recently, germline variants of armadillo repeat containing 5 (ARMC5) in patients with isolated BMAH and somatic, second-hit mutations in tumor nodules, were identified. OBJECTIVE Our objective was to identify the genetic basis of familial BMAH. DESIGN We performed whole exome capture and sequencing of 2 affected individuals from each of 4 BMAH families (BMAH-01, BMAH-02, BMAH-03, and BMAH-05). Based on clinical evaluation, there were 7, 3, 3, and 4 affected individuals in these families, respectively. Sanger sequencing of ARMC5 was performed in 1 other BMAH kindred, BMAH-06. RESULTS Exome sequencing identified novel variants Chr16:g.31477540, c.2139delT, p.(Thr715Leufs*1) (BMAH-02) and Chr16:g.31473811, c.943C→T, p.(Arg315Trp) (BMAH-03) in ARMC5 (GRch37/hg19), validated by Sanger sequencing. BMAH-01 had a recently reported mutation Chr16:g.31476121, c.1777C→T, p.(Arg593Trp). Sanger sequencing of ARMC5 in BMAH-06 identified a previously reported mutation, Chr16:g. 31473688; c.799C→T, p.(Arg267*). The genetic basis of BMAH in BMAH-05 was not identified. CONCLUSIONS Our studies have detected ARMC5 mutations in 4 of 5 BMAH families tested, confirming that these mutations are a frequent cause of BMAH. Two of the 4 families had novel mutations, indicating allelic heterogeneity. Preclinical evaluation did not predict mutation status. The ARMC5-negative family had unusual prominent hyperaldosteronism. Further studies are needed to determine the penetrance of BMAH in ARMC5 mutation-positive relatives of affected patients, the practical utility of genetic screening and genotype-phenotype correlations.
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Affiliation(s)
- Lucia Gagliardi
- Endocrine and Metabolic Unit (L.G., D.J.T.), Royal Adelaide Hospital; Department of Genetics and Molecular Pathology (L.G., C.N.H., B.E.O., H.S.S.) and ACRF Cancer Genomics Facility (A.W.S., J.F., H.S.S.), Centre for Cancer Biology, SA Pathology; and School of Pharmacy and Medical Sciences (H.S.S.), Division of Health Sciences, University of South Australia, Adelaide SA 5000, Australia; Schools of Medicine (L.G., C.N.H., D.J.T., H.S.S.) and Molecular and Biomedical Science (A.W.S., J.F., D.L.A., H.S.S.), University of Adelaide SA 5005, Australia; Oxford Medical Genetics Laboratories (T.C., H.B.), Oxford University Hospitals National Health Service Trust, and Oxford Centre for Diabetes, Endocrinology and Metabolism (A.B.G.), Churchill Hospital, University of Oxford, Oxford OX3 7LE, United Kingdom; Department of Endocrinology (C.H.), Greenlane Clinical Centre, Auckland District Health Board, Auckland 1051, New Zealand; Department of Clinical Science (B.E.O.), University of Bergen, 5021 Bergen, Norway; Department of Endocrinology (R.C.), North Shore Hospital, Waitemata District Health Board, Auckland 0622, New Zealand; Department of Endocrinology (W.J.B.), Flinders Medical Centre, Bedford Park, SA 5042 Australia; School of Medicine (R.D.G.), University of Queensland, Brisbane QLD 4072, Australia; Endocrine Hypertension Research Centre (R.D.G.), Greenslopes and Princess Alexandra Hospitals, Brisbane QLD 4120, Australia; and Centre for Endocrine and Diabetes Sciences (D.A.R.), School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
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