251
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Hendelman A, Zebell S, Rodriguez-Leal D, Dukler N, Robitaille G, Wu X, Kostyun J, Tal L, Wang P, Bartlett ME, Eshed Y, Efroni I, Lippman ZB. Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection. Cell 2021; 184:1724-1739.e16. [PMID: 33667348 DOI: 10.1016/j.cell.2021.02.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 01/09/2023]
Abstract
Divergence of gene function is a hallmark of evolution, but assessing functional divergence over deep time is not trivial. The few alleles available for cross-species studies often fail to expose the entire functional spectrum of genes, potentially obscuring deeply conserved pleiotropic roles. Here, we explore the functional divergence of WUSCHEL HOMEOBOX9 (WOX9), suggested to have species-specific roles in embryo and inflorescence development. Using a cis-regulatory editing drive system, we generate a comprehensive allelic series in tomato, which revealed hidden pleiotropic roles for WOX9. Analysis of accessible chromatin and conserved cis-regulatory sequences identifies the regions responsible for this pleiotropic activity, the functions of which are conserved in groundcherry, a tomato relative. Mimicking these alleles in Arabidopsis, distantly related to tomato and groundcherry, reveals new inflorescence phenotypes, exposing a deeply conserved pleiotropy. We suggest that targeted cis-regulatory mutations can uncover conserved gene functions and reduce undesirable effects in crop improvement.
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Affiliation(s)
- Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Sophia Zebell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Noah Dukler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xuelin Wu
- The Salk Institute for Biological Research, San Diego, CA, USA
| | - Jamie Kostyun
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Lior Tal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Peipei Wang
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot, Israel
| | | | - Yuval Eshed
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Idan Efroni
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot, Israel.
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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252
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Hu J, Wuitchik SJS, Barry TN, Jamniczky HA, Rogers SM, Barrett RDH. Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus). Genetics 2021; 217:1-15. [PMID: 33683369 PMCID: PMC8045681 DOI: 10.1093/genetics/iyab001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24-35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.
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Affiliation(s)
- Juntao Hu
- National Observation and Research Station for Yangtze Estuarine Wetland Ecosystems, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai 200438, China
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
| | - Sara J S Wuitchik
- Informatics Group, Harvard University, Cambridge, MA 02138, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Tegan N Barry
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
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253
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Strable J. Developmental genetics of maize vegetative shoot architecture. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:19. [PMID: 37309417 PMCID: PMC10236122 DOI: 10.1007/s11032-021-01208-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/25/2021] [Indexed: 06/13/2023]
Abstract
More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01208-1.
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Affiliation(s)
- Josh Strable
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
- Present Address: Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 USA
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254
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Wos G, Bohutínská M, Nosková J, Mandáková T, Kolář F. Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1211-1224. [PMID: 33258160 DOI: 10.1111/tpj.15105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/13/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Parallel adaptation results from the independent evolution of similar traits between closely related lineages and allows us to test to what extent evolution is repeatable. Similar gene expression changes are often detected but the identity of genes shaped by parallel selection and the causes of expression parallelism remain largely unknown. By comparing genomes and transcriptomes of four distinct foothill-alpine population pairs across four treatments, we addressed the genetic underpinnings, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of eight populations of Arabidopsis arenosa were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in differential gene expression between the foothill and alpine ecotypes was quantified by RNA-seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (i.e., gene-environment interaction, GEI). In spite of global non-parallel patterns transcriptome wide, we found significant parallelism in gene expression at the level of individual loci with an over-representation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI, indicating a shared differential response of the originally foothill versus alpine populations to environmental variation across mountain regions. A fraction of genes showing expression parallelism also encompassed parallel outliers for genomic differentiation, with greater enrichment of such variants in cis-regulatory elements in some mountain regions. In summary, our results suggest frequent evolutionary repeatability in gene expression changes associated with the colonization of a challenging environment that combines constitutive expression differences and plastic interaction with the surrounding environment.
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Affiliation(s)
- Guillaume Wos
- Department of Botany, Charles University, Prague, 128 01, Czech Republic
| | - Magdalena Bohutínská
- Department of Botany, Charles University, Prague, 128 01, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Jana Nosková
- Department of Botany, Charles University, Prague, 128 01, Czech Republic
| | - Terezie Mandáková
- Central European Institute of Technology and Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Filip Kolář
- Department of Botany, Charles University, Prague, 128 01, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
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255
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Semenov GA, Linck E, Enbody ED, Harris RB, Khaydarov DR, Alström P, Andersson L, Taylor SA. Asymmetric introgression reveals the genetic architecture of a plumage trait. Nat Commun 2021; 12:1019. [PMID: 33589637 PMCID: PMC7884433 DOI: 10.1038/s41467-021-21340-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/20/2021] [Indexed: 01/04/2023] Open
Abstract
Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression. Hybrid zones are windows into the evolutionary process. Semenov et al. find that the head plumage differences between white wagtail subspecies have a simple genetic basis involving two small genetic regions, in which partially dominant and epistatic interactions help to explain how this sexual signal has become decoupled from other plumage traits.
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Affiliation(s)
- Georgy A Semenov
- Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Ethan Linck
- UNM Biology, University of New Mexico, Albuquerque, NM, Mexico
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Scott A Taylor
- Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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256
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Pespeni MH, Moczek AP. Signals of selection beyond bottlenecks between exotic populations of the bull-headed dung beetle, Onthophagus taurus. Evol Dev 2021; 23:86-99. [PMID: 33522675 DOI: 10.1111/ede.12367] [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: 07/29/2019] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 11/27/2022]
Abstract
Colonization of new environments can lead to population bottlenecks and rapid phenotypic evolution that could be due to neutral and selective processes. Exotic populations of the bull-headed dung beetle (Onthophagus taurus) have differentiated in opposite directions from native beetles in male horn-to-body size allometry and female fecundity. Here we test for genetic and transcriptional differences among two exotic and one native O. taurus populations after three generations in common garden conditions. We sequenced RNA from 24 individuals for each of the three populations including both sexes, and spanning four developmental stages for the two exotic, differentiated populations. Identifying 270,400 high-quality single nucleotide polymorphisms, we revealed a strong signal of genetic differentiation between the three populations, and evidence of recent bottlenecks within and an excess of outlier loci between exotic populations. Differences in gene expression between populations were greatest in prepupae and early adult life stages, stages during which differences in male horn development and female fecundity manifest. Finally, genes differentially expressed between exotic populations also had greater genetic differentiation and performed functions related to chitin biosynthesis and nutrient sensing, possibly underlying allometry and fecundity trait divergences. Our results suggest that beyond bottlenecks, recent introductions have led to genetic and transcriptional differences in genes correlated with observed phenotypic differences.
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Affiliation(s)
- Melissa H Pespeni
- Department of Biology, University of Vermont, Burlington, Vermont, USA.,Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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257
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LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate. Nat Commun 2021; 12:626. [PMID: 33504790 PMCID: PMC7840934 DOI: 10.1038/s41467-020-20883-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/22/2020] [Indexed: 01/31/2023] Open
Abstract
Master transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet little is known about pioneer transcription factors in this kingdom. Here, we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1. Upon binding, LFY 'unlocks' chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between LFY and animal pioneer transcription factor.
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258
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Margres MJ, Rautsaw RM, Strickland JL, Mason AJ, Schramer TD, Hofmann EP, Stiers E, Ellsworth SA, Nystrom GS, Hogan MP, Bartlett DA, Colston TJ, Gilbert DM, Rokyta DR, Parkinson CL. The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype. Proc Natl Acad Sci U S A 2021; 118:e2014634118. [PMID: 33468678 PMCID: PMC7848695 DOI: 10.1073/pnas.2014634118] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Variation in gene regulation is ubiquitous, yet identifying the mechanisms producing such variation, especially for complex traits, is challenging. Snake venoms provide a model system for studying the phenotypic impacts of regulatory variation in complex traits because of their genetic tractability. Here, we sequence the genome of the Tiger Rattlesnake, which possesses the simplest and most toxic venom of any rattlesnake species, to determine whether the simple venom phenotype is the result of a simple genotype through gene loss or a complex genotype mediated through regulatory mechanisms. We generate the most contiguous snake-genome assembly to date and use this genome to show that gene loss, chromatin accessibility, and methylation levels all contribute to the production of the simplest, most toxic rattlesnake venom. We provide the most complete characterization of the venom gene-regulatory network to date and identify key mechanisms mediating phenotypic variation across a polygenic regulatory network.
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Affiliation(s)
- Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Biology, University of South Alabama, Mobile, AL 36688
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Tristan D Schramer
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erin Stiers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
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259
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McGirr JA, Martin CH. Few Fixed Variants between Trophic Specialist Pupfish Species Reveal Candidate Cis-Regulatory Alleles Underlying Rapid Craniofacial Divergence. Mol Biol Evol 2021; 38:405-423. [PMID: 32877534 PMCID: PMC7826174 DOI: 10.1093/molbev/msaa218] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Investigating closely related species that rapidly evolved divergent feeding morphology is a powerful approach to identify genetic variation underlying variation in complex traits. This can also lead to the discovery of novel candidate genes influencing natural and clinical variation in human craniofacial phenotypes. We combined whole-genome resequencing of 258 individuals with 50 transcriptomes to identify candidate cis-acting genetic variation underlying rapidly evolving craniofacial phenotypes within an adaptive radiation of Cyprinodon pupfishes. This radiation consists of a dietary generalist species and two derived trophic niche specialists-a molluscivore and a scale-eating species. Despite extensive morphological divergence, these species only diverged 10 kya and produce fertile hybrids in the laboratory. Out of 9.3 million genome-wide SNPs and 80,012 structural variants, we found very few alleles fixed between species-only 157 SNPs and 87 deletions. Comparing gene expression across 38 purebred F1 offspring sampled at three early developmental stages, we identified 17 fixed variants within 10 kb of 12 genes that were highly differentially expressed between species. By measuring allele-specific expression in F1 hybrids from multiple crosses, we found that the majority of expression divergence between species was explained by trans-regulatory mechanisms. We also found strong evidence for two cis-regulatory alleles affecting expression divergence of two genes with putative effects on skeletal development (dync2li1 and pycr3). These results suggest that SNPs and structural variants contribute to the evolution of novel traits and highlight the utility of the San Salvador Island pupfish system as an evolutionary model for craniofacial development.
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Affiliation(s)
- Joseph A McGirr
- Environmental Toxicology Department, University of California, Davis, CA
| | - Christopher H Martin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA
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260
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Liu C, Huang R, Wang L, Liang G. Functional Identification of EjGIF1 in Arabidopsis and Preliminary Analysis of Its Regulatory Mechanisms in the Formation of Triploid Loquat Leaf Heterosis. FRONTIERS IN PLANT SCIENCE 2021; 11:612055. [PMID: 33510754 PMCID: PMC7835675 DOI: 10.3389/fpls.2020.612055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Although several results have been obtained in triploid loquat heterosis (i.e., leaf size of triploid loquat) studies in the past years, the underlying mechanisms of the heterosis are still largely unknown, especially the regulation effects of one specific gene on the corresponding morphology heterosis. In this study, we sought to further illustrate the regulatory mechanisms of one specific gene on the leaf size heterosis of triploid loquats. A leaf size development-related gene (EjGIF1) and its promoter were successfully cloned. Ectopic expression of EjGIF1 in Arabidopsis showed that the leaf size of transgenic plantlets was larger than that of WTs, and the transgenic plantlets had more leaves than WTs. Quantitative Reverse Transcription PCR (qRT-PCR) showed that the expression level of EjGIF1 showed an AHP expression pattern in most of the hybrids, and this was consistent with our previous phenotype observations. Structure analysis of EjGIF1 promoter showed that there were significantly more light-responsive elements than other elements. To further ascertain the regulatory mechanisms of EjGIF1 on triploid loquat heterosis, the methylation levels of EjGIF1 promoter in different ploidy loquats were analyzed by using bisulfite sequencing. Surprisingly, the total methylation levels of EjGIF1 promoter in triploid showed a decreasing trend compared with the mid-parent value (MPV), and this was also consistent with the qRT-PCR results of EjGIF1. Taken together, our results suggested that EjGIF1 played an important role in promoting leaf size development of loquat, and demethylation of EjGIF1 promoter in triploid loquats caused EjGIF1 to exhibit over-dominance expression pattern and then further to promote leaf heterosis formation. In conclusion, EjGIF1 played an important role in the formation of triploid loquat leaf size heterosis.
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Affiliation(s)
- Chao Liu
- College of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Renwei Huang
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
| | - Lingli Wang
- Technical Advice Station of Economic Crop, Chongqing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
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261
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Hatleberg WL, Hinman VF. Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change. Curr Top Dev Biol 2021; 141:39-73. [DOI: 10.1016/bs.ctdb.2020.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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262
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Dussex N, Kutschera VE, Wiberg RAW, Parker DJ, Hunt GR, Gray RD, Rutherford K, Abe H, Fleischer RC, Ritchie MG, Rutz C, Wolf JBW, Gemmell NJ. A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows. Mol Ecol 2020; 30:973-986. [PMID: 33305388 DOI: 10.1111/mec.15775] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 12/30/2022]
Abstract
Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.
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Affiliation(s)
- Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Department of Bioinformatics and Genetics, Centre for Palaeogenetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Verena E Kutschera
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - R Axel W Wiberg
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.,Department of Environmental Sciences, Evolutionary Biology, University of Basel, Basel, Switzerland
| | - Darren J Parker
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Gavin R Hunt
- University of Auckland, Science Centre 302, Auckland, New Zealand
| | - Russell D Gray
- University of Auckland, Science Centre 302, Auckland, New Zealand.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hideaki Abe
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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263
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Mosharaf MP, Rahman H, Ahsan MA, Akond Z, Ahmed FF, Islam MM, Moni MA, Mollah MNH. In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.). PLoS One 2020; 15:e0228233. [PMID: 33347517 PMCID: PMC7751981 DOI: 10.1371/journal.pone.0228233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
RNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which are involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families and their regulatory elements. However, these RNAi gene families and their sub-cellular locations, functional pathways and regulatory components were not extensively investigated in the case of economically and nutritionally important fruit plant sweet orange (Citrus sinensis L.). Therefore, in silico characterization, gene diversity and regulatory factor analysis of RNA silencing genes in C. sinensis were conducted by using the integrated bioinformatics approaches. Genome-wide comparison analysis based on phylogenetic tree approach detected 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi candidate genes in C. sinensis corresponding to the RNAi genes of model plant Arabidopsis thaliana. The domain and motif composition and gene structure analyses for all three gene families exhibited almost homogeneity within the same group members. The Gene Ontology enrichment analysis clearly indicated that the predicted genes have direct involvement into the gene-silencing and other important pathways. The key regulatory transcription factors (TFs) MYB, Dof, ERF, NAC, MIKC_MADS, WRKY and bZIP were identified by their interaction network analysis with the predicted genes. The cis-acting regulatory elements associated with the predicted genes were detected as responsive to light, stress and hormone functions. Furthermore, the expressed sequence tag (EST) analysis showed that these RNAi candidate genes were highly expressed in fruit and leaves indicating their organ specific functions. Our genome-wide comparison and integrated bioinformatics analyses provided some necessary information about sweet orange RNA silencing components that would pave a ground for further investigation of functional mechanism of the predicted genes and their regulatory factors.
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Affiliation(s)
- Md. Parvez Mosharaf
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Hafizur Rahman
- Department of Microbiology, Rajshahi Institute of Biosciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Asif Ahsan
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Zobaer Akond
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Institute of Environmental Science, University of Rajshahi, Rajshahi, Bangladesh
- Agricultural Statistics and ICT Division, Bangladesh Agricultural Research Institute (BARI), Gazipur, Bangladesh
| | - Fee Faysal Ahmed
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Mazharul Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohammad Ali Moni
- The University of Sydney, Sydney Medical School, School of Medical Sciences, Discipline of Biomedical Science, Sydney, New South Wales, Australia
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- * E-mail:
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264
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Yang Z, Zhang Q, Yu H, Du H, Li L, He Y, Zhu S, Li C, Zhang S, Luo B, Gao Y. Genetic association study of a novel indel polymorphism in HSPA1B with the risk of sudden cardiac death in the Chinese populations. Forensic Sci Int 2020; 318:110637. [PMID: 33309992 DOI: 10.1016/j.forsciint.2020.110637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/16/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022]
Abstract
Sudden cardiac death (SCD) has become a global problem due to its high mortality in the general population. Identification of genetic factors predisposed to SCD is significant since it enables genetic testing that would contribute to molecular diagnosis and risk stratification of SCD. It has been reported that HSPA1B gene mutations might be related with SCD. In this study, based on candidate-gene-based approach and systematic screening strategy, a 5-base pair insertion/deletion (Indel) polymorphism (rs3036297) in the 3'UTR of HSPA1B gene was selected to perform a case-control study aiming to investigate its association with SCD susceptibility in Chinese populations. Logistic regression analysis showed that the insertion allele of rs3036297 was correlated with a comparatively lower risk for SCD [OR=0.58, 95%CI=0.43-0.77, P=1.28×10-4] compared with the deletion allele. Luciferase activity assay indicated that HSPA1B expression could be regulated by rs3036297 through interfering binding with miR-134-5p. Furthermore, analysis of database from Haploreg and GTEx revealed that the rs3036297 variant was involved in potential cis-regulatory element with the promoter of HLA-DRB5 through a long-range interaction and the deletion allele of rs3036297 increased HLA-DRB5 expression. In conclusion, the rs3036297 variant may regulate HSPA1B expression via a mechanism of miRNA binding and HLA-DRB5 expression via a long-range promoter interaction through which contributed to SCD susceptibility. Therefore, rs3036297 would be a potential marker for molecular diagnosis and genetic counseling of SCD.
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Affiliation(s)
- Zhenzhen Yang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China; Institute of Forensic Sciences, Henan University of Economics and Law, Zhengzhou, China
| | - Qing Zhang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Huan Yu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Hailin Du
- Nanjing Red Cross Blood Center, Nanjing, China
| | - Lijuan Li
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yan He
- Department of Epidemiology, Medical College of Soochow University, Suzhou, China
| | - Shaohua Zhu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Bin Luo
- Department of Forensic Pathology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
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265
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Molecular and evolutionary processes generating variation in gene expression. Nat Rev Genet 2020; 22:203-215. [PMID: 33268840 DOI: 10.1038/s41576-020-00304-w] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/18/2022]
Abstract
Heritable variation in gene expression is common within and between species. This variation arises from mutations that alter the form or function of molecular gene regulatory networks that are then filtered by natural selection. High-throughput methods for introducing mutations and characterizing their cis- and trans-regulatory effects on gene expression (particularly, transcription) are revealing how different molecular mechanisms generate regulatory variation, and studies comparing these mutational effects with variation seen in the wild are teasing apart the role of neutral and non-neutral evolutionary processes. This integration of molecular and evolutionary biology allows us to understand how the variation in gene expression we see today came to be and to predict how it is most likely to evolve in the future.
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266
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Ullah F, Xu Q, Zhao Y, Zhou DX. Histone deacetylase HDA710 controls salt tolerance by regulating ABA signaling in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 63:451-467. [PMID: 33289304 DOI: 10.1111/jipb.13042] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/30/2020] [Indexed: 05/08/2023]
Abstract
Plants have evolved numerous mechanisms that assist them in withstanding environmental stresses. Histone deacetylases (HDACs) play crucial roles in plant stress responses; however, their regulatory mechanisms remain poorly understood. Here, we explored the function of HDA710/OsHDAC2, a member of the HDAC RPD3/HDA1 family, in stress tolerance in rice (Oryza sativa). We established that HDA710 localizes to both the nucleus and cytoplasm and is involved in regulating the acetylation of histone H3 and H4, specifically targeting H4K5 and H4K16 under normal conditions. HDA710 transcript accumulation levels were strongly induced by abiotic stresses including drought and salinity, as well as by the phytohormones jasmonic acid (JA) and abscisic acid (ABA). hda710 knockout mutant plants showed enhanced salinity tolerance and reduced ABA sensitivity, whereas transgenic plants overexpressing HDA710 displayed the opposite phenotypes. Moreover, ABA- and salt-stress-responsive genes, such as OsLEA3, OsABI5, OsbZIP72, and OsNHX1, were upregulated in hda710 compared with wild-type plants. These expression differences corresponded with higher levels of histone H4 acetylation in gene promoter regions in hda710 compared with the wild type under ABA and salt-stress treatment. Collectively, these results suggest that HDA710 is involved in regulating ABA- and salt-stress-responsive genes by altering H4 acetylation levels in their promoters. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Farhan Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Qiutao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
- Institute of Plant Science of Paris-Saclay (IPS2), University Paris-Saclay, CNRS, INRAE, 91405, Orsay, France
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267
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Josephs EB. Gene expression links genotype and phenotype during rapid adaptation. Mol Ecol 2020; 30:30-32. [PMID: 33187015 DOI: 10.1111/mec.15729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/06/2020] [Indexed: 12/27/2022]
Abstract
Natural environments can change quickly and organisms living in these environments can either move, go extinct, or persist through rapid adaptation. Understanding the genetic and phenotypic changes that occur during rapid adaptation is crucial for predicting how populations will respond to sudden environmental changes. Since gene expression links genotype to phenotype, determining how rapid adaptation shapes the transcriptome will be useful for identifying both the traits and the genes important for adaptation, especially in cases where adaptation involves changes in quantitative traits. However, we lack a clear understanding of how rapid adaptation can cause and be caused by changes in gene expression. In this issue of Molecular Ecology, Hamann et al. (2020) investigate how gene expression has evolved during rapid adaptation to drought in two populations of the plant species Brassica rapa.
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Affiliation(s)
- Emily B Josephs
- Department of Plant Biology and the Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
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268
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Zrimec J, Börlin CS, Buric F, Muhammad AS, Chen R, Siewers V, Verendel V, Nielsen J, Töpel M, Zelezniak A. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nat Commun 2020; 11:6141. [PMID: 33262328 PMCID: PMC7708451 DOI: 10.1038/s41467-020-19921-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression levels remains unclear. Here we apply deep learning on over 20,000 mRNA datasets to examine the genetic regulatory code controlling mRNA abundance in 7 model organisms ranging from bacteria to Human. In all organisms, we can predict mRNA abundance directly from DNA sequence, with up to 82% of the variation of transcript levels encoded in the gene regulatory structure. By searching for DNA regulatory motifs across the gene regulatory structure, we discover that motif interactions could explain the whole dynamic range of mRNA levels. Co-evolution across coding and non-coding regions suggests that it is not single motifs or regions, but the entire gene regulatory structure and specific combination of regulatory elements that define gene expression levels.
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Affiliation(s)
- Jan Zrimec
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Christoph S Börlin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Filip Buric
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Azam Sheikh Muhammad
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Rhongzen Chen
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Vilhelm Verendel
- Computer Science and Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center (GGBC), Box 461, 40530, Gothenburg, Sweden
| | - Aleksej Zelezniak
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23a, SE-171 65, Stockholm, Sweden.
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269
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Zhang Y, Rodriguez L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. SCIENCE ADVANCES 2020; 6:6/50/eabc8895. [PMID: 33310852 PMCID: PMC7732203 DOI: 10.1126/sciadv.abc8895] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/26/2020] [Indexed: 05/31/2023]
Abstract
Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants.
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Affiliation(s)
- Yuzhou Zhang
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Lesia Rodriguez
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Lanxin Li
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Xixi Zhang
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria.
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270
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Akman M, Carlson JE, Latimer AM. Climate explains population divergence in drought-induced plasticity of functional traits and gene expression in a South African Protea. Mol Ecol 2020; 30:255-273. [PMID: 33098695 DOI: 10.1111/mec.15705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022]
Abstract
Long-term environmental variation often drives local adaptation and leads to trait differentiation across populations. Additionally, when traits change in an environment-dependent way through phenotypic plasticity, the genetic variation underlying plasticity will also be under selection. These processes could create a landscape of differentiation across populations in traits and their plasticity. Here, we performed a dry-down experiment under controlled conditions to measure responses in seedlings of a shrub species from the Cape Floristic Region, the common sugarbush (Protea repens). We measured morphological and physiological traits, and sequenced whole transcriptomes of leaf tissues from eight populations that represent both the climatic and the geographical distribution of this species. We found that there is substantial variation in how populations respond to drought, but we also observed common patterns such as reduced leaf size and leaf thickness, and up-regulation of stress-related and down-regulation of growth-related gene groups. Both high environmental heterogeneity and milder source site climates were associated with higher plasticity in various traits and co-expression gene networks. Associations between traits, trait plasticity, gene networks and the source site climate suggest that temperature may play a greater role in shaping these patterns when compared to precipitation, in line with recent changes in the region due to climate change. We also found that traits respond to climatic variation in an environment-dependent manner: some associations between traits and climate were apparent only under certain growing conditions. Together, our results uncover common responses of P. repens populations to drought, and climatic drivers of population differentiation in functional traits, gene expression and their plasticity.
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Affiliation(s)
- Melis Akman
- Department of Plant Sciences, UC Davis, Davis, CA, USA.,Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
| | - Jane E Carlson
- Department of Biology, Nicholls State University, Thibodaux, LA, USA.,Gulf Coast Network Inventory and Monitoring Program, National Park Services, Washington, DC, USA
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271
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Loaeza-Loaeza J, Beltran AS, Hernández-Sotelo D. DNMTs and Impact of CpG Content, Transcription Factors, Consensus Motifs, lncRNAs, and Histone Marks on DNA Methylation. Genes (Basel) 2020; 11:genes11111336. [PMID: 33198240 PMCID: PMC7696963 DOI: 10.3390/genes11111336] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
DNA methyltransferases (DNMTs) play an essential role in DNA methylation and transcriptional regulation in the genome. DNMTs, along with other poorly studied elements, modulate the dynamic DNA methylation patterns of embryonic and adult cells. We summarize the current knowledge on the molecular mechanism of DNMTs’ functional targeting to maintain genome-wide DNA methylation patterns. We focus on DNMTs’ intrinsic characteristics, transcriptional regulation, and post-transcriptional modifications. Furthermore, we focus special attention on the DNMTs’ specificity for target sites, including key cis-regulatory factors such as CpG content, common motifs, transcription factors (TF) binding sites, lncRNAs, and histone marks to regulate DNA methylation. We also review how complexes of DNMTs/TFs or DNMTs/lncRNAs are involved in DNA methylation in specific genome regions. Understanding these processes is essential because the spatiotemporal regulation of DNA methylation modulates gene expression in health and disease.
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Affiliation(s)
- Jaqueline Loaeza-Loaeza
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, NC 39087 Chilpancingo, Mexico;
| | - Adriana S. Beltran
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, NC 39087 Chilpancingo, Mexico;
- Correspondence:
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272
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Zhou H, Simion V, Pierce JB, Haemmig S, Chen AF, Feinberg MW. LncRNA-MAP3K4 regulates vascular inflammation through the p38 MAPK signaling pathway and cis-modulation of MAP3K4. FASEB J 2020; 35:e21133. [PMID: 33184917 DOI: 10.1096/fj.202001654rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/23/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
Abstract
Chronic vascular inflammation plays a key role in the pathogenesis of atherosclerosis. Long non-coding RNAs (lncRNAs) have emerged as essential inflammation regulators. We identify a novel lncRNA termed lncRNA-MAP3K4 that is enriched in the vessel wall and regulates vascular inflammation. In the aortic intima, lncRNA-MAP3K4 expression was reduced by 50% during the progression of atherosclerosis (chronic inflammation) and 70% during endotoxemia (acute inflammation). lncRNA-MAP3K4 knockdown reduced the expression of key inflammatory factors (eg, ICAM-1, E-selectin, MCP-1) in endothelial cells or vascular smooth muscle cells and decreased monocytes adhesion to endothelium, as well as reducing TNF-α, IL-1β, COX2 expression in macrophages. Mechanistically, lncRNA-MAP3K4 regulates inflammation through the p38 MAPK signaling pathway. lncRNA-MAP3K4 shares a bidirectional promoter with MAP3K4, an upstream regulator of the MAPK signaling pathway, and regulates its transcription in cis. lncRNA-MAP3K4 and MAP3K4 show coordinated expression in response to inflammation in vivo and in vitro. Similar to lncRNA-MAP3K4, MAP3K4 knockdown reduced the expression of inflammatory factors in several different vascular cells. Furthermore, lncRNA-MAP3K4 and MAP3K4 knockdown showed cooperativity in reducing inflammation in endothelial cells. Collectively, these findings unveil the role of a novel lncRNA in vascular inflammation by cis-regulating MAP3K4 via a p38 MAPK pathway.
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Affiliation(s)
- Haoyang Zhou
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Viorel Simion
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jacob B Pierce
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Stefan Haemmig
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alex F Chen
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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273
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Kozlenkov A, Vermunt MW, Apontes P, Li J, Hao K, Sherwood CC, Hof PR, Ely JJ, Wegner M, Mukamel EA, Creyghton MP, Koonin EV, Dracheva S. Evolution of regulatory signatures in primate cortical neurons at cell-type resolution. Proc Natl Acad Sci U S A 2020; 117:28422-28432. [PMID: 33109720 PMCID: PMC7668098 DOI: 10.1073/pnas.2011884117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type-specific regulatory landscapes in the cortex remain largely unexplored. Here we report epigenomic and transcriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. Using genome-wide profiling of the H3K27ac histone modification, we identify neuron-subtype-specific regulatory elements that previously went undetected in bulk brain tissue samples. Human-specific regulatory changes are uncovered in multiple genes, including those associated with language, autism spectrum disorder, and drug addiction. We observe preferential evolutionary divergence in neuron subtype-specific regulatory elements and show that a substantial fraction of pan-neuronal regulatory elements undergoes subtype-specific evolutionary changes. This study sheds light on the interplay between regulatory evolution and cell-type-dependent gene-expression programs, and provides a resource for further exploration of human brain evolution and function.
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Affiliation(s)
- Alexey Kozlenkov
- Research & Development, James J. Peters VA Medical Center, Bronx, NY 10468
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Marit W Vermunt
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Pasha Apontes
- Research & Development, James J. Peters VA Medical Center, Bronx, NY 10468
| | - Junhao Li
- Department of Cognitive Science, University of California San Diego, La Jolla, CA 92037
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - John J Ely
- Alamogordo Primate Facility, Holloman Air Force Base, Alamogordo, NM 88330
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Eran A Mukamel
- Department of Cognitive Science, University of California San Diego, La Jolla, CA 92037
| | - Menno P Creyghton
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands;
- Department of Developmental Biology, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Stella Dracheva
- Research & Development, James J. Peters VA Medical Center, Bronx, NY 10468;
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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274
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Mugal CF, Wang M, Backström N, Wheatcroft D, Ålund M, Sémon M, McFarlane SE, Dutoit L, Qvarnström A, Ellegren H. Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F 1 hybrids. Genome Res 2020; 30:1727-1739. [PMID: 33144405 PMCID: PMC7706733 DOI: 10.1101/gr.254508.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/28/2020] [Indexed: 12/27/2022]
Abstract
Changes in interacting cis- and trans-regulatory elements are important candidates for Dobzhansky-Muller hybrid incompatibilities and may contribute to hybrid dysfunction by giving rise to misexpression in hybrids. To gain insight into the molecular mechanisms and determinants of gene expression evolution in natural populations, we analyzed the transcriptome from multiple tissues of two recently diverged Ficedula flycatcher species and their naturally occurring F1 hybrids. Differential gene expression analysis revealed that the extent of differentiation between species and the set of differentially expressed genes varied across tissues. Common to all tissues, a higher proportion of Z-linked genes than autosomal genes showed differential expression, providing evidence for a fast-Z effect. We further found clear signatures of hybrid misexpression in brain, heart, kidney, and liver. However, while testis showed the highest divergence of gene expression among tissues, it showed no clear signature of misexpression in F1 hybrids, even though these hybrids were found to be sterile. It is therefore unlikely that incompatibilities between cis-trans regulatory changes explain the observed sterility. Instead, we found evidence that cis-regulatory changes play a significant role in the evolution of gene expression in testis, which illustrates the tissue-specific nature of cis-regulatory evolution bypassing constraints associated with pleiotropic effects of genes.
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Affiliation(s)
- Carina F Mugal
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
| | - Mi Wang
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
| | - Niclas Backström
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
| | - David Wheatcroft
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Murielle Ålund
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Marie Sémon
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,ENS de Lyon, Laboratory of Biology and Modelling of the Cell, Lyon University, 69364 Lyon Cedex 07, France
| | - S Eryn McFarlane
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Ludovic Dutoit
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,Department of Zoology, University of Otago, Dunedin 9016, New Zealand
| | - Anna Qvarnström
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
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275
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Morris J, Hanly JJ, Martin SH, Van Belleghem SM, Salazar C, Jiggins CD, Dasmahapatra KK. Deep Convergence, Shared Ancestry, and Evolutionary Novelty in the Genetic Architecture of Heliconius Mimicry. Genetics 2020; 216:765-780. [PMID: 32883703 PMCID: PMC7648585 DOI: 10.1534/genetics.120.303611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/25/2020] [Indexed: 01/31/2023] Open
Abstract
Convergent evolution can occur through different genetic mechanisms in different species. It is now clear that convergence at the genetic level is also widespread, and can be caused by either (i) parallel genetic evolution, where independently evolved convergent mutations arise in different populations or species, or (ii) collateral evolution in which shared ancestry results from either ancestral polymorphism or introgression among taxa. The adaptive radiation of Heliconius butterflies shows color pattern variation within species, as well as mimetic convergence between species. Using comparisons from across multiple hybrid zones, we use signals of shared ancestry to identify and refine multiple putative regulatory elements in Heliconius melpomene and its comimics, Heliconius elevatus and Heliconius besckei, around three known major color patterning genes: optix, WntA, and cortex While we find that convergence between H. melpomene and H. elevatus is caused by a complex history of collateral evolution via introgression in the Amazon, convergence between these species in the Guianas appears to have evolved independently. Thus, we find adaptive convergent genetic evolution to be a key driver of regulatory changes that lead to rapid phenotypic changes. Furthermore, we uncover evidence of parallel genetic evolution at some loci around optix and WntA in H. melpomene and its distant comimic Heliconius erato Ultimately, we show that all three of convergence, conservation, and novelty underlie the modular architecture of Heliconius color pattern mimicry.
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Affiliation(s)
- Jake Morris
- Department of Biology, University of York, Heslington YO10 5DD, United Kingdom
| | - Joseph J Hanly
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | - Simon H Martin
- Institute of Evolutionary Biology, The University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3FL, United Kingdom
| | - Steven M Van Belleghem
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá 111221, Colombia
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
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276
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Maney DL, Merritt JR, Prichard MR, Horton BM, Yi SV. Inside the supergene of the bird with four sexes. Horm Behav 2020; 126:104850. [PMID: 32937166 PMCID: PMC7725849 DOI: 10.1016/j.yhbeh.2020.104850] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/04/2020] [Accepted: 09/06/2020] [Indexed: 02/07/2023]
Abstract
The white-throated sparrow (Zonotrichia albicollis) offers unique opportunities to understand the adaptive value of supergenes, particularly their role in alternative phenotypes. In this species, alternative plumage morphs segregate with a nonrecombining segment of chromosome 2, which has been called a 'supergene'. The species mates disassortatively with respect to the supergene; that is, each breeding pair consists of one individual with it and one without it. This species has therefore been called the "bird with four sexes". The supergene segregates with a behavioral phenotype; birds with it are more aggressive and less parental than birds without it. Here, we review our efforts to identify the genes inside the supergene that are responsible for the behavioral polymorphism. The gene ESR1, which encodes estrogen receptor α, differs between the morphs and predicts both territorial and parental behavior. Variation in the regulatory regions of ESR1 causes an imbalance in expression of the two alleles, and the degree to which this imbalance favors the supergene allele predicts territorial singing. In heterozygotes, knockdown of ESR1 causes a phenotypic switch, from more aggressive to less aggressive. We recently showed that another gene important for social behavior, vasoactive intestinal peptide (VIP), is differentially expressed between the morphs and predicts territorial singing. We hypothesize that ESR1 and VIP contribute to behavior in a coordinated way and could represent co-adapted alleles. Because the supergene contains more than 1000 individual genes, this species provides rich possibilities for discovering alleles that work together to mediate life-history trade-offs and maximize the fitness of alternative complex phenotypes.
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Affiliation(s)
- Donna L Maney
- Department of Psychology, Emory University, Atlanta, GA, USA.
| | | | | | - Brent M Horton
- Department of Biology, Millersville University, Millersville, PA, USA
| | - Soojin V Yi
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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277
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Fuqua T, Jordan J, van Breugel ME, Halavatyi A, Tischer C, Polidoro P, Abe N, Tsai A, Mann RS, Stern DL, Crocker J. Dense and pleiotropic regulatory information in a developmental enhancer. Nature 2020; 587:235-239. [PMID: 33057197 DOI: 10.1038/s41586-020-2816-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/22/2020] [Indexed: 01/08/2023]
Abstract
Changes in gene regulation underlie much of phenotypic evolution1. However, our understanding of the potential for regulatory evolution is biased, because most evidence comes from either natural variation or limited experimental perturbations2. Using an automated robotics pipeline, we surveyed an unbiased mutation library for a developmental enhancer in Drosophila melanogaster. We found that almost all mutations altered gene expression and that parameters of gene expression-levels, location, and state-were convolved. The widespread pleiotropic effects of most mutations may constrain the evolvability of developmental enhancers. Consistent with these observations, comparisons of diverse Drosophila larvae revealed apparent biases in the phenotypes influenced by the enhancer. Developmental enhancers may encode a higher density of regulatory information than has been appreciated previously, imposing constraints on regulatory evolution.
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Affiliation(s)
- Timothy Fuqua
- European Molecular Biology Laboratory, Heidelberg, Germany.,Joint PhD Collaboration, EMBL and Faculty of Biosciences Heidelberg University, Heidelberg, Germany
| | | | | | | | | | | | - Namiko Abe
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Albert Tsai
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Richard S Mann
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Justin Crocker
- European Molecular Biology Laboratory, Heidelberg, Germany.
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278
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Reddy PC, Gungi A, Ubhe S, Galande S. Epigenomic landscape of enhancer elements during Hydra head organizer formation. Epigenetics Chromatin 2020; 13:43. [PMID: 33046126 PMCID: PMC7552563 DOI: 10.1186/s13072-020-00364-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/26/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Axis patterning during development is accompanied by large-scale gene expression changes. These are brought about by changes in the histone modifications leading to dynamic alterations in chromatin architecture. The cis regulatory DNA elements also play an important role towards modulating gene expression in a context-dependent manner. Hydra belongs to the phylum Cnidaria where the first asymmetry in the body plan was observed and the oral-aboral axis originated. Wnt signaling has been shown to determine the head organizer function in the basal metazoan Hydra. RESULTS To gain insights into the evolution of cis regulatory elements and associated chromatin signatures, we ectopically activated the Wnt signaling pathway in Hydra and monitored the genome-wide alterations in key histone modifications. Motif analysis of putative intergenic enhancer elements from Hydra revealed the conservation of bilaterian cis regulatory elements that play critical roles in development. Differentially regulated enhancer elements were identified upon ectopic activation of Wnt signaling and found to regulate many head organizer specific genes. Enhancer activity of many of the identified cis regulatory elements was confirmed by luciferase reporter assay. Quantitative chromatin immunoprecipitation analysis upon activation of Wnt signaling further confirmed the enrichment of H3K27ac on the enhancer elements of Hv_Wnt5a, Hv_Wnt11 and head organizer genes Hv_Bra1, CnGsc and Hv_Pitx1. Additionally, perturbation of the putative H3K27me3 eraser activity using a specific inhibitor affected the ectopic activation of Wnt signaling indicating the importance of the dynamic changes in the H3K27 modifications towards regulation of the genes involved in the head organizer activity. CONCLUSIONS The activation-associated histone marks H3K4me3, H3K27ac and H3K9ac mark chromatin in a similar manner as seen in bilaterians. We identified intergenic cis regulatory elements which harbor sites for key transcription factors involved in developmental processes. Differentially regulated enhancers exhibited motifs for many zinc-finger, T-box and ETS related TFs whose homologs have a head specific expression in Hydra and could be a part of the pioneer TF network in the patterning of the head. The ability to differentially modify the H3K27 residue is critical for the patterning of Hydra axis revealing a dynamic acetylation/methylation switch to regulate gene expression and chromatin architecture.
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Affiliation(s)
- Puli Chandramouli Reddy
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Akhila Gungi
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Suyog Ubhe
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India.
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279
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Lang Y, Liu Z. Basic Helix-Loop-Helix (bHLH) transcription factor family in Yellow horn (Xanthoceras sorbifolia Bunge): Genome-wide characterization, chromosome location, phylogeny, structures and expression patterns. Int J Biol Macromol 2020; 160:711-723. [DOI: 10.1016/j.ijbiomac.2020.05.253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/27/2022]
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280
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Yarahmadov T, Robinson S, Hanemian M, Pulver V, Kuhlemeier C. Identification of transcription factors controlling floral morphology in wild Petunia species with contrasting pollination syndromes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:289-301. [PMID: 32780443 PMCID: PMC7693086 DOI: 10.1111/tpj.14962] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 07/15/2020] [Indexed: 05/29/2023]
Abstract
Adaptation to different pollinators is an important driver of speciation in the angiosperms. Genetic approaches such as QTL mapping have been successfully used to identify the underlying speciation genes. However, these methods are often limited by widespread suppression of recombination due to divergence between species. While the mutations that caused the interspecific differences in floral color and scent have been elucidated in a variety of plant genera, the genes that are responsible for morphological differences remain mostly unknown. Differences in floral organ length determine the pollination efficiency of hawkmoths and hummingbirds, and therefore the genes that control these differences are potential speciation genes. Identifying such genes is challenging, especially in non-model species and when studying complex traits for which little prior genetic and biochemical knowledge is available. Here we combine transcriptomics with detailed growth analysis to identify candidate transcription factors underlying interspecific variation in the styles of Petunia flowers. Starting from a set of 2284 genes, stepwise filtering for expression in styles, differential expression between species, correlation with growth-related traits, allele-specific expression in interspecific hybrids, and/or high-impact polymorphisms resulted in a set of 43 candidate speciation genes. Validation by virus-induced gene silencing identified two MYB transcription factors, EOBI and EOBII, that were previously shown to regulate floral scent emission, a trait associated with pollination by hawkmoths.
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Affiliation(s)
- Tural Yarahmadov
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
- Department of BioMedical ResearchUniversity of BernBernCH‐3008Switzerland
| | - Sarah Robinson
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
- Sainsbury LaboratoryUniversity of CambridgeCambridgeCB2 1LRUK
| | - Mathieu Hanemian
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
- LIPMUniversité de ToulouseINRAECNRSCastanet‐TolosanFrance
| | - Valentin Pulver
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
| | - Cris Kuhlemeier
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
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281
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Cano AV, Payne JL. Mutation bias interacts with composition bias to influence adaptive evolution. PLoS Comput Biol 2020; 16:e1008296. [PMID: 32986712 PMCID: PMC7571706 DOI: 10.1371/journal.pcbi.1008296] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 10/19/2020] [Accepted: 08/30/2020] [Indexed: 11/19/2022] Open
Abstract
Mutation is a biased stochastic process, with some types of mutations occurring more frequently than others. Previous work has used synthetic genotype-phenotype landscapes to study how such mutation bias affects adaptive evolution. Here, we consider 746 empirical genotype-phenotype landscapes, each of which describes the binding affinity of target DNA sequences to a transcription factor, to study the influence of mutation bias on adaptive evolution of increased binding affinity. By using empirical genotype-phenotype landscapes, we need to make only few assumptions about landscape topography and about the DNA sequences that each landscape contains. The latter is particularly important because the set of sequences that a landscape contains determines the types of mutations that can occur along a mutational path to an adaptive peak. That is, landscapes can exhibit a composition bias—a statistical enrichment of a particular type of mutation relative to a null expectation, throughout an entire landscape or along particular mutational paths—that is independent of any bias in the mutation process. Our results reveal the way in which composition bias interacts with biases in the mutation process under different population genetic conditions, and how such interaction impacts fundamental properties of adaptive evolution, such as its predictability, as well as the evolution of genetic diversity and mutational robustness. Mutation is often depicted as a random process due its unpredictable nature. However, such randomness does not imply uniformly distributed outcomes, because some DNA sequence changes happen more frequently than others. Mutation bias can be an orienting factor in adaptive evolution, influencing the mutational trajectories populations follow toward higher-fitness genotypes. Because these trajectories are typically just a small subset of all possible mutational trajectories, they can exhibit composition bias—an enrichment of a particular kind of DNA sequence change, such as transition or transversion mutations. Here, we use empirical data from eukaryotic transcriptional regulation to study how mutation bias and composition bias interact to influence adaptive evolution.
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Affiliation(s)
- Alejandro V. Cano
- Institute of Integrative Biology, ETH, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
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282
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Li Y, Schwalie PC, Bast-Habersbrunner A, Mocek S, Russeil J, Fromme T, Deplancke B, Klingenspor M. Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning. Cell Rep 2020; 29:4099-4113.e5. [PMID: 31851936 DOI: 10.1016/j.celrep.2019.11.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/02/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Recruitment of brite/beige cells, known as browning of white adipose tissue (WAT), is an efficient way to turn an energy-storing organ into an energy-dissipating one and may therefore be of therapeutic value in combating obesity. However, a comprehensive understanding of the regulatory mechanisms mediating WAT browning is still lacking. Here, we exploit the large natural variation in WAT browning propensity between inbred mouse strains to gain an inclusive view of the core regulatory network coordinating this cellular process. Combining comparative transcriptomics, perturbation-based validations, and gene network analyses, we present a comprehensive gene regulatory network of inguinal WAT browning, revealing up to four distinct regulatory modules with key roles for uncovered transcriptional factors, while also providing deep insights into the genetic architecture of brite adipogenesis. The presented findings therefore greatly increase our understanding of the molecular drivers mediating the intriguing cellular heterogeneity and plasticity of adipose tissue.
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Affiliation(s)
- Yongguo Li
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Petra C Schwalie
- Institute of Bio-engineering, School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Andrea Bast-Habersbrunner
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Sabine Mocek
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Julie Russeil
- Institute of Bio-engineering, School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tobias Fromme
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Bart Deplancke
- Institute of Bio-engineering, School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Martin Klingenspor
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany.
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283
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Abstract
New species arise as the genomes of populations diverge. The developmental 'alarm clock' of speciation sounds off when sufficient divergence in genetic control of development leads hybrid individuals to infertility or inviability, the world awoken to the dawn of new species with intrinsic post-zygotic reproductive isolation. Some developmental stages will be more prone to hybrid dysfunction due to how molecular evolution interacts with the ontogenetic timing of gene expression. Considering the ontogeny of hybrid incompatibilities provides a profitable connection between 'evo-devo' and speciation genetics to better link macroevolutionary pattern, microevolutionary process, and molecular mechanisms. Here, we explore speciation alongside development, emphasizing their mutual dependence on genetic network features, fitness landscapes, and developmental system drift. We assess models for how ontogenetic timing of reproductive isolation can be predictable. Experiments and theory within this synthetic perspective can help identify new rules of speciation as well as rules in the molecular evolution of development.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of TorontoTorontoCanada
| | - Joanna D Bundus
- Department of Integrative Biology, University of Wisconsin – MadisonMadisonUnited States
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284
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Gramazio P, Takayama M, Ezura H. Challenges and Prospects of New Plant Breeding Techniques for GABA Improvement in Crops: Tomato as an Example. FRONTIERS IN PLANT SCIENCE 2020; 11:577980. [PMID: 33014001 PMCID: PMC7500313 DOI: 10.3389/fpls.2020.577980] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/20/2020] [Indexed: 05/28/2023]
Abstract
Over the last seven decades, γ-aminobutyric acid (GABA) has attracted great attention from scientists for its ubiquity in plants, animals and microorganisms and for its physiological implications as a signaling molecule involved in multiple pathways and processes. Recently, the food and pharmaceutical industries have also shown significantly increased interest in GABA, because of its great potential benefits for human health and the consumer demand for health-promoting functional compounds, resulting in the release of a plethora of GABA-enriched products. Nevertheless, many crop species accumulate appreciable GABA levels in their edible parts and could help to meet the daily recommended intake of GABA for promoting positive health effects. Therefore, plant breeders are devoting much effort into breeding elite varieties with improved GABA contents. In this regard, tomato (Solanum lycopersicum), the most produced and consumed vegetable worldwide and a fruit-bearing model crop, has received much consideration for its accumulation of remarkable GABA levels. Although many different strategies have been implemented, from classical crossbreeding to induced mutagenesis, new plant breeding techniques (NPBTs) have achieved the best GABA accumulation results in red ripe tomato fruits along with shedding light on GABA metabolism and gene functions. In this review, we summarize, analyze and compare all the studies that have substantially contributed to tomato GABA breeding with further discussion and proposals regarding the most recent NPBTs that could bring this process to the next level of precision and efficiency. This document also provides guidelines with which researchers of other crops might take advantage of the progress achieved in tomato for more efficient GABA breeding programs.
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Affiliation(s)
- Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mariko Takayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Japan
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285
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Anderson J, Song BH. Plant adaptation to climate change - Where are we? JOURNAL OF SYSTEMATICS AND EVOLUTION 2020; 58:533-545. [PMID: 33584833 PMCID: PMC7875155 DOI: 10.1111/jse.12649] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Climate change poses critical challenges for population persistence in natural communities, agriculture and environmental sustainability, and food security. In this review, we discuss recent progress in climatic adaptation in plants. We evaluate whether climate change exerts novel selection and disrupts local adaptation, whether gene flow can facilitate adaptive responses to climate change, and if adaptive phenotypic plasticity could sustain populations in the short term. Furthermore, we discuss how climate change influences species interactions. Through a more in-depth understanding of these eco-evolutionary dynamics, we will increase our capacity to predict the adaptive potential of plants under climate change. In addition, we review studies that dissect the genetic basis of plant adaptation to climate change. Finally, we highlight key research gaps, ranging from validating gene function, to elucidating molecular mechanisms, expanding research systems from model species to other natural species, testing the fitness consequences of alleles in natural environments, and designing multifactorial studies that more closely reflect the complex and interactive effects of multiple climate change factors. By leveraging interdisciplinary tools (e.g., cutting-edge omics toolkits, novel ecological strategies, newly-developed genome editing technology), researchers can more accurately predict the probability that species can persist through this rapid and intense period of environmental change, as well as cultivate crops to withstand climate change, and conserve biodiversity in natural systems.
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Affiliation(s)
- Jill Anderson
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Authors for correspondence. Bao-Hua Song. ; Jill Anderson.
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Authors for correspondence. Bao-Hua Song. ; Jill Anderson.
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286
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Courtier‐Orgogozo V, Danchin A, Gouyon P, Boëte C. Evaluating the probability of CRISPR-based gene drive contaminating another species. Evol Appl 2020; 13:1888-1905. [PMID: 32908593 PMCID: PMC7463340 DOI: 10.1111/eva.12939] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
The probability D that a given clustered regularly interspaced short palindromic repeats (CRISPR)-based gene drive element contaminates another, nontarget species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = h y b + t r a n s f × e x p r e s s × c u t × f l a n k × i m m u n e × n o n e x t i n c t with hyb = probability of hybridization between the target species and a nontarget species; transf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a nontarget species (with no hybridization); express = probability that the Cas9 and guide RNA genes are expressed; cut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the new host; flank = probability that the gene drive cassette inserts at the cut site; immune = probability that the immune system does not reject Cas9-expressing cells; nonextinct = probability of invasion of the drive within the population. We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. We conclude from current data that the probability of a gene drive cassette to contaminate another species is not insignificant. We propose strategies to reduce this risk and call for more work on estimating all the parameters of the formula.
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Affiliation(s)
| | - Antoine Danchin
- Institut Cochin INSERM U1016 – CNRS UMR8104 – Université Paris DescartesParisFrance
| | - Pierre‐Henri Gouyon
- Institut de Systématique, Évolution, BiodiversitéMuséum National d'Histoire NaturelleCNRSSorbonne UniversitéEPHEUAParisFrance
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287
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Soyk S, Benoit M, Lippman ZB. New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation. Annu Rev Genet 2020; 54:287-307. [PMID: 32870731 DOI: 10.1146/annurev-genet-050720-122916] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Uncovering the genes, variants, and interactions underlying crop diversity is a frontier in plant genetics. Phenotypic variation often does not reflect the cumulative effect of individual gene mutations. This deviation is due to epistasis, in which interactions between alleles are often unpredictable and quantitative in effect. Recent advances in genomics and genome-editing technologies are elevating the study of epistasis in crops. Using the traits and developmental pathways that were major targets in domestication and breeding, we highlight how epistasis is central in guiding the behavior of the genetic variation that shapes quantitative trait variation. We outline new strategies that illuminate how quantitative epistasis from modified gene dosage defines background dependencies. Advancing our understanding of epistasis in crops can reveal new principles and approaches to engineering targeted improvements in agriculture.
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Affiliation(s)
- Sebastian Soyk
- Center for Integrative Genomics, University of Lausanne, CH-1005 Lausanne, Switzerland;
| | - Matthias Benoit
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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288
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Satokangas I, Martin SH, Helanterä H, Saramäki J, Kulmuni J. Multi-locus interactions and the build-up of reproductive isolation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190543. [PMID: 32654649 PMCID: PMC7423273 DOI: 10.1098/rstb.2019.0543] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
All genes interact with other genes, and their additive effects and epistatic interactions affect an organism's phenotype and fitness. Recent theoretical and empirical work has advanced our understanding of the role of multi-locus interactions in speciation. However, relating different models to one another and to empirical observations is challenging. This review focuses on multi-locus interactions that lead to reproductive isolation (RI) through reduced hybrid fitness. We first review theoretical approaches and show how recent work incorporating a mechanistic understanding of multi-locus interactions recapitulates earlier models, but also makes novel predictions concerning the build-up of RI. These include high variance in the build-up rate of RI among taxa, the emergence of strong incompatibilities producing localized barriers to introgression, and an effect of population size on the build-up of RI. We then review recent experimental approaches to detect multi-locus interactions underlying RI using genomic data. We argue that future studies would benefit from overlapping methods like ancestry disequilibrium scans, genome scans of differentiation and analyses of hybrid gene expression. Finally, we highlight a need for further overlap between theoretical and empirical work, and approaches that predict what kind of patterns multi-locus interactions resulting in incompatibilities will leave in genome-wide polymorphism data. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- I. Satokangas
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 1, PO Box 65, 00014 Helsinki, Finland
| | - S. H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3FL, UK
| | - H. Helanterä
- Ecology and Genetics research unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - J. Saramäki
- Department of Computer Science, Aalto University, PO Box 11000, 00076 Aalto, Espoo, Finland
| | - J. Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 1, PO Box 65, 00014 Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, J. A. Palménin tie 260, 10900 Hanko, Finland
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289
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Kuriyama T, Murakami A, Brandley M, Hasegawa M. Blue, Black, and Stripes: Evolution and Development of Color Production and Pattern Formation in Lizards and Snakes. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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290
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Sundararajan V, Pang QY, Choolani M, Huang RYJ. Spotlight on the Granules (Grainyhead-Like Proteins) - From an Evolutionary Conserved Controller of Epithelial Trait to Pioneering the Chromatin Landscape. Front Mol Biosci 2020; 7:213. [PMID: 32974388 PMCID: PMC7471608 DOI: 10.3389/fmolb.2020.00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022] Open
Abstract
Among the transcription factors that are conserved across phylogeny, the grainyhead family holds vital roles in driving the epithelial cell fate. In Drosophila, the function of grainyhead (grh) gene is essential during developmental processes such as epithelial differentiation, tracheal tube formation, maintenance of wing and hair polarity, and epidermal barrier wound repair. Three main mammalian orthologs of grh: Grainyhead-like 1-3 (GRHL1, GRHL2, and GRHL3) are highly conserved in terms of their gene structures and functions. GRHL proteins are essentially associated with the development and maintenance of the epithelial phenotype across diverse physiological conditions such as epidermal differentiation and craniofacial development as well as pathological functions including hearing impairment and neural tube defects. More importantly, through direct chromatin binding and induction of epigenetic alterations, GRHL factors function as potent suppressors of oncogenic cellular dedifferentiation program – epithelial-mesenchymal transition and its associated tumor-promoting phenotypes such as tumor cell migration and invasion. On the contrary, GRHL factors also induce pro-tumorigenic effects such as increased migration and anchorage-independent growth in certain tumor types. Furthermore, investigations focusing on the epithelial-specific activation of grh and GRHL factors have revealed that these factors potentially act as a pioneer factor in establishing a cell-type/cell-state specific accessible chromatin landscape that is exclusive for epithelial gene transcription. In this review, we highlight the essential roles of grh and GRHL factors during embryogenesis and pathogenesis, with a special focus on its emerging pioneering function.
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Affiliation(s)
- Vignesh Sundararajan
- Center for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Qing You Pang
- Center for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Obstetrics and Gynaecology, National University of Singapore, Singapore, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, National University of Singapore, Singapore, Singapore
| | - Ruby Yun-Ju Huang
- Department of Obstetrics and Gynaecology, National University of Singapore, Singapore, Singapore.,School of Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
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291
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He J, Bouwmeester HJ, Dicke M, Kappers IF. Genome-Wide Analysis Reveals Transcription Factors Regulated by Spider-Mite Feeding in Cucumber ( Cucumis sativus). PLANTS (BASEL, SWITZERLAND) 2020; 9:E1014. [PMID: 32796676 PMCID: PMC7465836 DOI: 10.3390/plants9081014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 11/16/2022]
Abstract
To gain insight into the regulatory networks that underlie the induced defense in cucumber against spider mites, genes encoding transcription factors (TFs) were identified in the cucumber (Cucumissativus) genome and their regulation by two-spotted spider mite (Tetranychusurticae) herbivory was analyzed using RNA-seq. Of the total 1212 annotated TF genes in the cucumber genome, 119 were differentially regulated upon spider-mite herbivory during a period of 3 days. These TF genes belong to different categories but the MYB, bHLH, AP2/ERF and WRKY families had the highest relative numbers of differentially expressed genes. Correlation analysis of the expression of TF genes with defense-associated genes during herbivory and pathogen infestation, and in different organs resulted in the putative identification of regulators of herbivore-induced terpenoid and green-leaf-volatile biosynthesis. Analysis of the cis-acting regulatory elements (CAREs) present in the promoter regions of the genes responsive to spider-mite feeding revealed potential TF regulators. This study describes the TF genes in cucumber that are potentially involved in the regulation of induced defense against herbivory by spider mites.
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Affiliation(s)
- Jun He
- Citrus Research Institute, Southwest University, Chongqing 400712, China
- Laboratory of Plant Physiology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
| | - Harro J. Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1000 BE Amsterdam, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
| | - Iris F. Kappers
- Laboratory of Plant Physiology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
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292
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Han J, Wang P, Wang Q, Lin Q, Chen Z, Yu G, Miao C, Dao Y, Wu R, Schnable JC, Tang H, Wang K. Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses. THE PLANT CELL 2020; 32:2457-2473. [PMID: 32471863 PMCID: PMC7401015 DOI: 10.1105/tpc.19.00716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/11/2020] [Accepted: 05/23/2020] [Indexed: 05/05/2023]
Abstract
Deep sequencing of DNase-I treated chromatin (DNase-seq) can be used to identify DNase I-hypersensitive sites (DHSs) and facilitates genome-scale mining of de novo cis-regulatory DNA elements. Here, we adapted DNase-seq to generate genome-wide maps of DHSs using control and cold-treated leaf, stem, and root tissues of three widely studied grass species: Brachypodium distachyon, foxtail millet (Setaria italica), and sorghum (Sorghum bicolor). Functional validation demonstrated that 12 of 15 DHSs drove reporter gene expression in transiently transgenic B. distachyon protoplasts. DHSs under both normal and cold treatment substantially differed among tissues and species. Intriguingly, the putative DHS-derived transcription factors (TFs) are largely colocated among tissues and species and include 17 ubiquitous motifs covering all grass taxa and all tissues examined in this study. This feature allowed us to reconstruct a regulatory network that responds to cold stress. Ethylene-responsive TFs SHINE3, ERF2, and ERF9 occurred frequently in cold feedback loops in the tissues examined, pointing to their possible roles in the regulatory network. Overall, we provide experimental annotation of 322,713 DHSs and 93 derived cold-response TF binding motifs in multiple grasses, which could serve as a valuable resource for elucidating the transcriptional networks that function in the cold-stress response and other physiological processes.
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Affiliation(s)
- Jinlei Han
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Pengxi Wang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Qiongli Wang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Qingfang Lin
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Zhiyong Chen
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Guangrun Yu
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Chenyong Miao
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Yihang Dao
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Ruoxi Wu
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Haibao Tang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Kai Wang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
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293
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Thompson JD, Ou J, Lee N, Shin K, Cigliola V, Song L, Crawford GE, Kang J, Poss KD. Identification and requirements of enhancers that direct gene expression during zebrafish fin regeneration. Development 2020; 147:dev.191262. [PMID: 32665240 DOI: 10.1242/dev.191262] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022]
Abstract
To identify candidate tissue regeneration enhancer elements (TREEs) important for zebrafish fin regeneration, we performed ATAC-seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified tens of thousands of DNA regions from each sample type with dynamic accessibility during regeneration, and assigned these regions to proximal genes with corresponding expression changes by RNA-seq. To determine whether these profiles reveal bona fide TREEs, we tested the sufficiency and requirements of several sequences in stable transgenic lines and mutant lines with homozygous deletions. These experiments validated new non-coding regulatory sequences near induced and/or essential genes during fin regeneration, including fgf20a, mdka and cx43, identifying distinct domains of directed expression for each confirmed TREE. Whereas deletion of the previously identified LEN enhancer abolished detectable induction of the nearby leptin b gene during regeneration, deletions of enhancers linked to fgf20a, mdka and cx43 had no effect or partially reduced gene expression. Our study generates a new resource for dissecting the regulatory mechanisms of appendage generation and reveals a range of requirements for individual TREEs in control of regeneration programs.
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Affiliation(s)
- John D Thompson
- Regeneration Next, Duke University, Durham, NC 27710, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jianhong Ou
- Regeneration Next, Duke University, Durham, NC 27710, USA
| | - Nutishia Lee
- Regeneration Next, Duke University, Durham, NC 27710, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kwangdeok Shin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Valentina Cigliola
- Regeneration Next, Duke University, Durham, NC 27710, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lingyun Song
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center; Center for Genomic and Computational Biology; Center for Advanced Genomic Technologies, Durham, NC 27710, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center; Center for Genomic and Computational Biology; Center for Advanced Genomic Technologies, Durham, NC 27710, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kenneth D Poss
- Regeneration Next, Duke University, Durham, NC 27710, USA .,Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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294
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Gao H, Li J, Wang L, Zhang J, He C. Transcriptomic variation of the flower-fruit transition in Physalis and Solanum. PLANTA 2020; 252:28. [PMID: 32720160 DOI: 10.1007/s00425-020-03434-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
Gene expression variations in response to fertilization between Physalis and Solanum might play essential roles in species divergence and fruit evolution. Fertilization triggers variation in fruit development and morphology. The Chinese lantern, a morphological novelty derived from the calyx, is formed upon fertilization in Physalis but is not observed in Solanum. The underlying genetic variations are largely unknown. Here, we documented the developmental and morphological differences in the flower and fruit between Physalis floridana and Solanum pimpinellifolium and then evaluated both the transcript sequence variation and gene expression at the transcriptomic level at fertilization between the two species. In Physalis transcriptomic analysis, 468 unigenes were identified as differentially expressed genes (DEGs) that were strongly regulated by fertilization across 3 years. In comparison with tomato, 14,536 strict single-copy orthologous gene pairs were identified between P. floridana and S. pimpinellifolium in the flower-fruit transcriptome. Nine types of gene variations with specific GO-enriched patterns were identified, covering 58.82% orthologous gene pairs that were DEGs in either trend or dosage at the flower-fruit transition between the two species, which could adequately distinguish Solanum and Physalis, implying that differential gene expression at fertilization might play essential roles during the divergence and fruit evolution of Solanum-Physalis. Virus-induced gene silencing analyses revealed the developmental roles of some transcription factor genes in fertility, Chinese lantern development, and fruit weight control in Physalis. This study presents the first floral transcriptomic resource of Physalis, and reveals some candidate genetic variations accounting for the early fruit developmental evolution in Physalis in comparison to Solanum.
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Affiliation(s)
- Huihui Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
| | - Jisi Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
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295
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An osmolality/salinity-responsive enhancer 1 (OSRE1) in intron 1 promotes salinity induction of tilapia glutamine synthetase. Sci Rep 2020; 10:12103. [PMID: 32694739 PMCID: PMC7374092 DOI: 10.1038/s41598-020-69090-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/11/2020] [Indexed: 01/02/2023] Open
Abstract
Euryhaline tilapia (Oreochromis mossambicus) are fish that tolerate a wide salinity range from fresh water to > 3× seawater. Even though the physiological effector mechanisms of osmoregulation that maintain plasma homeostasis in fresh water and seawater fish are well known, the corresponding molecular mechanisms that control switching between hyper- (fresh water) and hypo-osmoregulation (seawater) remain mostly elusive. In this study we show that hyperosmotic induction of glutamine synthetase represents a prominent part of this switch. Proteomics analysis of the O. mossambicus OmB cell line revealed that glutamine synthetase is transcriptionally regulated by hyperosmolality. Therefore, the 5' regulatory sequence of O. mossambicus glutamine synthetase was investigated. Using an enhancer trapping assay, we discovered a novel osmosensitive mechanism by which intron 1 positively mediates glutamine synthetase transcription. Intron 1 includes a single, functional copy of an osmoresponsive element, osmolality/salinity-responsive enhancer 1 (OSRE1). Unlike for conventional enhancers, the hyperosmotic induction of glutamine synthetase by intron 1 is position dependent. But irrespective of intron 1 position, OSRE1 deletion from intron 1 abolishes hyperosmotic enhancer activity. These findings indicate that proper intron 1 positioning and the presence of an OSRE1 in intron 1 are required for precise enhancement of hyperosmotic glutamine synthetase expression.
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296
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Sánchez-Gaya V, Mariner-Faulí M, Rada-Iglesias A. Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies. Front Genet 2020; 11:688. [PMID: 32765580 PMCID: PMC7379850 DOI: 10.3389/fgene.2020.00688] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
In the last few years, the role of non-coding regulatory elements and their involvement in human disease have received great attention. Among the non-coding regulatory sequences, enhancers are particularly important for the proper establishment of cell type-specific gene-expression programs. Furthermore, the disruption of enhancers can lead to human disease through two main mechanisms: (i) Mutations or copy number variants can directly alter the enhancer sequences and thereby affect expression of their target genes; (ii) structural variants can provoke changes in 3-D chromatin organization that alter neither the enhancers nor their target genes, but rather the physical communication between them. In this review, these pathomechanisms are mostly discussed in the context of neurocristopathies, congenital disorders caused by defects that occur during neural crest development. We highlight why, due to its contribution to multiple tissues and organs, the neural crest represents an important, yet understudied, cell type involved in multiple congenital disorders. Moreover, we discuss currently available resources and experimental models for the study of human neurocristopathies. Last, we provide some practical guidelines that can be followed when investigating human neurocristopathies caused by structural variants. Importantly, these guidelines can be useful not only to uncover the etiology of human neurocristopathies, but also of other human congenital disorders in which enhancer disruption is involved.
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Affiliation(s)
- Víctor Sánchez-Gaya
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas-University of Cantabria-Sociedad para el Desarrollo de Cantabria, Santander, Spain
| | - Maria Mariner-Faulí
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas-University of Cantabria-Sociedad para el Desarrollo de Cantabria, Santander, Spain
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas-University of Cantabria-Sociedad para el Desarrollo de Cantabria, Santander, Spain
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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297
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Dukler N, Huang YF, Siepel A. Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data. Mol Biol Evol 2020; 37:2137-2152. [PMID: 32176292 PMCID: PMC7306682 DOI: 10.1093/molbev/msaa073] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Evolutionary changes in gene expression are often driven by gains and losses of cis-regulatory elements (CREs). The dynamics of CRE evolution can be examined using multispecies epigenomic data, but so far such analyses have generally been descriptive and model-free. Here, we introduce a probabilistic modeling framework for the evolution of CREs that operates directly on raw chromatin immunoprecipitation and sequencing (ChIP-seq) data and fully considers the phylogenetic relationships among species. Our framework includes a phylogenetic hidden Markov model, called epiPhyloHMM, for identifying the locations of multiply aligned CREs, and a combined phylogenetic and generalized linear model, called phyloGLM, for accounting for the influence of a rich set of genomic features in describing their evolutionary dynamics. We apply these methods to previously published ChIP-seq data for the H3K4me3 and H3K27ac histone modifications in liver tissue from nine mammals. We find that enhancers are gained and lost during mammalian evolution at about twice the rate of promoters, and that turnover rates are negatively correlated with DNA sequence conservation, expression level, and tissue breadth, and positively correlated with distance from the transcription start site, consistent with previous findings. In addition, we find that the predicted dosage sensitivity of target genes positively correlates with DNA sequence constraint in CREs but not with turnover rates, perhaps owing to differences in the effect sizes of the relevant mutations. Altogether, our probabilistic modeling framework enables a variety of powerful new analyses.
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Affiliation(s)
- Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY
| | - Yi-Fei Huang
- Department of Biology and Huck Institute of Life Sciences, Pennsylvania State University, University Park, PA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Yang Y, Chu X, Nie M, Song A, Jiang Y, Li M, Xia W, Xing X, Wang O. A novel long-range deletion spanning STX16 and NPEPL1 causing imprinting defects of the GNAS locus discovered in a patient with autosomal-dominant pseudohypoparathyroidism type 1B. Endocrine 2020; 69:212-219. [PMID: 32337648 DOI: 10.1007/s12020-020-02304-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/04/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND Pseudohypoparathyroidism (PHP) is a rare disorder characterized by hypocalcemia, hyperphosphatemia, and resistance to parathyroid hormone (PTH). According to different GNAS mutations, PHP is divided into several subtypes, among which autosomal-dominant PHP1B (AD-PHP1B) is caused by STX16 deletion and epigenetic alteration of GNAS. Although the deletion of STX16 exons 2-6 is commonly observed, other mutations involving STX16 can also result in AD-PHP1B. MATERIALS AND METHODS The clinical information of a 38-year-old male PHP patient was collected. The genomic DNA from peripheral blood cells was extracted for genetic analysis of GNAS and upstream STX16 by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) and whole-exome sequencing (WES). Sanger sequencing was performed to verify the break point of the novel long-range deletion. RESULTS The patient's medical history of tetany and seizure as well as laboratory examination showing hypocalcemia and elevated PTH levels indicated the diagnosis of PHP. The results of MS-MLPA showed loss of methylation of GNAS A/B:TSS-DMR and half-reduced copy number of STX16 exon 1-9, which revealed the subtype of AD-PHP1B. Furthermore, the WES study displayed a 87.5 kb missing upstream of GNAS. A 87.5 kb deletion spanning STX16 and NPEPL1 together with an insertion of 28 bp of unknown origin was verified by PCR along with Sanger sequencing. CONCLUSIONS A novel deletion of 87.5 kb spanning STX16 and NPEPL1 was discovered in an AD-PHP1B patient, which provides new information on molecular defects leading to AD-PHP1B.
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Affiliation(s)
- Yi Yang
- Key Laboratory of Endocrinology of the Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China
| | - Xueying Chu
- Key Laboratory of Endocrinology of the Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China
| | - Min Nie
- Key Laboratory of Endocrinology of the Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China
| | - An Song
- Key Laboratory of Endocrinology of the Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China
| | - Yan Jiang
- Key Laboratory of Endocrinology of the Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China
| | - Mei Li
- Key Laboratory of Endocrinology of the Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China
| | - Weibo Xia
- Key Laboratory of Endocrinology of the Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China
| | - Xiaoping Xing
- Key Laboratory of Endocrinology of the Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China
| | - Ou Wang
- Key Laboratory of Endocrinology of the Ministry of Health, Department of Endocrinology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China.
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299
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Hassan MM, Yuan G, Chen JG, Tuskan GA, Yang X. Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research. BIODESIGN RESEARCH 2020; 2020:9350905. [PMID: 37849904 PMCID: PMC10530660 DOI: 10.34133/2020/9350905] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 10/19/2023] Open
Abstract
Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as "prime editing," has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.
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Affiliation(s)
- Md. Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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300
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Dong K, Zhang S. Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data. Brief Bioinform 2020; 22:5860691. [PMID: 32578841 PMCID: PMC8138825 DOI: 10.1093/bib/bbaa120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
The rapid accumulation of single-cell chromatin accessibility data offers a unique opportunity to investigate common and specific regulatory mechanisms across different cell types. However, existing methods for cis-regulatory network reconstruction using single-cell chromatin accessibility data were only designed for cells belonging to one cell type, and resulting networks may be incomparable directly due to diverse cell numbers of different cell types. Here, we adopt a computational method to jointly reconstruct cis-regulatory interaction maps (JRIM) of multiple cell populations based on patterns of co-accessibility in single-cell data. We applied JRIM to explore common and specific regulatory interactions across multiple tissues from single-cell ATAC-seq dataset containing ~80 000 cells across 13 mouse tissues. Reconstructed common interactions among 13 tissues indeed relate to basic biological functions, and individual cis-regulatory networks show strong tissue specificity and functional relevance. More importantly, tissue-specific regulatory interactions are mediated by coordination of histone modifications and tissue-related TFs, and many of them may reveal novel regulatory mechanisms.
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Affiliation(s)
- Kangning Dong
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences
| | - Shihua Zhang
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences
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