1
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Ergin EK, Myung JJ, Lange PF. Statistical Testing for Protein Equivalence Identifies Core Functional Modules Conserved across 360 Cancer Cell Lines and Presents a General Approach to Investigating Biological Systems. J Proteome Res 2024; 23:2169-2185. [PMID: 38804581 PMCID: PMC11166143 DOI: 10.1021/acs.jproteome.4c00131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/04/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024]
Abstract
Quantitative proteomics has enhanced our capability to study protein dynamics and their involvement in disease using various techniques, including statistical testing, to discern the significant differences between conditions. While most focus is on what is different between conditions, exploring similarities can provide valuable insights. However, exploring similarities directly from the analyte level, such as proteins, genes, or metabolites, is not a standard practice and is not widely adopted. In this study, we propose a statistical framework called QuEStVar (Quantitative Exploration of Stability and Variability through statistical hypothesis testing), enabling the exploration of quantitative stability and variability of features with a combined statistical framework. QuEStVar utilizes differential and equivalence testing to expand statistical classifications of analytes when comparing conditions. We applied our method to an extensive data set of cancer cell lines and revealed a quantitatively stable core proteome across diverse tissues and cancer subtypes. The functional analysis of this set of proteins highlighted the molecular mechanism of cancer cells to maintain constant conditions of the tumorigenic environment via biological processes, including transcription, translation, and nucleocytoplasmic transport.
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Affiliation(s)
- Enes K. Ergin
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 2H4, Canada
| | - Junia J.K. Myung
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 2H4, Canada
| | - Philipp F. Lange
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 2H4, Canada
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2
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Hu Z, Chen J, Olatoye MO, Zhang H, Lin Z. Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum. THE PLANT GENOME 2024; 17:e20448. [PMID: 38602082 DOI: 10.1002/tpg2.20448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.
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Affiliation(s)
- Zhenbin Hu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Junhao Chen
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Marcus O Olatoye
- USDA-ARS, Forage Seed and Cereal Research Unit, Prosser, Washington, USA
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
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3
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Balogun EJ, Ness RW. The Effects of De Novo Mutation on Gene Expression and the Consequences for Fitness in Chlamydomonas reinhardtii. Mol Biol Evol 2024; 41:msae035. [PMID: 38366781 PMCID: PMC10910851 DOI: 10.1093/molbev/msae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/01/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Mutation is the ultimate source of genetic variation, the bedrock of evolution. Yet, predicting the consequences of new mutations remains a challenge in biology. Gene expression provides a potential link between a genotype and its phenotype. But the variation in gene expression created by de novo mutation and the fitness consequences of mutational changes to expression remain relatively unexplored. Here, we investigate the effects of >2,600 de novo mutations on gene expression across the transcriptome of 28 mutation accumulation lines derived from 2 independent wild-type genotypes of the green algae Chlamydomonas reinhardtii. We observed that the amount of genetic variance in gene expression created by mutation (Vm) was similar to the variance that mutation generates in typical polygenic phenotypic traits and approximately 15-fold the variance seen in the limited species where Vm in gene expression has been estimated. Despite the clear effect of mutation on expression, we did not observe a simple additive effect of mutation on expression change, with no linear correlation between the total expression change and mutation count of individual MA lines. We therefore inferred the distribution of expression effects of new mutations to connect the number of mutations to the number of differentially expressed genes (DEGs). Our inferred DEE is highly L-shaped with 95% of mutations causing 0-1 DEG while the remaining 5% are spread over a long tail of large effect mutations that cause multiple genes to change expression. The distribution is consistent with many cis-acting mutation targets that affect the expression of only 1 gene and a large target of trans-acting targets that have the potential to affect tens or hundreds of genes. Further evidence for cis-acting mutations can be seen in the overabundance of mutations in or near differentially expressed genes. Supporting evidence for trans-acting mutations comes from a 15:1 ratio of DEGs to mutations and the clusters of DEGs in the co-expression network, indicative of shared regulatory architecture. Lastly, we show that there is a negative correlation with the extent of expression divergence from the ancestor and fitness, providing direct evidence of the deleterious effects of perturbing gene expression.
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Affiliation(s)
- Eniolaye J Balogun
- Department of Biology, William G. Davis Building, University of Toronto, Mississauga L5L-1C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto M5S-3B2, Canada
| | - Rob W Ness
- Department of Biology, William G. Davis Building, University of Toronto, Mississauga L5L-1C6, Canada
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4
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Daybog I, Kolodny O. A computational framework for resolving the microbiome diversity conundrum. Nat Commun 2023; 14:7977. [PMID: 38042865 PMCID: PMC10693575 DOI: 10.1038/s41467-023-42768-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 10/20/2023] [Indexed: 12/04/2023] Open
Abstract
Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term 'the microbial β- diversity conundrum'. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.
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Affiliation(s)
- Itay Daybog
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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5
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 2023; 624:390-402. [PMID: 38092918 PMCID: PMC10719095 DOI: 10.1038/s41586-023-06819-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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Affiliation(s)
- Nathan R Zemke
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Wenliang Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seoyeon Lee
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jingtian Zhou
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Xu
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Lei Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Keyi Dong
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hannah S Indralingam
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jonathan A Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Miller
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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6
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Kang M, Wu H, Liu H, Liu W, Zhu M, Han Y, Liu W, Chen C, Song Y, Tan L, Yin K, Zhao Y, Yan Z, Lou S, Zan Y, Liu J. The pan-genome and local adaptation of Arabidopsis thaliana. Nat Commun 2023; 14:6259. [PMID: 37802986 PMCID: PMC10558531 DOI: 10.1038/s41467-023-42029-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 09/27/2023] [Indexed: 10/08/2023] Open
Abstract
Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.
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Affiliation(s)
- Minghui Kang
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Haolin Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huanhuan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wenyu Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yu Han
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wei Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chunlin Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yan Song
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Luna Tan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Kangqun Yin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yusen Zhao
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhen Yan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Shangling Lou
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Yanjun Zan
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266000, China.
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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7
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Zhang X, Wolinska J, Blair D, Hu W, Yin M. Responses to predation pressure involve similar sets of genes in two divergent species of Daphnia. J Anim Ecol 2023; 92:1743-1758. [PMID: 37337454 DOI: 10.1111/1365-2656.13969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Species that are not closely related can express similar inducible traits, but molecular mechanisms underlying the observed responses are often unknown, nor is it known if these mechanisms are shared between such species. Here, we compared transcriptional profiles of two Daphnia species (D. mitsukuri and D. sinensis) from different subgenera, at both juvenile and adult developmental stages. Both species were exposed to the same predation threat (fish kairomones), and both showed similar induced morphological changes (reduced body length). At the early developmental stage, response to predation risk resulted in similar changes in expression levels of 23 orthologues in both species. These orthologues, involved in 107 GO categories, changed in the same direction in both species (over- or underexpressed), in comparison to non-exposed controls. Several of these orthologues were associated with DNA replication, structural constituents of cuticle or innate immune response. In both species, the differentially expressed (DE) genes on average had higher ω (dN /dS ) values than non-DE genes, suggesting that these genes had experienced greater positive selection or lower purifying selection than non-DE genes. Overall, our results suggest that similar suites of genes, responding in similar ways to predation pressure, have been retained in Daphnia for many millions of years.
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Affiliation(s)
- Xiuping Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
- Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
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8
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Roberts M, Josephs EB. Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana. Genetics 2023; 224:iyad074. [PMID: 37094602 PMCID: PMC10484170 DOI: 10.1093/genetics/iyad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/06/2023] [Accepted: 04/07/2023] [Indexed: 04/26/2023] Open
Abstract
Differential gene expression between environments often underlies phenotypic plasticity. However, environment-specific expression patterns are hypothesized to relax selection on genes, and thus limit plasticity evolution. We collated over 27 terabases of RNA-sequencing data on Arabidopsis thaliana from over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Consistent with relaxed selection, genes with more treatment-specific expression have higher levels of nucleotide diversity and divergence at nonsynonymous sites but lack stronger signals of positive selection. This result persisted even after controlling for expression level, gene length, GC content, the tissue specificity of expression, and technical variation between studies. Overall, our investigation supports the existence of a hypothesized trade-off between the environment specificity of a gene's expression and the strength of selection on said gene in A. thaliana. Future studies should leverage multiple genome-scale datasets to tease apart the contributions of many variables in limiting plasticity evolution.
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Affiliation(s)
- Miles Roberts
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI 48824, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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9
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Behrens MM, Lein ES, Ecker JR, Ren B. Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.08.536119. [PMID: 37066152 PMCID: PMC10104177 DOI: 10.1101/2023.04.08.536119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Sequence divergence of cis- regulatory elements drives species-specific traits, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome, and chromosomal conformation profiles from a total of over 180,000 cells. For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes and that epigenetic status at distal candidate cis -regulatory elements (cCREs) evolves faster than promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity helps uncover functional cis -regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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10
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Mezzavilla M, Cocca M. Insights into gene tissue specificity and protein-protein interactions in the context of purifying selection in humans. Ann Hum Genet 2023; 87:75-79. [PMID: 36704895 DOI: 10.1111/ahg.12497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/28/2023]
Abstract
BACKGROUND How much are natural selection and gene characteristics, such as the number of protein-protein interactions (PPIs), tissue specificity (𝞽), and expression level, connected? METHODS In order to investigate these relationships, we combined different metrics linked to genetic constraints and analyzed their distribution concerning PPIs, 𝞽 and expression levels. RESULTS We discovered a positive correlation between genetic constraints, PPIs, and expression levels in all tissues. On the other hand, we obtained a negative correlation between genetic constraints and 𝞽. Furthermore, the fraction of variance in PPI and 𝞽 explained by the constraints metrics is around 6% and 10%, respectively. CONCLUSIONS We observed that the variance of expression of tissue-specific genes seems not related to their level of selection constraints, which is the opposite of what is found on non-tissue-specific genes. Overall these observations would help to elucidate the relationship between natural selection and gene features.
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Affiliation(s)
- Massimo Mezzavilla
- Department of Biology, University of Padua, Padua, Italy.,Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Massimiliano Cocca
- Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
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11
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Expression Profile of Housekeeping Genes and Tissue-Specific Genes in Multiple Tissues of Pigs. Animals (Basel) 2022; 12:ani12243539. [PMID: 36552460 PMCID: PMC9774903 DOI: 10.3390/ani12243539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Pigs have become an ideal model system for human disease research and development and an important farm animal that provides a valuable source of nutrition. To profile the all-sided gene expression and their biological functions across multiple tissues, we conducted a comprehensive analysis of gene expression on a large scale around the side of housekeeping genes (HKGs), tissue specific genes (TSGs), and the co-expressed genes in 14 various tissues. In this study, we identified 2351 HKGs and 3018 TSGs across tissues, among which 4 HKGs (COX1, UBB, OAZ1/NPFF) exhibited low variation and high expression levels, and 31 particular TSGs (e.g., PDC, FKBP6, STAT2, and COL1A1) were exclusively expressed in several tissues, including endocrine brain, ovaries, livers, backfat, jejunum, kidneys, lungs, and longissimus dorsi muscles. We also obtained 17 modules with 230 hub genes (HUBGs) by weighted gene co-expression network analysis. On the other hand, HKGs functions were enriched in the signaling pathways of the ribosome, spliceosome, thermogenesis, oxidative phosphorylation, and nucleocytoplasmic transport, which have been highly suggested to involve in the basic biological tissue activities. While TSGs were highly enriched in the signaling pathways that were involved in specific physiological processes, such as the ovarian steroidogenesis pathway in ovaries and the renin-angiotensin system pathway in kidneys. Collectively, these stable, specifical, and co-expressed genes provided useful information for the investigation of the molecular mechanism for an understanding of the genetic and biological processes of complex traits in pigs.
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12
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Yang M, Harrison BR, Promislow DEL. In search of a Drosophila core cellular network with single-cell transcriptome data. G3 GENES|GENOMES|GENETICS 2022; 12:6670625. [PMID: 35976114 PMCID: PMC9526075 DOI: 10.1093/g3journal/jkac212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
Along with specialized functions, cells of multicellular organisms also perform essential functions common to most if not all cells. Whether diverse cells do this by using the same set of genes, interacting in a fixed coordinated fashion to execute essential functions, or a subset of genes specific to certain cells, remains a central question in biology. Here, we focus on gene coexpression to search for a core cellular network across a whole organism. Single-cell RNA-sequencing measures gene expression of individual cells, enabling researchers to discover gene expression patterns that contribute to the diversity of cell functions. Current efforts to study cellular functions focus primarily on identifying differentially expressed genes across cells. However, patterns of coexpression between genes are probably more indicative of biological processes than are the expression of individual genes. We constructed cell-type-specific gene coexpression networks using single-cell transcriptome datasets covering diverse cell types from the fruit fly, Drosophila melanogaster. We detected a set of highly coordinated genes preserved across cell types and present this as the best estimate of a core cellular network. This core is very small compared with cell-type-specific gene coexpression networks and shows dense connectivity. Gene members of this core tend to be ancient genes and are enriched for those encoding ribosomal proteins. Overall, we find evidence for a core cellular network in diverse cell types of the fruit fly. The topological, structural, functional, and evolutionary properties of this core indicate that it accounts for only a minority of essential functions.
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Affiliation(s)
- Ming Yang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine , Seattle, WA 98195, USA
| | - Benjamin R Harrison
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine , Seattle, WA 98195, USA
| | - Daniel E L Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine , Seattle, WA 98195, USA
- Department of Biology, University of Washington , Seattle, WA 98195, USA
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13
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Swargiary P, Boruah N, Singh CS, Chatterjee A. Genome-wide analysis of DNaseI hypersensitivity unveils open chromatin associated with histone H3 modifications after areca nut with lime exposure. Mutagenesis 2022; 37:182-190. [DOI: 10.1093/mutage/geac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Research over the years revealed that precocious anaphase, securin overexpression, and genome instability in both target and nontarget cells are significantly associated with the increased risk of areca nut (AN) and lime-induced oral, esophageal, and gastric cancers. Further, hyperphosphorylation of Rb and histone H3 epigenetic modifications both globally and in the promoter region of the securin gene were demonstrated after AN + lime exposure. This study aims whether the extract of raw AN + lime relaxes chromatin structure which further facilitates the histone H3 epigenetic modifications during the initial phase of carcinogenesis. Three groups of mice (10 in each group) were used. The treated group consumed 1 mg/day/mice of AN extract with lime ad libitum in the drinking water for 60 days. The dose was increased by 1 mg every 60 days. Isolated nuclei were digested with DNaseI and 2 kb and below DNA was eluted from the agarose gel, purified and PCR amplified by using securin and GAPDH primers. Securin and E2F1 expression, pRb phosphorylation, and histone epigenetic modifications were analyzed by immunohistochemistry. The number of DNA fragments within 2 kb in size after DNaseI treatment was higher significantly in AN + lime exposed tissue samples than in the untreated one. The PCR result showed that the number of fragments bearing securin gene promoter and GAPDH gene was significantly higher in AN + lime exposed DNaseI-treated samples. Immunohistochemistry data revealed increased Rb hyperphosphorylation, upregulation of E2F1, and securin in the AN + lime-treated samples. Increased trimethylation of histone H3 lysine 4 and acetylation of H3 lysine 9 and 18 were observed globally in the treated samples. Therefore, the results of this study have led to the hypothesis that AN + lime exposure relaxes the chromatin, changes the epigenetic landscape, and deregulates the Rb–E2F1 circuit which might be involved in the upregulation of securin and some other proto-oncogenes that might play an important role in the initial phases of AN + lime mediated carcinogenesis.
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Affiliation(s)
- Pooja Swargiary
- Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya 793022 , India
| | - Nabamita Boruah
- Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya 793022 , India
| | - Chongtham Sovachandra Singh
- Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya 793022 , India
| | - Anupam Chatterjee
- Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya 793022 , India
- Department of Biotechnology, Royal School of Biosciences, The Assam Royal Global University , Guwahati, Assam 781035 , India
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14
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Irie M, Itoh J, Matsuzawa A, Ikawa M, Kiyonari H, Kihara M, Suzuki T, Hiraoka Y, Ishino F, Kaneko-Ishino T. Retrovirus-derived RTL5 and RTL6 genes are novel constituents of the innate immune system in the eutherian brain. Development 2022; 149:dev200976. [PMID: 36162816 PMCID: PMC9641642 DOI: 10.1242/dev.200976] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/14/2022] [Indexed: 09/26/2023]
Abstract
Retrotransposon Gag-like 5 [RTL5, also known as sushi-ichi-related retrotransposon homolog 8 (SIRH8)] and RTL6 (also known as SIRH3) are eutherian-specific genes presumably derived from a retrovirus and phylogenetically related to each other. They, respectively, encode a strongly acidic and extremely basic protein, and are well conserved among the eutherians. Here, we report that RTL5 and RTL6 are microglial genes with roles in the front line of innate brain immune response. Venus and mCherry knock-in mice exhibited expression of RTL5-mCherry and RTL6-Venus fusion proteins in microglia and appeared as extracellular dots and granules in the central nervous system. These proteins display a rapid response to pathogens such as lipopolysaccharide (LPS), double-stranded (ds) RNA analog and non-methylated CpG DNA, acting both cooperatively and/or independently. Experiments using Rtl6 or Rtl5 knockout mice provided additional evidence that RTL6 and RTL5 act as factors against LPS and dsRNA, respectively, in the brain, providing the first demonstration that retrovirus-derived genes play a role in the eutherian innate immune system. Finally, we propose a model emphasizing the importance of extra-embryonic tissues as the origin site of retrovirus-derived genes. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Masahito Irie
- Faculty of Nursing, School of Medicine, Tokai University, Kanagawa 259-1193, Japan
- Department of Epigenetics, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Johbu Itoh
- Department of Pathology, School of Medicine, Tokai University, Kanagawa 259-1193, Japan
| | - Ayumi Matsuzawa
- Department of Epigenetics, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
- Department of Genomic Function and Diversity, MRI, TMDU, Tokyo 113-8510, Japan
| | - Masahito Ikawa
- Animal Resource Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka 565-0871, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Miho Kihara
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Toru Suzuki
- Laboratory of Genome Editing for Biomedical Research, MRI, TMDU, Tokyo 113-8510, Japan
| | - Yuichi Hiraoka
- Laboratory of Genome Editing for Biomedical Research, MRI, TMDU, Tokyo 113-8510, Japan
- Laboratory of Molecular Neuroscience, MRI, TMDU, Tokyo 113-8510, Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Tomoko Kaneko-Ishino
- Faculty of Nursing, School of Medicine, Tokai University, Kanagawa 259-1193, Japan
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Identification and Validation of Reference Genes for Expression Analysis in Nitrogen-Fixing Bacteria under Environmental Stress. Life (Basel) 2022; 12:life12091379. [PMID: 36143415 PMCID: PMC9505014 DOI: 10.3390/life12091379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/15/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Reference genes, also referred to as housekeeping genes (HKGs), play an important role in gene expression analysis by serving as an internal control. These HKGs are usually involved in basic cellular functions and their expression should remain at relatively constant levels. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) has been used to measure gene expression. Since the normalization of gene expression data depends on baseline expression of HKGs, it is important to identify and verify true HKGs for the qRT-PCR analysis. The goal of this study is to identify and confirm HKGs in Bradyrhizobium diazoefficiens, a nitrogen fixing bacterium which forms a symbiotic relationship with soybean. By revealing such HKGs, the normalization of gene expression would be more robust, reliable, and consistent. Here, we analyzed previous gene expression data for B. diazoefficiens under multiple environmental conditions. As a result, we identified seven constitutively expressed genes among 8453 genes across all conditions. Their fold-change values were within a range of −1.25-fold < x < 1.25-fold. We adopted GeNorm, NormFinder, and comparative ∆Ct methods to rank the seven candidate genes based on their expression stability. To validate these potential HKGs, we measured their expression in various experimental conditions, such as heat, pH, and heavy metal stress. The HKGs that were found in B. diazoefficiens were also applied in closely related species by identifying their homologs.
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16
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Tilk S, Tkachenko S, Curtis C, Petrov DA, McFarland CD. Most cancers carry a substantial deleterious load due to Hill-Robertson interference. eLife 2022; 11:67790. [PMID: 36047771 PMCID: PMC9499534 DOI: 10.7554/elife.67790] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer genomes exhibit surprisingly weak signatures of negative selection1,2. This may be because selective pressures are relaxed or because genome-wide linkage prevents deleterious mutations from being removed (Hill-Robertson interference)3. By stratifying tumors by their genome-wide mutational burden, we observe negative selection (dN/dS ~ 0.56) in low mutational burden tumors, while remaining cancers exhibit dN/dS ratios ~1. This suggests that most tumors do not remove deleterious passengers. To buffer against deleterious passengers, tumors upregulate heat shock pathways as their mutational burden increases. Finally, evolutionary modeling finds that Hill-Robertson interference alone can reproduce patterns of attenuated selection and estimates the total fitness cost of passengers to be 46% per cell on average. Collectively, our findings suggest that the lack of observed negative selection in most tumors is not due to relaxed selective pressures, but rather the inability of selection to remove deleterious mutations in the presence of genome-wide linkage.
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Affiliation(s)
- Susanne Tilk
- Department of Biology, Stanford University, Stanford, United States
| | - Svyatoslav Tkachenko
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Christina Curtis
- Department of Genetics, Stanford University, Stanford, United States
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, United States
| | - Christopher D McFarland
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
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17
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Wang YP, Yang LN, Feng YY, Liu S, Zhan J. Single Amino Acid Substitution the DNA Repairing Gene Radiation-Sensitive 4 Contributes to Ultraviolet Tolerance of a Plant Pathogen. Front Microbiol 2022; 13:927139. [PMID: 35910660 PMCID: PMC9330021 DOI: 10.3389/fmicb.2022.927139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
To successfully survive and reproduce, all species constantly modify the structure and expression of their genomes to cope with changing environmental conditions including ultraviolet (UV) radiation. Thus, knowledge of species adaptation to environmental changes is a central theme of evolutionary studies which could have important implication for disease management and social-ecological sustainability in the future but is generally insufficient. Here, we investigated the evolution of UV adaptation in organisms by population genetic analysis of sequence structure, physiochemistry, transcription, and fitness variation in the radiation-sensitive 4 (RAD4) gene of the Irish potato famine pathogen Phytophthora infestans sampled from various altitudes. We found that RAD4 is a key gene determining the resistance of the pathogen to UV stress as indicated by strong phenotype-genotype-geography associations and upregulated transcription after UV exposure. We also found conserved evolution in the RAD4 gene. Only five nucleotide haplotypes corresponding to three protein isoforms generated by point mutations were detected in the 140 sequences analyzed and the mutations were constrained to the N-terminal domain of the protein. Physiochemical changes associated with non-synonymous mutations generate severe fitness penalty to mutants, which are purged out by natural selection, leading to the conserved evolution observed in the gene.
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Affiliation(s)
- Yan-Ping Wang
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
| | - Li-Na Yang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Yuan-Yuan Feng
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
| | - Songqing Liu
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
- *Correspondence: Songqing Liu,
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Jiasui Zhan,
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18
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Joshi CJ, Ke W, Drangowska-Way A, O’Rourke EJ, Lewis NE. What are housekeeping genes? PLoS Comput Biol 2022; 18:e1010295. [PMID: 35830477 PMCID: PMC9312424 DOI: 10.1371/journal.pcbi.1010295] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/25/2022] [Accepted: 06/10/2022] [Indexed: 12/26/2022] Open
Abstract
The concept of "housekeeping gene" has been used for four decades but remains loosely defined. Housekeeping genes are commonly described as "essential for cellular existence regardless of their specific function in the tissue or organism", and "stably expressed irrespective of tissue type, developmental stage, cell cycle state, or external signal". However, experimental support for the tenet that gene essentiality is linked to stable expression across cell types, conditions, and organisms has been limited. Here we use genome-scale functional genomic screens together with bulk and single-cell sequencing technologies to test this link and optimize a quantitative and experimentally validated definition of housekeeping gene. Using the optimized definition, we identify, characterize, and provide as resources, housekeeping gene lists extracted from several human datasets, and 10 other animal species that include primates, chicken, and C. elegans. We find that stably expressed genes are not necessarily essential, and that the individual genes that are essential and stably expressed can considerably differ across organisms; yet the pathways enriched among these genes are conserved. Further, the level of conservation of housekeeping genes across the analyzed organisms captures their taxonomic groups, showing evolutionary relevance for our definition. Therefore, we present a quantitative and experimentally supported definition of housekeeping genes that can contribute to better understanding of their unique biological and evolutionary characteristics.
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Affiliation(s)
- Chintan J. Joshi
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, California, United States of America
| | - Wenfan Ke
- Department of Biology and Cell Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Anna Drangowska-Way
- Department of Biology and Cell Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eyleen J. O’Rourke
- Department of Biology and Cell Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, California, United States of America
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- National Biologics Facility, Technical University of Denmark, Kongens Lyngby, Denmark
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19
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Li Z, Zhang Y, Li W, Irwin AJ, Finkel ZV. Conservation and architecture of housekeeping genes in the model marine diatom Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2022; 234:1363-1376. [PMID: 35179783 DOI: 10.1111/nph.18039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
Housekeeping genes (HKGs) are constitutively expressed with low variation across tissues/conditions. They are thought to be highly conserved and fundamental to cellular maintenance, with distinctive genomic features. Here, we identify 1505 HKGs in the unicellular marine diatom Thalassiosira pseudonana based on an RNA-seq analysis of 232 samples taken under 12 experimental conditions over 0-72 h. We identify promising internal reference genes (IRGs) for T. pseudonana from the most stably expressed HKGs. A comparative analysis indicates < 18% of HKGs in T. pseudonana have orthologs in other eukaryotes, including other diatom species. Contrary to work on human tissues, T. pseudonana HKGs are longer than non-HKGs, due to elongated introns. More ancient HKGs tend to be shorter than more recent HKGs, and expression levels of HKGs decrease more rapidly with gene length relative to non-HKGs. Our results indicate that HKGs are highly variable across the tree of life and thus unlikely to be universally fundamental for cellular maintenance. We hypothesize that the distinct genomic features of HKGs of T. pseudonana may be a consequence of selection pressures associated with high expression and low variance across conditions.
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Affiliation(s)
- Zhengke Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Weiyang University Park, Xi'an, Shaanxi, 710021, China
- Department of Oceanography, Dalhousie University, 1355 Oxford St, Halifax, NS, B3H 4R2, Canada
| | - Yong Zhang
- Department of Oceanography, Dalhousie University, 1355 Oxford St, Halifax, NS, B3H 4R2, Canada
- College of Environmental Science and Engineering, Fujian Key Laboratory of Pollution Control and Resource Recycling, Fujian Normal University, No. 8 Shangsan Road, Fuzhou, Fujian, 350007, China
| | - Wei Li
- College of Life and Environmental Sciences, Huangshan University, 39 Xihai Road, Huangshan, Anhui, 245041, China
| | - Andrew J Irwin
- Department of Mathematics & Statistics, Dalhousie University, 1355 Oxford St, Halifax, NS, B3H 4R2, Canada
| | - Zoe V Finkel
- Department of Oceanography, Dalhousie University, 1355 Oxford St, Halifax, NS, B3H 4R2, Canada
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Functional buffering via cell-specific gene expression promotes tissue homeostasis and cancer robustness. Sci Rep 2022; 12:2974. [PMID: 35194081 PMCID: PMC8863889 DOI: 10.1038/s41598-022-06813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/03/2022] [Indexed: 11/08/2022] Open
Abstract
Functional buffering that ensures biological robustness is critical for maintaining tissue homeostasis, organismal survival, and evolution of novelty. However, the mechanism underlying functional buffering, particularly in multicellular organisms, remains largely elusive. Here, we proposed that functional buffering can be mediated via expression of buffering genes in specific cells and tissues, by which we named Cell-specific Expression-BUffering (CEBU). We developed an inference index (C-score) for CEBU by computing C-scores across 684 human cell lines using genome-wide CRISPR screens and transcriptomic RNA-seq. We report that C-score-identified putative buffering gene pairs are enriched for members of the same duplicated gene family, pathway, and protein complex. Furthermore, CEBU is especially prevalent in tissues of low regenerative capacity (e.g., bone and neuronal tissues) and is weakest in highly regenerative blood cells, linking functional buffering to tissue regeneration. Clinically, the buffering capacity enabled by CEBU can help predict patient survival for multiple cancers. Our results suggest CEBU as a potential buffering mechanism contributing to tissue homeostasis and cancer robustness in humans.
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Dang Y, Wei Y, Batool W, Sun X, Li X, Zhang SH. Contribution of the Mitochondrial Carbonic Anhydrase (MoCA1) to Conidiogenesis and Pathogenesis in Magnaporthe oryzae. Front Microbiol 2022; 13:845570. [PMID: 35250959 PMCID: PMC8891501 DOI: 10.3389/fmicb.2022.845570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/24/2022] [Indexed: 01/12/2023] Open
Abstract
The interconversion of CO2 and HCO3− catalyzed by carbonic anhydrases (CAs) is a fundamental biochemical process in organisms. During mammalian–pathogen interaction, both host and pathogen CAs play vital roles in resistance and pathogenesis; during planta–pathogen interaction, however, plant CAs function in host resistance but whether pathogen CAs are involved in pathogenesis is unknown. Here, we biologically characterized the Magnaporthe oryzae CA (MoCA1). Through detecting the DsRED-tagged proteins, we observed the fusion MoCA1 in the mitochondria of M. oryzae. Together with the measurement of CA activity, we confirmed that MoCA1 is a mitochondrial zinc-binding CA. MoCA1 expression, upregulated with H2O2 or NaHCO3 treatment, also showed a drastic upregulation during conidiogenesis and pathogenesis. When MoCA1 was deleted, the mutant ΔMoCA1 was defective in conidiophore development and pathogenicity. 3,3′-Diaminobenzidine (DAB) staining indicated that more H2O2 accumulated in ΔMoCA1; accordingly, ATPase genes were downregulated and ATP content decreased in ΔMoCA1. Summarily, our data proved the involvement of the mitochondrial MoCA1 in conidiogenesis and pathogenesis in the rice blast fungus. Considering the previously reported HCO3− transporter MoAE4, we propose that MoCA1 in cooperation with MoAE4 constitutes a HCO3− homeostasis-mediated disease pathway, in which MoCA1 and MoAE4 can be a drug target for disease control.
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Affiliation(s)
- Yuejia Dang
- Center for Extreme-Environmental Microorganisms, Shenyang Agricultural University, Shenyang, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yi Wei
- Center for Extreme-Environmental Microorganisms, Shenyang Agricultural University, Shenyang, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Wajjiha Batool
- Center for Extreme-Environmental Microorganisms, Shenyang Agricultural University, Shenyang, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Xicen Sun
- Center for Extreme-Environmental Microorganisms, Shenyang Agricultural University, Shenyang, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Xiaoqian Li
- Center for Extreme-Environmental Microorganisms, Shenyang Agricultural University, Shenyang, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Shi-Hong Zhang
- Center for Extreme-Environmental Microorganisms, Shenyang Agricultural University, Shenyang, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Shi-Hong Zhang,
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22
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Li R, Ma Z, Zhou C. The First Two Complete Mitochondrial Genomes of Neoephemeridae (Ephemeroptera): Comparative Analysis and Phylogenetic Implication for Furcatergalia. Genes (Basel) 2021; 12:genes12121875. [PMID: 34946823 PMCID: PMC8702025 DOI: 10.3390/genes12121875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/05/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
Mayflies of the family Neoephemeridae are widespread in the Holarctic and Oriental regions, and its phylogenetic position is still unstable in the group Furcatergalia (mayflies with fringed gills). In the present study, we determined the complete mitogenomes of two species, namely Potamanthellus edmundsi and Pulchephemera projecta, of this family. The lengths of two mitogenomes were 15,274 bp and 16,031 bp with an A + T content of 73.38% and 73.07%, respectively. Two neoephemerid mitogenomes had a similar gene size, base composition, and codon usage of protein-coding genes (PCGs), and the sequenced gene arrangements were consistent with the putative ancestral insect mitogenomes as understood today. The most variable gene of Furcatergalia mitogenomes was ND2, while the most conserved gene was COI. Meanwhile, the analysis of selection pressures showed that ND6 and ATP8 exhibited a relaxed purifying selection, and COI was under the strongest purifying selection. Phylogenetic trees reconstructed based on two concatenated nucleotide datasets using both maximum likelihood (ML) and Bayesian inference (BI) estimations yielded robust identical topologies. These results corroborated the monophyly of seven studied families and supported the family Leptophlebiidae as being of the basal lineage of Furcatergalia. Additionally, the sister-group relationship of Caenidae and Neoephemeridae was well supported. Methodologically, our present study provides a general reference for future phylogenetic studies of Ephemeroptera at the mitogenome level.
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Affiliation(s)
- Ran Li
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (R.L.); (Z.M.)
- School of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Zhenxing Ma
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (R.L.); (Z.M.)
| | - Changfa Zhou
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (R.L.); (Z.M.)
- Correspondence:
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23
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Huang YF. Dissecting genomic determinants of positive selection with an evolution-guided regression model. Mol Biol Evol 2021; 39:6379733. [PMID: 34597406 PMCID: PMC8763110 DOI: 10.1093/molbev/msab291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In evolutionary genomics, it is fundamentally important to understand how characteristics of genomic sequences, such as gene expression level, determine the rate of adaptive evolution. While numerous statistical methods, such as the McDonald–Kreitman (MK) test, are available to examine the association between genomic features and the rate of adaptation, we currently lack a statistical approach to disentangle the independent effect of a genomic feature from the effects of other correlated genomic features. To address this problem, I present a novel statistical model, the MK regression, which augments the MK test with a generalized linear model. Analogous to the classical multiple regression model, the MK regression can analyze multiple genomic features simultaneously to infer the independent effect of a genomic feature, holding constant all other genomic features. Using the MK regression, I identify numerous genomic features driving positive selection in chimpanzees. These features include well-known ones, such as local mutation rate, residue exposure level, tissue specificity, and immune genes, as well as new features not previously reported, such as gene expression level and metabolic genes. In particular, I show that highly expressed genes may have a higher adaptation rate than their weakly expressed counterparts, even though a higher expression level may impose stronger negative selection. Also, I show that metabolic genes may have a higher adaptation rate than their nonmetabolic counterparts, possibly due to recent changes in diet in primate evolution. Overall, the MK regression is a powerful approach to elucidate the genomic basis of adaptation.
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Affiliation(s)
- Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
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24
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Skinnider MA, Scott NE, Prudova A, Kerr CH, Stoynov N, Stacey RG, Chan QWT, Rattray D, Gsponer J, Foster LJ. An atlas of protein-protein interactions across mouse tissues. Cell 2021; 184:4073-4089.e17. [PMID: 34214469 DOI: 10.1016/j.cell.2021.06.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Cellular processes arise from the dynamic organization of proteins in networks of physical interactions. Mapping the interactome has therefore been a central objective of high-throughput biology. However, the dynamics of protein interactions across physiological contexts remain poorly understood. Here, we develop a quantitative proteomic approach combining protein correlation profiling with stable isotope labeling of mammals (PCP-SILAM) to map the interactomes of seven mouse tissues. The resulting maps provide a proteome-scale survey of interactome rewiring across mammalian tissues, revealing more than 125,000 unique interactions at a quality comparable to the highest-quality human screens. We identify systematic suppression of cross-talk between the evolutionarily ancient housekeeping interactome and younger, tissue-specific modules. Rewired proteins are tightly regulated by multiple cellular mechanisms and are implicated in disease. Our study opens up new avenues to uncover regulatory mechanisms that shape in vivo interactome responses to physiological and pathophysiological stimuli in mammalian systems.
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Affiliation(s)
- Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nichollas E Scott
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Peter Doherty Institute, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Anna Prudova
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Craig H Kerr
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nikolay Stoynov
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Queenie W T Chan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - David Rattray
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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25
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Fjell AM, Grydeland H, Wang Y, Amlien IK, Bartres-Faz D, Brandmaier AM, Düzel S, Elman J, Franz CE, Håberg AK, Kietzmann TC, Kievit RA, Kremen WS, Krogsrud SK, Kühn S, Lindenberger U, Macía D, Mowinckel AM, Nyberg L, Panizzon MS, Solé-Padullés C, Sørensen Ø, Westerhausen R, Walhovd KB. The genetic organization of longitudinal subcortical volumetric change is stable throughout the lifespan. eLife 2021; 10:66466. [PMID: 34180395 PMCID: PMC8260220 DOI: 10.7554/elife.66466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/26/2021] [Indexed: 11/13/2022] Open
Abstract
Development and aging of the cerebral cortex show similar topographic organization and are governed by the same genes. It is unclear whether the same is true for subcortical regions, which follow fundamentally different ontogenetic and phylogenetic principles. We tested the hypothesis that genetically governed neurodevelopmental processes can be traced throughout life by assessing to which degree brain regions that develop together continue to change together through life. Analyzing over 6000 longitudinal MRIs of the brain, we used graph theory to identify five clusters of coordinated development, indexed as patterns of correlated volumetric change in brain structures. The clusters tended to follow placement along the cranial axis in embryonic brain development, suggesting continuity from prenatal stages, and correlated with cognition. Across independent longitudinal datasets, we demonstrated that developmental clusters were conserved through life. Twin-based genetic correlations revealed distinct sets of genes governing change in each cluster. Single-nucleotide polymorphisms-based analyses of 38,127 cross-sectional MRIs showed a similar pattern of genetic volume–volume correlations. In conclusion, coordination of subcortical change adheres to fundamental principles of lifespan continuity and genetic organization.
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Affiliation(s)
- Anders Martin Fjell
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway.,Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | - Hakon Grydeland
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Yunpeng Wang
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Inge K Amlien
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - David Bartres-Faz
- Departament de Medicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, and Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Andreas M Brandmaier
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany.,Max Planck UCL Centre for Computational Psychiatry and Ageing Research, Berlin, Germany
| | - Sandra Düzel
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Jeremy Elman
- Center for Behavioral Genomics Twin Research Laboratory, University of California, San Diego, La Jolla, United States
| | - Carol E Franz
- Center for Behavioral Genomics Twin Research Laboratory, University of California, San Diego, La Jolla, United States
| | - Asta K Håberg
- Department of Radiology and Nuclear Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Tim C Kietzmann
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Rogier Andrew Kievit
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, United Kingdom
| | - William S Kremen
- Center for Behavioral Genomics Twin Research Laboratory, University of California, San Diego, La Jolla, United States.,Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla, United States
| | - Stine K Krogsrud
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Simone Kühn
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany.,Lise Meitner Group for Environmental Neuroscience, Max Planck Institute for Human Development, Berlin, Germany
| | - Ulman Lindenberger
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany.,Max Planck UCL Centre for Computational Psychiatry and Ageing Research, Berlin, Germany
| | - Didac Macía
- Departament de Medicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, and Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Athanasia Monika Mowinckel
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Lars Nyberg
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway.,Department of Radiation Sciences, Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
| | - Matthew S Panizzon
- Center for Behavioral Genomics Twin Research Laboratory, University of California, San Diego, La Jolla, United States.,Department of Psychiatry, University of California, San Diego, La Jolla, United States
| | - Cristina Solé-Padullés
- Departament de Medicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, and Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Øystein Sørensen
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Rene Westerhausen
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway
| | - Kristine Beate Walhovd
- Center for Lifespan Changes in Brain and Cognition, Department of Psychology, University of Oslo, Oslo, Norway.,Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
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26
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Innovation, conservation, and repurposing of gene function in root cell type development. Cell 2021; 184:3333-3348.e19. [PMID: 34010619 DOI: 10.1016/j.cell.2021.04.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/19/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022]
Abstract
Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.
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27
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Wang J, Zhang YJ, Yang L, Chen XS. The complete mitochondrial genome of Trifida elongate and comparative analysis of 43 leafhoppers. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100843. [PMID: 33962105 DOI: 10.1016/j.cbd.2021.100843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/13/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
In this study, the mitochondrial genome of Trifida elongate was sequenced, and comparative analysis of T. elongate and other 43 leafhoppers was performed based on the mitochondrial genome. The mitochondrial genome sequence length of T. elongate was 14,924 bp. It comprised 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transport RNA (tRNA) genes, and 1 non-coding control region. The control region is located between the rrnS and trnI genes, is characterized by two tandem repeats and three simple sequence repeats. Phylogenetic analysis showed that T. elongate is closely related with Bolanusoides shaanxiensis and Limassolla lingchuanensis (bootstrap value = 92% and posterior probabilities = 1). Analysis of synonymous and non-synonymous nucleotide substitutions showed that Ka/Ks value of the 13 protein-coding genes of 8 subfamily leafhoppers were less than 1 ranging from 0.0315 to 0.9928. atp8 had the highest Ka/Ks value whereas cox1 had the lowest Ka/Ks value. This study provides information on the structure and sequence characteristics of the mitochondrial genome of T. elongata. Typhlocybinae is clustered with (Cicadellinae+(Idiocerinae+(Mileewinae+(Nirvaninae+(Evacanthinae+Ledrinae))))).
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Affiliation(s)
- Jing Wang
- Institute of Entomology, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory for Plant Pest Management of Mountainous Region, Guizhou University, Guiyang 550025, China
| | - Yu-Jie Zhang
- Institute of Entomology, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory for Plant Pest Management of Mountainous Region, Guizhou University, Guiyang 550025, China
| | - Lin Yang
- Institute of Entomology, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory for Plant Pest Management of Mountainous Region, Guizhou University, Guiyang 550025, China
| | - Xiang-Sheng Chen
- Institute of Entomology, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory for Plant Pest Management of Mountainous Region, Guizhou University, Guiyang 550025, China.
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28
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Wang YP, Wu EJ, Lurwanu Y, Ding JP, He DC, Waheed A, Nkurikiyimfura O, Liu ST, Li WY, Wang ZH, Yang L, Zhan J. Evidence for a synergistic effect of post-translational modifications and genomic composition of eEF-1α on the adaptation of Phytophthora infestans. Ecol Evol 2021; 11:5484-5496. [PMID: 34026022 PMCID: PMC8131795 DOI: 10.1002/ece3.7442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 12/18/2022] Open
Abstract
Genetic variation plays a fundamental role in pathogen's adaptation to environmental stresses. Pathogens with low genetic variation tend to survive and proliferate more poorly due to their lack of genotypic/phenotypic polymorphisms in responding to fluctuating environments. Evolutionary theory hypothesizes that the adaptive disadvantage of genes with low genomic variation can be compensated for structural diversity of proteins through post-translation modification (PTM) but this theory is rarely tested experimentally and its implication to sustainable disease management is hardly discussed. In this study, we analyzed nucleotide characteristics of eukaryotic translation elongation factor-1α (eEF-lα) gene from 165 Phytophthora infestans isolates and the physical and chemical properties of its derived proteins. We found a low sequence variation of eEF-lα protein, possibly attributable to purifying selection and a lack of intra-genic recombination rather than reduced mutation. In the only two isoforms detected by the study, the major one accounted for >95% of the pathogen collection and displayed a significantly higher fitness than the minor one. High lysine representation enhances the opportunity of the eEF-1α protein to be methylated and the absence of disulfide bonds is consistent with the structural prediction showing that many disordered regions are existed in the protein. Methylation, structural disordering, and possibly other PTMs ensure the ability of the protein to modify its functions during biological, cellular and biochemical processes, and compensate for its adaptive disadvantage caused by sequence conservation. Our results indicate that PTMs may function synergistically with nucleotide codes to regulate the adaptive landscape of eEF-1α, possibly as well as other housekeeping genes, in P. infestans. Compensatory evolution between pre- and post-translational phase in eEF-1α could enable pathogens quickly adapting to disease management strategies while efficiently maintaining critical roles of the protein playing in biological, cellular, and biochemical activities. Implications of these results to sustainable plant disease management are discussed.
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Affiliation(s)
- Yan-Ping Wang
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - E-Jiao Wu
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Yahuza Lurwanu
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
- Department of Crop Protection Bayero University Kano Kano Nigeria
| | - Ji-Peng Ding
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Dun-Chun He
- School of Economics and Trade Fujian Jiangxia University Fuzhou China
| | - Abdul Waheed
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Oswald Nkurikiyimfura
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Shi-Ting Liu
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Wen-Yang Li
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Zong-Hua Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction College of Life Sciences Fujian Agriculture and Forestry University Fuzhou China
- Institute of Oceanography Minjiang University Fuzhou China
| | - Lina Yang
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
- Institute of Oceanography Minjiang University Fuzhou China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden
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29
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Vancaester E, Depuydt T, Osuna-Cruz CM, Vandepoele K. Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms. Mol Biol Evol 2021; 37:3243-3257. [PMID: 32918458 DOI: 10.1093/molbev/msaa182] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favorable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A large-scale phylogeny-based prokaryotic HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. Genes derived from HGT are implicated in several processes including environmental sensing and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Five consecutive genes involved in the final synthesis of the cobalamin biosynthetic pathway, which could function as scavenging and repair genes, were detected as HGT. The full suite of these genes was detected in the cold-adapted diatom Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.
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Affiliation(s)
- Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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30
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Göktay M, Fulgione A, Hancock AM. A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes. Mol Biol Evol 2021; 38:1498-1511. [PMID: 33247723 PMCID: PMC8042739 DOI: 10.1093/molbev/msaa309] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genomic variation in the model plant Arabidopsis thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focusing on single-nucleotide polymorphisms. Conversely, structural variation has been largely ignored in spite of its potential to dramatically affect phenotype. Here, we identify 155,440 indels and structural variants ranging in size from 1 bp to 10 kb, including presence/absence variants (PAVs), inversions, and tandem duplications in 1,301 A. thaliana natural accessions from Morocco, Madeira, Europe, Asia, and North America. We show evidence for strong purifying selection on PAVs in genes, in particular for housekeeping genes and homeobox genes, and we find that PAVs are concentrated in defense-related genes (R-genes, secondary metabolites) and F-box genes. This implies the presence of a "core" genome underlying basic cellular processes and a "flexible" genome that includes genes that may be important in spatially or temporally varying selection. Further, we find an excess of intermediate frequency PAVs in defense response genes in nearly all populations studied, consistent with a history of balancing selection on this class of genes. Finally, we find that PAVs in genes involved in the cold requirement for flowering (vernalization) and drought response are strongly associated with temperature at the sites of origin.
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Affiliation(s)
- Mehmet Göktay
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrea Fulgione
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angela M Hancock
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
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31
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Hounkpe BW, Chenou F, de Lima F, De Paula E. HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets. Nucleic Acids Res 2021; 49:D947-D955. [PMID: 32663312 PMCID: PMC7778946 DOI: 10.1093/nar/gkaa609] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/08/2020] [Indexed: 12/18/2022] Open
Abstract
Housekeeping (HK) genes are constitutively expressed genes that are required for the maintenance of basic cellular functions. Despite their importance in the calibration of gene expression, as well as the understanding of many genomic and evolutionary features, important discrepancies have been observed in studies that previously identified these genes. Here, we present Housekeeping and Reference Transcript Atlas (HRT Atlas v1.0, www.housekeeping.unicamp.br) a web-based database which addresses some of the previously observed limitations in the identification of these genes, and offers a more accurate database of human and mouse HK genes and transcripts. The database was generated by mining massive human and mouse RNA-seq data sets, including 11 281 and 507 high-quality RNA-seq samples from 52 human non-disease tissues/cells and 14 healthy tissues/cells of C57BL/6 wild type mouse, respectively. User can visualize the expression and download lists of 2158 human HK transcripts from 2176 HK genes and 3024 mouse HK transcripts from 3277 mouse HK genes. HRT Atlas also offers the most stable and suitable tissue selective candidate reference transcripts for normalization of qPCR experiments. Specific primers and predicted modifiers of gene expression for some of these HK transcripts are also proposed. HRT Atlas has also been integrated with a regulatory elements resource from Epiregio server.
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Affiliation(s)
| | - Francine Chenou
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil
| | - Franciele de Lima
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil
| | - Erich Vinicius De Paula
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil
- Hematology and Hemotherapy Center, University of Campinas, Campinas, SP, Brazil
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32
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Batool W, Shabbir A, Lin L, Chen X, An Q, He X, Pan S, Chen S, Chen Q, Wang Z, Norvienyeku J. Translation Initiation Factor eIF4E Positively Modulates Conidiogenesis, Appressorium Formation, Host Invasion and Stress Homeostasis in the Filamentous Fungi Magnaporthe oryzae. FRONTIERS IN PLANT SCIENCE 2021; 12:646343. [PMID: 34220879 PMCID: PMC8244596 DOI: 10.3389/fpls.2021.646343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/21/2021] [Indexed: 05/14/2023]
Abstract
Translation initiation factor eIF4E generally mediates the recognition of the 5'cap structure of mRNA during the recruitment of the ribosomes to capped mRNA. Although the eIF4E has been shown to regulate stress response in Schizosaccharomyces pombe positively, there is no direct experimental evidence for the contributions of eIF4E to both physiological and pathogenic development of filamentous fungi. We generated Magnaporthe oryzae eIF4E (MoeIF4E3) gene deletion strains using homologous recombination strategies. Phenotypic and biochemical analyses of MoeIF4E3 defective strains showed that the deletion of MoeIF4E3 triggered a significant reduction in growth and conidiogenesis. We also showed that disruption of MoeIF4E3 partially impaired conidia germination, appressorium integrity and attenuated the pathogenicity of ΔMoeif4e3 strains. In summary, this study provides experimental insights into the contributions of the eIF4E3 to the development of filamentous fungi. Additionally, these observations underscored the need for a comprehensive evaluation of the translational regulatory machinery in phytopathogenic fungi during pathogen-host interaction progression.
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Affiliation(s)
- Wajjiha Batool
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ammarah Shabbir
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lili Lin
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaomin Chen
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiuli An
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiongjie He
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shu Pan
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuzun Chen
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinghe Chen
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Zonghua Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
- Institute of Oceanography, Minjiang University, Fuzhou, China
- *Correspondence: Zonghua Wang,
| | - Justice Norvienyeku
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
- Justice Norvienyeku, ;
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Do M, Kim H, Yeo I, Lee J, Park IA, Ryu HS, Kim Y. Clinical Application of Multiple Reaction Monitoring-Mass Spectrometry to Human Epidermal Growth Factor Receptor 2 Measurements as a Potential Diagnostic Tool for Breast Cancer Therapy. Clin Chem 2020; 66:1339-1348. [DOI: 10.1093/clinchem/hvaa178] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022]
Abstract
Abstract
Background
Human epidermal growth factor receptor 2 (HER2) is often overexpressed in breast cancer and correlates with a worse prognosis. Thus, the accurate detection of HER2 is crucial for providing the appropriate measures for patients. However, the current techniques used to detect HER2 status, immunohistochemistry and fluorescence in situ hybridization (FISH), have limitations. Specifically, FISH, which is mandatory for arbitrating 2+ cases, is time-consuming and costly. To address this shortcoming, we established a multiple reaction monitoring-mass spectrometry (MRM-MS) assay that improves on existing methods for differentiating HER2 status.
Methods
We quantified HER2 expression levels in 210 breast cancer formalin-fixed paraffin-embedded (FFPE) tissue samples by MRM-MS. We aimed to improve the accuracy and precision of HER2 quantification by simplifying the sample preparation through predicting the number of FFPE slides required to ensure an adequate amount of protein and using the expression levels of an epithelial cell-specific protein as a normalization factor when measuring HER2 expression levels.
Results
To assess the correlation between MRM-MS and IHC/FISH data, HER2 quantitative data from MRM-MS were divided by the expression levels of junctional adhesion molecule A, an epithelial cell-specific protein, prior to statistical analysis. The normalized HER2 amounts distinguished between HER2 2+/FISH-negative and 2+/FISH-positive groups (AUROC = 0.908), which could not be differentiated by IHC. In addition, all HER2 status were discriminated by MRM-MS.
Conclusions
This MRM-MS assay yields more accurate HER2 expression levels relative to immunohistochemistry and should help to guide clinicians toward the proper treatment for breast cancer patients, based on their HER2 expression.
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Affiliation(s)
- Misol Do
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyunsoo Kim
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Injoon Yeo
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jihyeon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - In Ae Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Republic of Korea
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Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution. Nat Commun 2020; 11:4459. [PMID: 32900997 PMCID: PMC7479108 DOI: 10.1038/s41467-020-18090-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
The origins of multicellular physiology are tied to evolution of gene expression. Genes can shift expression as organisms evolve, but how ancestral expression influences altered descendant expression is not well understood. To examine this, we amalgamate 1,903 RNA-seq datasets from 182 research projects, including 6 organs in 21 vertebrate species. Quality control eliminates project-specific biases, and expression shifts are reconstructed using gene-family-wise phylogenetic Ornstein-Uhlenbeck models. Expression shifts following gene duplication result in more drastic changes in expression properties than shifts without gene duplication. The expression properties are tightly coupled with protein evolutionary rate, depending on whether and how gene duplication occurred. Fluxes in expression patterns among organs are nonrandom, forming modular connections that are reshaped by gene duplication. Thus, if expression shifts, ancestral expression in some organs induces a strong propensity for expression in particular organs in descendants. Regardless of whether the shifts are adaptive or not, this supports a major role for what might be termed preadaptive pathways of gene expression evolution.
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35
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Evans P, Cox NJ, Gamazon ER. The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes. PeerJ 2020; 8:e9554. [PMID: 32765967 PMCID: PMC7380284 DOI: 10.7717/peerj.9554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/24/2020] [Indexed: 11/20/2022] Open
Abstract
The development of explanatory models of protein sequence evolution has broad implications for our understanding of cellular biology, population history, and disease etiology. Here we analyze the GTEx transcriptome resource to quantify the effect of the transcriptome on protein sequence evolution in a multi-tissue framework. We find substantial variation among the central nervous system tissues in the effect of expression variance on evolutionary rate, with highly variable genes in the cortex showing significantly greater purifying selection than highly variable genes in subcortical regions (Mann-Whitney U p = 1.4 × 10-4). The remaining tissues cluster in observed expression correlation with evolutionary rate, enabling evolutionary analysis of genes in diverse physiological systems, including digestive, reproductive, and immune systems. Importantly, the tissue in which a gene attains its maximum expression variance significantly varies (p = 5.55 × 10-284) with evolutionary rate, suggesting a tissue-anchored model of protein sequence evolution. Using a large-scale reference resource, we show that the tissue-anchored model provides a transcriptome-based approach to predicting the primary affected tissue of developmental disorders. Using gradient boosted regression trees to model evolutionary rate under a range of model parameters, selected features explain up to 62% of the variation in evolutionary rate and provide additional support for the tissue model. Finally, we investigate several methodological implications, including the importance of evolutionary-rate-aware gene expression imputation models using genetic data for improved search for disease-associated genes in transcriptome-wide association studies. Collectively, this study presents a comprehensive transcriptome-based analysis of a range of factors that may constrain molecular evolution and proposes a novel framework for the study of gene function and disease mechanism.
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Affiliation(s)
- Patrick Evans
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Eric R Gamazon
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America.,Clare Hall, University of Cambridge, Cambridge, United Kingdom.,MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom.,Data Science Institute, Vanderbilt University, Nashville, TN, United States of America
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36
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Licini C, Montalbano G, Ciapetti G, Cerqueni G, Vitale-Brovarone C, Mattioli-Belmonte M. Analysis of multiple protein detection methods in human osteoporotic bone extracellular matrix: From literature to practice. Bone 2020; 137:115363. [PMID: 32298836 DOI: 10.1016/j.bone.2020.115363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 11/15/2022]
Abstract
The punctual analysis of bone Extracellular Matrix (ECM) proteins represents a pivotal point for medical research in bone diseases like osteoporosis. Studies in this field, historically done to appreciate bone biology, were mainly conducted on animal samples and, up to today, only a few studies on protein detection in human bone are present. The challenges in bone ECM protein extraction and quantitation protocols are related to both the separation of proteins from the mineral content (i.e. hydroxyapatite) and the difficulty of avoiding protein denaturation during the extraction processes. The aim of the present work was to define appropriate protocol(s) for bone ECM protein extraction that could be applied to investigate both normal and pathological conditions. We compared and optimised some of the most used protocols present in the literature, modifying the protein precipitation method, the buffer used for resuspension and/or the volume of reagent used. Bradford and BCA assays and Western Blotting were used to evaluate the variations in the total protein recovery and the amount of selected proteins (Type I Collagen, TGF-β, IGF-1, Decorin, Osteopontin, Bone Sialoprotein-2 and Osteocalcin). Collectively, we were capable to draw-up two single-extract protocols with optimal recovery and ideal protein content, that can be used for a detailed analysis of ECM proteins in pathological bone samples. Time-consuming multi-extract procedures, optimised in their precipitation methods, are however crucial for a precise detection of specific proteins, like osteocalcin. As the matter of fact, also the demineralization processes, commonly suggested and performed in several protocols, could hinder an accurate protein detection, thus inherently affecting the study of a pathological bone ECM. This study represents a starting point for the definition of appropriate strategies in the study of bone extracellular matrix proteins involved in the onset and maintenance of bone diseases, as well as a tool for the development of customized scaffolds capable to modulate a proper feedback loop in bone remodelling, altered in case of diseases like osteoporosis.
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Affiliation(s)
- Caterina Licini
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica delle Marche, Via Tronto 10/A, 60126 Ancona, Italy
| | - Giorgia Montalbano
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Gabriela Ciapetti
- Laboratorio di Fisiopatologia Ortopedica e Medicina Rigenerativa, Istituto Ortopedico Rizzoli, IRCCS, Via di Barbiano 1/10, 40136 Bologna, Italy
| | - Giorgia Cerqueni
- Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica delle Marche, Via Tronto 10/A, 60126 Ancona, Italy
| | - Chiara Vitale-Brovarone
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
| | - Monica Mattioli-Belmonte
- Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica delle Marche, Via Tronto 10/A, 60126 Ancona, Italy
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37
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Cheema AS, Stinson LF, Lai CT, Geddes DT, Payne MS. DNA extraction method influences human milk bacterial profiles. J Appl Microbiol 2020; 130:142-156. [PMID: 32654260 DOI: 10.1111/jam.14780] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022]
Abstract
AIMS To evaluate four DNA extraction methods to elucidate the most effective method for bacterial DNA recovery from human milk (HM). METHODS AND RESULTS Human milk DNA was extracted using the following methods: (i) Qiagen MagAttract Microbial DNA Isolation Kit (kit QM), (ii) Norgen Milk Bacterial DNA Isolation Kit (kit NM), (iii) Qiagen MagAttract Microbiome DNA/RNA Isolation Kit (kit MM) and (iv) TRIzol LS Reagent (method LS). The full-length 16S rRNA gene was sequenced. Kits MM and method LS were unable to extract detectable levels of DNA in 9/11 samples. Detectable levels of DNA were recovered from all samples using kits NM (mean = 0·68 ng μl-1 ) and QM (mean = 0·55 ng μl-1 ). For kits NM and QM, the greatest number of reads were associated with Staphylococcus epidermidis, Streptococcus vestibularis, Propionibacterium acnes, Veillonella dispar and Rothia mucilaginosa. Contamination profiles varied substantially between kits, with one bacterial species detected in negative extraction controls generated with kit QM and six with kit NM. CONCLUSIONS Kit QM is the most suitable of the kits tested for the extraction of bacterial DNA from human milk. SIGNIFICANCE AND IMPACT OF THE STUDY Choice of extraction method impacts the efficiency of bacterial DNA extraction from human milk and the resultant bacterial community profiles generated from these samples.
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Affiliation(s)
- A S Cheema
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - L F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - C T Lai
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - D T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - M S Payne
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, WA, Australia
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38
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Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D. Trends Genet 2020; 36:967-980. [PMID: 32713597 DOI: 10.1016/j.tig.2020.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
In eukaryotes, DNA replication progresses through a finely orchestrated temporal and spatial program. The 3D genome structure and nuclear architecture have recently emerged as fundamental determinants of the replication program. Factors with established roles in replication have been recognized as genome organization regulators. Exploiting paradigms from yeasts and mammals, we discuss how DNA replication is regulated in time and space through DNA-associated trans-acting factors, diffusible limiting replication initiation factors, higher-order chromatin folding, dynamic origin localization, and specific nuclear microenvironments. We present an integrated model for the regulation of DNA replication in 3D and highlight the importance of accurate spatio-temporal regulation of DNA replication in physiology and disease.
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39
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Abstract
Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly optimized for their specific functions. The 20th-century modern synthesis, structural biology, and the central dogma explained the machinery of evolution, and nearly neutral theory explained how selection competes with random fixation dynamics that produce molecular clocks essential e.g. for dating evolutionary histories. However, quantitative proteomics revealed that selection pressures not relating to optimal function play much larger roles than previously thought, acting perhaps most importantly via protein expression levels. This paper first summarizes recent progress in the 21st century toward recovering this universal selection pressure. Then, the paper argues that proteome cost minimization is the dominant, underlying 'non-function' selection pressure controlling most of the evolution of already functionally adapted living systems. A theory of proteome cost minimization is described and argued to have consequences for understanding evolutionary trade-offs, aging, cancer, and neurodegenerative protein-misfolding diseases.
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40
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Wang YJ, Wang HL, Wang XW, Liu SS. Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects. INSECTS 2020; 11:insects11060326. [PMID: 32466547 PMCID: PMC7349267 DOI: 10.3390/insects11060326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Females and males often differ obviously in morphology and behavior, and the differences between sexes are the result of natural selection and/or sexual selection. To a great extent, the differences between the two sexes are the result of differential gene expression. In haplodiploid insects, this phenomenon is obvious, since males develop from unfertilized zygotes and females develop from fertilized zygotes. Whiteflies of the Bemisia tabaci species complex are typical haplodiploid insects, and some species of this complex are important pests of many crops worldwide. Here, we report the transcriptome profiles of males and females in three species of this whitefly complex. Between-species comparisons revealed that non-sex-biased genes display higher variation than male-biased or female-biased genes. Sex-biased genes evolve at a slow rate in protein coding sequences and gene expression and have a pattern of evolution that differs from those of social haplodiploid insects and diploid animals. Genes with high evolutionary rates are more related to non-sex-biased traits-such as nutrition, immune system, and detoxification-than to sex-biased traits, indicating that the evolution of protein coding sequences and gene expression has been mainly driven by non-sex-biased traits.
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41
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Alvarez-Ponce D, Aguilar-Rodríguez J, Fares MA. Molecular Chaperones Accelerate the Evolution of Their Protein Clients in Yeast. Genome Biol Evol 2020; 11:2360-2375. [PMID: 31297528 PMCID: PMC6735891 DOI: 10.1093/gbe/evz147] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2019] [Indexed: 12/23/2022] Open
Abstract
Protein stability is a major constraint on protein evolution. Molecular chaperones, also known as heat-shock proteins, can relax this constraint and promote protein evolution by diminishing the deleterious effect of mutations on protein stability and folding. This effect, however, has only been stablished for a few chaperones. Here, we use a comprehensive chaperone–protein interaction network to study the effect of all yeast chaperones on the evolution of their protein substrates, that is, their clients. In particular, we analyze how yeast chaperones affect the evolutionary rates of their clients at two very different evolutionary time scales. We first study the effect of chaperone-mediated folding on protein evolution over the evolutionary divergence of Saccharomyces cerevisiae and S. paradoxus. We then test whether yeast chaperones have left a similar signature on the patterns of standing genetic variation found in modern wild and domesticated strains of S. cerevisiae. We find that genes encoding chaperone clients have diverged faster than genes encoding non-client proteins when controlling for their number of protein–protein interactions. We also find that genes encoding client proteins have accumulated more intraspecific genetic diversity than those encoding non-client proteins. In a number of multivariate analyses, controlling by other well-known factors that affect protein evolution, we find that chaperone dependence explains the largest fraction of the observed variance in the rate of evolution at both evolutionary time scales. Chaperones affecting rates of protein evolution mostly belong to two major chaperone families: Hsp70s and Hsp90s. Our analyses show that protein chaperones, by virtue of their ability to buffer destabilizing mutations and their role in modulating protein genotype–phenotype maps, have a considerable accelerating effect on protein evolution.
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Affiliation(s)
- David Alvarez-Ponce
- Biology Department, University of Nevada, Reno.,Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
| | - José Aguilar-Rodríguez
- Department of Biology, Stanford University, CA.,Department of Chemical and Systems Biology, Stanford University School of Medicine, CA
| | - Mario A Fares
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain.,Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Ireland
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42
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Karin BR, Gamble T, Jackman TR. Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements. Mol Biol Evol 2020; 37:904-922. [PMID: 31710677 PMCID: PMC7038749 DOI: 10.1093/molbev/msz263] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
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Affiliation(s)
- Benjamin R Karin
- Department of Biology, Villanova University, Villanova, PA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Milwaukee Public Museum, Milwaukee, WI
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN
| | - Todd R Jackman
- Department of Biology, Villanova University, Villanova, PA
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Cheng X, Garcés-Carrera S, Whitworth RJ, Fellers JP, Park Y, Chen MS. A Horizontal Gene Transfer Led to the Acquisition of a Fructan Metabolic Pathway in a Gall Midge. ACTA ACUST UNITED AC 2020; 4:e1900275. [PMID: 32293157 DOI: 10.1002/adbi.201900275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/30/2020] [Indexed: 01/19/2023]
Abstract
Animals are thought to use only glucose polymers (glycogen) as energy reserve, whereas both glucose (starch) and fructose polymers (fructans) are used by microbes and plants. Here, it is reported that the gall midge Mayetiola destructor, and likely other herbivorous animal species, gained the ability to utilize dietary fructans directly as storage polysaccharides by a single horizontal gene transfer (HGT) of bacterial levanase/inulinase gene followed by gene expansion and differentiation. Multiple genes encoding levanases/inulinases have their origin in a single HGT event from a bacterium and they show high expression levels and enzymatic activities in different tissues of the gall midge, including nondigestive fat bodies and eggs, both of which contained significant amounts of fructans. This study provides evidence that animals can also use fructans as energy reserve by incorporating bacterial genes in their genomes.
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Affiliation(s)
- Xiaoyan Cheng
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
| | | | - Robert Jeff Whitworth
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
| | - John P Fellers
- Hard Winter Wheat Genetics Research Unit, Center for Grain and Animal Health Research Center, USDA-ARS, 4008 Throckmorton, Manhattan, KS, 66506, USA
| | - Yoonseong Park
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
| | - Ming-Shun Chen
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
- Hard Winter Wheat Genetics Research Unit, Center for Grain and Animal Health Research Center, USDA-ARS, 4008 Throckmorton, Manhattan, KS, 66506, USA
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44
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The strength and pattern of natural selection on gene expression in rice. Nature 2020; 578:572-576. [PMID: 32051590 DOI: 10.1038/s41586-020-1997-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 12/13/2019] [Indexed: 01/12/2023]
Abstract
Levels of gene expression underpin organismal phenotypes1,2, but the nature of selection that acts on gene expression and its role in adaptive evolution remain unknown1,2. Here we assayed gene expression in rice (Oryza sativa)3, and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts4,5. Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions. Overall, more transcripts are conditionally neutral (2.83%) than are antagonistically pleiotropic6 (0.04%), and transcripts that display lower levels of expression and stochastic noise7-9 and higher levels of plasticity9 are under stronger selection. Selection strength was further weakly negatively associated with levels of cis-regulation and network connectivity9. Our multivariate analysis suggests that selection acts on the expression of photosynthesis genes4,5, but that the efficacy of selection is genetically constrained under drought conditions10. Drought selected for earlier flowering11,12 and a higher expression of OsMADS18 (Os07g0605200), which encodes a MADS-box transcription factor and is a known regulator of early flowering13-marking this gene as a drought-escape gene11,12. The ability to estimate selection strengths provides insights into how selection can shape molecular traits at the core of gene action.
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45
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Wilson J, Staley JM, Wyckoff GJ. Extinction of chromosomes due to specialization is a universal occurrence. Sci Rep 2020; 10:2170. [PMID: 32034231 PMCID: PMC7005762 DOI: 10.1038/s41598-020-58997-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/20/2020] [Indexed: 11/09/2022] Open
Abstract
The human X and Y chromosomes evolved from a pair of autosomes approximately 180 million years ago. Despite their shared evolutionary origin, extensive genetic decay has resulted in the human Y chromosome losing 97% of its ancestral genes while gene content and order remain highly conserved on the X chromosome. Five 'stratification' events, most likely inversions, reduced the Y chromosome's ability to recombine with the X chromosome across the majority of its length and subjected its genes to the erosive forces associated with reduced recombination. The remaining functional genes are ubiquitously expressed, functionally coherent, dosage-sensitive genes, or have evolved male-specific functionality. It is unknown, however, whether functional specialization is a degenerative phenomenon unique to sex chromosomes, or if it conveys a potential selective advantage aside from sexual antagonism. We examined the evolution of mammalian orthologs to determine if the selective forces that led to the degeneration of the Y chromosome are unique in the genome. The results of our study suggest these forces are not exclusive to the Y chromosome, and chromosomal degeneration may have occurred throughout our evolutionary history. The reduction of recombination could additionally result in rapid fixation through isolation of specialized functions resulting in a cost-benefit relationship during times of intense selective pressure.
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Affiliation(s)
- Jason Wilson
- University of Missouri-Kansas City School of Medicine, Department of Biomedical and Health Informatics, Kansas City, 64108, Missouri, USA.
| | - Joshua M Staley
- Kansas State University College of Veterinary Medicine, Department of Diagnostic Medicine/Pathobiology, Olathe, 66061, Kansas, USA
| | - Gerald J Wyckoff
- University of Missouri-Kansas City School of Medicine, Department of Biomedical and Health Informatics, Kansas City, 64108, Missouri, USA.,Kansas State University College of Veterinary Medicine, Department of Diagnostic Medicine/Pathobiology, Olathe, 66061, Kansas, USA.,University of Missouri-Kansas City School of Biological and Chemical Sciences, Department of Molecular Biology and Biochemistry, Kansas City, 64108, Missouri, USA
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46
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Muro EM, Ibn-Salem J, Andrade-Navarro MA. The distributions of protein coding genes within chromatin domains in relation to human disease. Epigenetics Chromatin 2019; 12:72. [PMID: 31805995 PMCID: PMC6894242 DOI: 10.1186/s13072-019-0317-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background Our understanding of the nuclear chromatin structure has increased hugely during the last years mainly as a consequence of the advances in chromatin conformation capture methods like Hi-C. The unprecedented resolution of genome-wide interaction maps shows functional consequences that extend the initial thought of an efficient DNA packaging mechanism: gene regulation, DNA repair, chromosomal translocations and evolutionary rearrangements seem to be only the peak of the iceberg. One key concept emerging from this research is the topologically associating domains (TADs) whose functional role in gene regulation and their association with disease is not fully untangled. Results We report that the lower the number of protein coding genes inside TADs, the higher the tendency of those genes to be associated with disease (p-value = 4 × \documentclass[12pt]{minimal}
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\begin{document}$$10^{-54}$$\end{document}10-54). Moreover, housekeeping genes are less associated with disease than other genes. Accordingly, they are depleted in TADs containing less than three protein coding genes (p-value = 3.9 × \documentclass[12pt]{minimal}
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\begin{document}$$10^{-34}$$\end{document}10-34). We observed that TADs with higher ratios of enhancers versus genes contained higher numbers of disease-associated genes. We interpret these results as an indication that sharing enhancers among genes reduces their involvement in disease. Larger TADs would have more chances to accommodate many genes and select for enhancer sharing along evolution. Conclusions Genes associated with human disease do not distribute randomly over the TADs. Our observations suggest general rules that confer functional stability to TADs, adding more evidence to the role of TADs as regulatory units.
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Affiliation(s)
- Enrique M Muro
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Jonas Ibn-Salem
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
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Guo Y, Peng Z, Liu J, Yuan N, Wang Z, Du J. Systematic Comparisons of Positively Selected Genes between Gossypium arboreum and Gossypium raimondii Genomes. Curr Bioinform 2019. [DOI: 10.2174/1574893614666190227151013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Studies of Positively Selected Genes (PSGs) in microorganisms and
mammals have provided insights into the dynamics of genome evolution and the genetic basis of
differences between species by using whole genome-wide scans. Systematic investigations and
comparisons of PSGs in plants, however, are still limited.
Objective:
A systematic comparison of PSGs between the genomes of two cotton species,
Gossypium arboreum (G. arboreum) and G. raimondii, will give the key answer for revealing
molecular evolutionary differences in plants.
Methods:
Genome sequences of G. arboreum and G. raimondii were compared, including Whole
Genome Duplication (WGD) events and genomic features such as gene number, gene length,
codon bias index, evolutionary rate, number of expressed genes, and retention of duplicated
copies.
Results:
Unlike the PSGs in G. raimondii, G. arboreum comprised more PSGs, smaller gene size
and fewer expressed gene. In addition, the PSGs evolved at a higher rate of synonymous
substitutions, but were subjected to lower selection pressure. The PSGs in G. arboreum were also
retained with a lower number of duplicate gene copies than G. raimondii after a single WGD event
involving Gossypium.
Conclusion:
These data indicate that PSGs in G. arboreum and G. raimondii differ not only in
Ka/Ks, but also in their evolutionary, structural, and expression properties, indicating that
divergence of G. arboreum and G. raimondii was associated with differences in PSGs in terms of
evolutionary rates, gene length, expression patterns, and WGD retention in Gossypium.
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Affiliation(s)
- Yue Guo
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhen Peng
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Liu
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Na Yuan
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhen Wang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jianchang Du
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Lin Y, Ghazanfar S, Strbenac D, Wang A, Patrick E, Lin DM, Speed T, Yang JYH, Yang P. Evaluating stably expressed genes in single cells. Gigascience 2019; 8:giz106. [PMID: 31531674 PMCID: PMC6748759 DOI: 10.1093/gigascience/giz106] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 05/22/2019] [Accepted: 08/09/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Single-cell RNA-seq (scRNA-seq) profiling has revealed remarkable variation in transcription, suggesting that expression of many genes at the single-cell level is intrinsically stochastic and noisy. Yet, on the cell population level, a subset of genes traditionally referred to as housekeeping genes (HKGs) are found to be stably expressed in different cell and tissue types. It is therefore critical to question whether stably expressed genes (SEGs) can be identified on the single-cell level, and if so, how can their expression stability be assessed? We have previously proposed a computational framework for ranking expression stability of genes in single cells for scRNA-seq data normalization and integration. In this study, we perform detailed evaluation and characterization of SEGs derived from this framework. RESULTS Here, we show that gene expression stability indices derived from the early human and mouse development scRNA-seq datasets and the "Mouse Atlas" dataset are reproducible and conserved across species. We demonstrate that SEGs identified from single cells based on their stability indices are considerably more stable than HKGs defined previously from cell populations across diverse biological systems. Our analyses indicate that SEGs are inherently more stable at the single-cell level and their characteristics reminiscent of HKGs, suggesting their potential role in sustaining essential functions in individual cells. CONCLUSIONS SEGs identified in this study have immediate utility both for understanding variation and stability of single-cell transcriptomes and for practical applications such as scRNA-seq data normalization. Our framework for calculating gene stability index, "scSEGIndex," is incorporated into the scMerge Bioconductor R package (https://sydneybiox.github.io/scMerge/reference/scSEGIndex.html) and can be used for identifying genes with stable expression in scRNA-seq datasets.
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Affiliation(s)
- Yingxin Lin
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
| | - Shila Ghazanfar
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Dario Strbenac
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
| | - Andy Wang
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Ellis Patrick
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
- Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, Australia
| | - David M Lin
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Terence Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jean Y H Yang
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
| | - Pengyi Yang
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
- Computational Systems Biology Group, Children’s Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
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A quantitative model of human neurodegenerative diseases involving protein aggregation. Neurobiol Aging 2019; 80:46-55. [DOI: 10.1016/j.neurobiolaging.2019.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/12/2022]
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50
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Wei K, Ma L, Zhang T. Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend. PeerJ 2019; 7:e7204. [PMID: 31275764 PMCID: PMC6598670 DOI: 10.7717/peerj.7204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/29/2019] [Indexed: 02/04/2023] Open
Abstract
It is vital to understand the conservation and evolution of gene promoter sequences in order to understand environmental adaptation. The level of promoter conservation varies greatly between housekeeping (HK) and tissue-specific (TS) genes, denoting differences in the strength of the evolutionary constraints. Here, we analyzed promoter conservation and evolution to exploit differential regulation between HK and TS genes. The analysis of conserved elements showed CpG islands, short tandem repeats and G-quadruplex sequences are highly enriched in HK promoters relative to TS promoters. In addition, the type and density of regulatory motifs in TS promoters are much higher than HK promoters, indicating that TS genes show more complex regulatory patterns than HK genes. Moreover, the evolutionary dynamics of promoters showed similar evolutionary trend to coding sequences. HK promoters suffer more stringent selective pressure in the long-term evolutionary process. HK genes tend to show increased upstream sequence conservation due to stringent selection pressures acting on the promoter regions. The specificity of TS gene expression may be due to complex regulatory motifs acting in different tissues or conditions. The results from this study can be used to deepen our understanding of adaptive evolution.
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Affiliation(s)
- Kai Wei
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China.,Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Byern, Germany
| | - Lei Ma
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Tingting Zhang
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
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