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Condic N, Amiji H, Patel D, Shropshire WC, Lermi NO, Sabha Y, John B, Hanson B, Karras GI. Selection for robust metabolism in domesticated yeasts is driven by adaptation to Hsp90 stress. Science 2024; 385:eadi3048. [PMID: 39052788 DOI: 10.1126/science.adi3048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 12/31/2023] [Accepted: 05/24/2024] [Indexed: 07/27/2024]
Abstract
Protein folding both promotes and constrains adaptive evolution. We uncover this surprising duality in the role of the protein-folding chaperone heat shock protein 90 (Hsp90) in maintaining the integrity of yeast metabolism amid proteotoxic stressors within industrial domestication niches. Ethanol disrupts critical Hsp90-dependent metabolic pathways and exerts strong selective pressure for redundant duplications of key genes within these pathways, yielding the classical genomic signatures of beer and bread domestication. This work demonstrates a mechanism of adaptive canalization in an ecology of major economic importance and highlights Hsp90-dependent variation as an important source of phantom heritability in complex traits.
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Affiliation(s)
- Natalia Condic
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hatim Amiji
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dipak Patel
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Charles Shropshire
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
| | - Nejla Ozirmak Lermi
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Youssef Sabha
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Beryl John
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Blake Hanson
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
| | - Georgios Ioannis Karras
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center, UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
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2
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Kooblall KG, Stevenson M, Heilig R, Stewart M, Wright B, Lockstone H, Buck D, Fischer R, Wells S, Lines KE, Teboul L, Hennekam RC, Thakker RV. Identification of cellular retinoic acid binding protein 2 (CRABP2) as downstream target of nuclear factor I/X (NFIX): implications for skeletal dysplasia syndromes. JBMR Plus 2024; 8:ziae060. [PMID: 38827116 PMCID: PMC11144382 DOI: 10.1093/jbmrpl/ziae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/04/2024] [Indexed: 06/04/2024] Open
Abstract
Nuclear factor I/X (NFIX) mutations are associated with 2 skeletal dysplasias, Marshall-Smith (MSS) and Malan (MAL) syndromes. NFIX encodes a transcription factor that regulates expression of genes, including Bobby sox (BBX) and glial fibrillary acidic protein (GFAP) in neural progenitor cells and astrocytes, respectively. To elucidate the role of NFIX mutations in MSS, we studied their effects in fibroblast cell lines obtained from 5 MSS unrelated patients and 3 unaffected individuals. The 5 MSS NFIX frameshift mutations in exons 6-8 comprised 3 deletions (c.819-732_1079-948del, c.819-471_1079-687del, c.819-592_1079-808del), an insertion (c.1037_1038insT), and a duplication (c.1090dupG). Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blot analyses using MSS and unrelated control fibroblasts and in vitro expression studies in monkey kidney fibroblast (COS-7) cells showed that frameshift mutations in NFIX exons 6-8 generated mutant transcripts that were not cleared by nonsense-mediated-decay mechanisms and encoded truncated NFIX proteins. Moreover, BBX or GFAP expression was unaffected in the majority of MSS fibroblasts. To identify novel NFIX downstream target genes, RNA sequencing and proteomics analyses were performed on mouse embryonic fibroblast (MEF) cells derived from control Nfix+/+, Nfix+/Del2, Nfix+/Del24, NfixDel24/Del24, Nfix+/Del140, and NfixDel140/Del140 mice, compared with NfixDel2/Del2 mice which had developmental, skeletal, and neural abnormalities. This identified 191 transcripts and 815 proteins misregulated in NfixDel2/Del2 MEFs with ≥2-fold-change (P <0 .05). Validation studies using qRT-PCR and western blot analyses confirmed that 2 genes, cellular retinoic acid binding protein 2 (Crabp2) and vascular cell adhesion molecule 1 (Vcam1), were misregulated at the RNA and protein levels in NfixDel2/Del2 MEFs, and that CRABP2 and VCAM1 expressions were altered in 60%-100% of MSS fibroblast cells. Furthermore, in vitro luciferase reporter assays confirmed that NFIX directly regulates CRABP2 promoter activity. Thus, these altered genes and pathways may represent possible targets for drugs as potential treatments and therapies for MSS.
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Affiliation(s)
- Kreepa G Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
| | - Raphael Heilig
- Target Discovery Unit, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Michelle Stewart
- MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Benjamin Wright
- Oxford Genomics Centre, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Helen Lockstone
- Oxford Genomics Centre, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - David Buck
- Oxford Genomics Centre, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Roman Fischer
- Target Discovery Unit, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Sara Wells
- MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Kate E Lines
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
| | - Lydia Teboul
- MRC Harwell, Mary Lyon Centre, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Raoul C Hennekam
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Churchill Hospital, Headington, Oxford OX3 7LJ, United Kingdom
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3
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Spirov AV, Myasnikova EM, Holloway DM. Body plan evolvability: The role of variability in gene regulatory networks. J Bioinform Comput Biol 2024; 22:2450011. [PMID: 39036846 DOI: 10.1142/s0219720024500112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Recent computational modeling of early fruit fly (Drosophila) development has characterized the degree to which gene regulation networks can be robust to natural variability. In the first few hours of development, broad spatial gradients of maternally derived transcription factors activate embryonic gap genes. These gap patterns determine the subsequent segmented insect body plan through pair-rule gene expression. Gap genes are expressed with greater spatial precision than the maternal patterns. Computational modeling of the gap-gap regulatory interactions provides a mechanistic understanding for this robustness to maternal variability in wild-type (WT) patterning. A long-standing question in evolutionary biology has been how a system which is robust, such as the developmental program creating any particular species' body plan, is also evolvable, i.e. how can a system evolve or speciate, if the WT form is strongly buffered and protected? In the present work, we use the WT model to explore the breakdown of such Waddington-type 'canalization'. What levels of variability will push the system out of the WT form; are there particular pathways in the gene regulatory mechanism which are more susceptible to losing the WT form; and when robustness is lost, what types of forms are most likely to occur (i.e. what forms lie near the WT)? Manipulating maternal effects in several different pathways, we find a common gap 'peak-to-step' pattern transition in the loss of WT. We discuss these results in terms of the evolvability of insect segmentation, and in terms of experimental perturbations and mutations which could test the model predictions. We conclude by discussing the prospects for using continuum models of pattern dynamics to investigate a wider range of evo-devo problems.
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Affiliation(s)
- Alexander V Spirov
- Lab Modeling of Evolution, I. M. Sechenov Institute of Evolutionary Physiology & Biochemistry, Russian Academy of Sciences, Thorez Pr. 44, St. Petersburg 2194223, Russia
| | - Ekaterina M Myasnikova
- Lab Modeling of Evolution, I. M. Sechenov Institute of Evolutionary Physiology & Biochemistry, Russian Academy of Sciences, Thorez Pr. 44, St. Petersburg 2194223, Russia
| | - David M Holloway
- Mathematics Department, British Columbia Institute of Technology, 3700 Willingdon Ave., Burnaby, B.C. V5G 3H2, Canada
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4
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Tawfeeq MT, Voordeckers K, van den Berg P, Govers SK, Michiels J, Verstrepen KJ. Mutational robustness and the role of buffer genes in evolvability. EMBO J 2024; 43:2294-2307. [PMID: 38719995 PMCID: PMC11183146 DOI: 10.1038/s44318-024-00109-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/19/2024] [Accepted: 04/17/2024] [Indexed: 06/19/2024] Open
Abstract
Organisms rely on mutations to fuel adaptive evolution. However, many mutations impose a negative effect on fitness. Cells may have therefore evolved mechanisms that affect the phenotypic effects of mutations, thus conferring mutational robustness. Specifically, so-called buffer genes are hypothesized to interact directly or indirectly with genetic variation and reduce its effect on fitness. Environmental or genetic perturbations can change the interaction between buffer genes and genetic variation, thereby unmasking the genetic variation's phenotypic effects and thus providing a source of variation for natural selection to act on. This review provides an overview of our understanding of mutational robustness and buffer genes, with the chaperone gene HSP90 as a key example. It discusses whether buffer genes merely affect standing variation or also interact with de novo mutations, how mutational robustness could influence evolution, and whether mutational robustness might be an evolved trait or rather a mere side-effect of complex genetic interactions.
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Affiliation(s)
- Mohammed T Tawfeeq
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Karin Voordeckers
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Pieter van den Berg
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Jan Michiels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.
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5
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Alexandre CM, Bubb KL, Schultz KM, Lempe J, Cuperus JT, Queitsch C. LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2024; 241:253-266. [PMID: 37865885 PMCID: PMC10843042 DOI: 10.1111/nph.19334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/26/2023] [Indexed: 10/23/2023]
Abstract
Isogenic individuals can display seemingly stochastic phenotypic differences, limiting the accuracy of genotype-to-phenotype predictions. The extent of this phenotypic variation depends in part on genetic background, raising questions about the genes involved in controlling stochastic phenotypic variation. Focusing on early seedling traits in Arabidopsis thaliana, we found that hypomorphs of the cuticle-related gene LIPID TRANSFER PROTEIN 2 (LTP2) greatly increased variation in seedling phenotypes, including hypocotyl length, gravitropism and cuticle permeability. Many ltp2 hypocotyls were significantly shorter than wild-type hypocotyls while others resembled the wild-type. Differences in epidermal properties and gene expression between ltp2 seedlings with long and short hypocotyls suggest a loss of cuticle integrity as the primary determinant of the observed phenotypic variation. We identified environmental conditions that reveal or mask the increased variation in ltp2 hypomorphs and found that increased expression of its closest paralog LTP1 is necessary for ltp2 phenotypes. Our results illustrate how decreased expression of a single gene can generate starkly increased phenotypic variation in isogenic individuals in response to an environmental challenge.
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Affiliation(s)
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Karla M Schultz
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Janne Lempe
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany 1099
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
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6
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Dandage R, Papkov M, Greco BM, Fishman D, Friesen H, Wang K, Styles E, Kraus O, Grys B, Boone C, Andrews B, Parts L, Kuzmin E. Single-cell imaging of protein dynamics of paralogs reveals mechanisms of gene retention. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.23.568466. [PMID: 38045359 PMCID: PMC10690282 DOI: 10.1101/2023.11.23.568466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Gene duplication is common across the tree of life, including yeast and humans, and contributes to genomic robustness. In this study, we examined changes in the subcellular localization and abundance of proteins in response to the deletion of their paralogs originating from the whole-genome duplication event, which is a largely unexplored mechanism of functional divergence. We performed a systematic single-cell imaging analysis of protein dynamics and screened subcellular redistribution of proteins, capturing their localization and abundance changes, providing insight into forces determining paralog retention. Paralogs showed dependency, whereby proteins required their paralog to maintain their native abundance or localization, more often than compensation. Network feature analysis suggested the importance of functional redundancy and rewiring of protein and genetic interactions underlying redistribution response of paralogs. Translation of non-canonical protein isoform emerged as a novel compensatory mechanism. This study provides new insights into paralog retention and evolutionary forces that shape genomes.
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7
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Keseroglu K, Zinani OQH, Keskin S, Seawall H, Alpay EE, Özbudak EM. Stochastic gene expression and environmental stressors trigger variable somite segmentation phenotypes. Nat Commun 2023; 14:6497. [PMID: 37838784 PMCID: PMC10576776 DOI: 10.1038/s41467-023-42220-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023] Open
Abstract
Mutations of several genes cause incomplete penetrance and variable expressivity of phenotypes, which are usually attributed to modifier genes or gene-environment interactions. Here, we show stochastic gene expression underlies the variability of somite segmentation defects in embryos mutant for segmentation clock genes her1 or her7. Phenotypic strength is further augmented by low temperature and hypoxia. By performing live imaging of the segmentation clock reporters, we further show that groups of cells with higher oscillation amplitudes successfully form somites while those with lower amplitudes fail to do so. In unfavorable environments, the number of cycles with high amplitude oscillations and the number of successful segmentations proportionally decrease. These results suggest that individual oscillation cycles stochastically fail to pass a threshold amplitude, resulting in segmentation defects in mutants. Our quantitative methodology is adaptable to investigate variable phenotypes of mutant genes in different tissues.
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Affiliation(s)
- Kemal Keseroglu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Oriana Q H Zinani
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Molecular and Developmental Biology Graduate Program, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Sevdenur Keskin
- Allergy and Immunology, University of Arkansas for Medical Science and Arkansas Children's Hospital, Little Rock, AR, 72202, USA
| | - Hannah Seawall
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Eslim E Alpay
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ertuğrul M Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
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8
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Alexandre CM, Bubb KL, Schultz KM, Lempe J, Cuperus JT, Queitsch C. LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540469. [PMID: 37214854 PMCID: PMC10197655 DOI: 10.1101/2023.05.11.540469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Isogenic individuals can display seemingly stochastic phenotypic differences, limiting the accuracy of genotype-to-phenotype predictions. The extent of this phenotypic variation depends in part on genetic background, raising questions about the genes involved in controlling stochastic phenotypic variation. Focusing on early seedling traits in Arabidopsis thaliana, we found that hypomorphs of the cuticle-related gene LTP2 greatly increased variation in seedling phenotypes, including hypocotyl length, gravitropism and cuticle permeability. Many ltp2 hypocotyls were significantly shorter than wild-type hypocotyls while others resembled the wild type. Differences in epidermal properties and gene expression between ltp2 seedlings with long and short hypocotyls suggest a loss of cuticle integrity as the primary determinant of the observed phenotypic variation. We identified environmental conditions that reveal or mask the increased variation in ltp2 hypomorphs, and found that increased expression of its closest paralog LTP1 is necessary for ltp2 phenotypes. Our results illustrate how decreased expression of a single gene can generate starkly increased phenotypic variation in isogenic individuals in response to an environmental challenge.
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Affiliation(s)
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Karla M Schultz
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Janne Lempe
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
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9
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Sun YH, Wu YL, Liao BY. Phenotypic heterogeneity in human genetic diseases: ultrasensitivity-mediated threshold effects as a unifying molecular mechanism. J Biomed Sci 2023; 30:58. [PMID: 37525275 PMCID: PMC10388531 DOI: 10.1186/s12929-023-00959-7] [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: 04/01/2023] [Accepted: 07/26/2023] [Indexed: 08/02/2023] Open
Abstract
Phenotypic heterogeneity is very common in genetic systems and in human diseases and has important consequences for disease diagnosis and treatment. In addition to the many genetic and non-genetic (e.g., epigenetic, environmental) factors reported to account for part of the heterogeneity, we stress the importance of stochastic fluctuation and regulatory network topology in contributing to phenotypic heterogeneity. We argue that a threshold effect is a unifying principle to explain the phenomenon; that ultrasensitivity is the molecular mechanism for this threshold effect; and discuss the three conditions for phenotypic heterogeneity to occur. We suggest that threshold effects occur not only at the cellular level, but also at the organ level. We stress the importance of context-dependence and its relationship to pleiotropy and edgetic mutations. Based on this model, we provide practical strategies to study human genetic diseases. By understanding the network mechanism for ultrasensitivity and identifying the critical factor, we may manipulate the weak spot to gently nudge the system from an ultrasensitive state to a stable non-disease state. Our analysis provides a new insight into the prevention and treatment of genetic diseases.
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Affiliation(s)
- Y Henry Sun
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Zhunan, Miaoli, Taiwan.
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
| | - Yueh-Lin Wu
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Zhunan, Miaoli, Taiwan
- Division of Nephrology, Department of Internal Medicine, Wei-Gong Memorial Hospital, Miaoli, Taiwan
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei, Taiwan
- Division of Nephrology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City, Taiwan
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institute, Zhunan, Miaoli, Taiwan
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10
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Patel D, Amiji H, Shropshire W, Condic N, Lermi NO, Sabha Y, John B, Hanson B, Karras GI. Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.547572. [PMID: 37745611 PMCID: PMC10516021 DOI: 10.1101/2023.07.21.547572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Protein folding promotes and constrains adaptive evolution. We uncover this surprising duality in the role the protein-folding chaperone Hsp90 plays in mediating the interplay between proteome and the genome which acts to maintain the integrity of yeast metabolism in the face of proteotoxic stressors in anthropic niches. Of great industrial relevance, ethanol concentrations generated by fermentation in the making of beer and bread disrupt critical Hsp90-dependent nodes of metabolism and exert strong selective pressure for increased copy number of key genes encoding components of these nodes, yielding the classical genetic signatures of beer and bread domestication. This work establishes a mechanism of adaptive canalization in an ecology of major economic significance and highlights Hsp90-contingent variation as an important source of phantom heritability in complex traits.
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11
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Kooblall KG, Stevenson M, Stewart M, Harris L, Zalucki O, Dewhurst H, Butterfield N, Leng H, Hough TA, Ma D, Siow B, Potter P, Cox RD, Brown SD, Horwood N, Wright B, Lockstone H, Buck D, Vincent TL, Hannan FM, Bassett JD, Williams GR, Lines KE, Piper M, Wells S, Teboul L, Hennekam RC, Thakker RV. A Mouse Model with a Frameshift Mutation in the Nuclear Factor I/X ( NFIX) Gene Has Phenotypic Features of Marshall-Smith Syndrome. JBMR Plus 2023; 7:e10739. [PMID: 37283649 PMCID: PMC10241085 DOI: 10.1002/jbm4.10739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
The nuclear factor I/X (NFIX) gene encodes a ubiquitously expressed transcription factor whose mutations lead to two allelic disorders characterized by developmental, skeletal, and neural abnormalities, namely, Malan syndrome (MAL) and Marshall-Smith syndrome (MSS). NFIX mutations associated with MAL mainly cluster in exon 2 and are cleared by nonsense-mediated decay (NMD) leading to NFIX haploinsufficiency, whereas NFIX mutations associated with MSS are clustered in exons 6-10 and escape NMD and result in the production of dominant-negative mutant NFIX proteins. Thus, different NFIX mutations have distinct consequences on NFIX expression. To elucidate the in vivo effects of MSS-associated NFIX exon 7 mutations, we used CRISPR-Cas9 to generate mouse models with exon 7 deletions that comprised: a frameshift deletion of two nucleotides (Nfix Del2); in-frame deletion of 24 nucleotides (Nfix Del24); and deletion of 140 nucleotides (Nfix Del140). Nfix +/Del2, Nfix +/Del24, Nfix +/Del140, Nfix Del24/Del24, and Nfix Del140/Del140 mice were viable, normal, and fertile, with no skeletal abnormalities, but Nfix Del2/Del2 mice had significantly reduced viability (p < 0.002) and died at 2-3 weeks of age. Nfix Del2 was not cleared by NMD, and NfixDel2/Del2 mice, when compared to Nfix +/+ and Nfix +/Del2 mice, had: growth retardation; short stature with kyphosis; reduced skull length; marked porosity of the vertebrae with decreased vertebral and femoral bone mineral content; and reduced caudal vertebrae height and femur length. Plasma biochemistry analysis revealed Nfix Del2/Del2 mice to have increased total alkaline phosphatase activity but decreased C-terminal telopeptide and procollagen-type-1-N-terminal propeptide concentrations compared to Nfix +/+ and Nfix +/Del2 mice. Nfix Del2/Del2 mice were also found to have enlarged cerebral cortices and ventricular areas but smaller dentate gyrus compared to Nfix +/+ mice. Thus, Nfix Del2/Del2 mice provide a model for studying the in vivo effects of NFIX mutants that escape NMD and result in developmental abnormalities of the skeletal and neural tissues that are associated with MSS. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Kreepa G. Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michelle Stewart
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | | | - Oressia Zalucki
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Hannah Dewhurst
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Natalie Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Houfu Leng
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Tertius A. Hough
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Da Ma
- Department of Internal MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | | | - Paul Potter
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Roger D. Cox
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Stephen D.M. Brown
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Nicole Horwood
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Benjamin Wright
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Helen Lockstone
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - David Buck
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Tonia L. Vincent
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Fadil M. Hannan
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
- Nuffield Department of Women's and Reproductive HealthUniversity of OxfordOxfordUK
| | - J.H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Kate E. Lines
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michael Piper
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Sara Wells
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Lydia Teboul
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Raoul C. Hennekam
- Department of Pediatrics, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Rajesh V. Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
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12
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van Oosten-Hawle P. Organismal Roles of Hsp90. Biomolecules 2023; 13:biom13020251. [PMID: 36830620 PMCID: PMC9952938 DOI: 10.3390/biom13020251] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is a highly conserved molecular chaperone that assists in the maturation of many client proteins involved in cellular signal transduction. As a regulator of cellular signaling processes, it is vital for the maintenance of cellular proteostasis and adaptation to environmental stresses. Emerging research shows that Hsp90 function in an organism goes well beyond intracellular proteostasis. In metazoans, Hsp90, as an environmentally responsive chaperone, is involved in inter-tissue stress signaling responses that coordinate and safeguard cell nonautonomous proteostasis and organismal health. In this way, Hsp90 has the capacity to influence evolution and aging, and effect behavioral responses to facilitate tissue-defense systems that ensure organismal survival. In this review, I summarize the literature on the organismal roles of Hsp90 uncovered in multicellular organisms, from plants to invertebrates and mammals.
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Affiliation(s)
- Patricija van Oosten-Hawle
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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13
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Parab L, Pal S, Dhar R. Transcription factor binding process is the primary driver of noise in gene expression. PLoS Genet 2022; 18:e1010535. [PMID: 36508455 PMCID: PMC9779669 DOI: 10.1371/journal.pgen.1010535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/22/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Noise in expression of individual genes gives rise to variations in activity of cellular pathways and generates heterogeneity in cellular phenotypes. Phenotypic heterogeneity has important implications for antibiotic persistence, mutation penetrance, cancer growth and therapy resistance. Specific molecular features such as the presence of the TATA box sequence and the promoter nucleosome occupancy have been associated with noise. However, the relative importance of these features in noise regulation is unclear and how well these features can predict noise has not yet been assessed. Here through an integrated statistical model of gene expression noise in yeast we found that the number of regulating transcription factors (TFs) of a gene was a key predictor of noise, whereas presence of the TATA box and the promoter nucleosome occupancy had poor predictive power. With an increase in the number of regulatory TFs, there was a rise in the number of cooperatively binding TFs. In addition, an increased number of regulatory TFs meant more overlaps in TF binding sites, resulting in competition between TFs for binding to the same region of the promoter. Through modeling of TF binding to promoter and application of stochastic simulations, we demonstrated that competition and cooperation among TFs could increase noise. Thus, our work uncovers a process of noise regulation that arises out of the dynamics of gene regulation and is not dependent on any specific transcription factor or specific promoter sequence.
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Affiliation(s)
- Lavisha Parab
- Department of Biotechnology, Indian Institute of Technology (IIT) Kharagpur, Kharagpur, West Bengal, India
- Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Sampriti Pal
- Department of Biotechnology, Indian Institute of Technology (IIT) Kharagpur, Kharagpur, West Bengal, India
| | - Riddhiman Dhar
- Department of Biotechnology, Indian Institute of Technology (IIT) Kharagpur, Kharagpur, West Bengal, India
- * E-mail:
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14
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Bhattacharya K, Maiti S, Zahoran S, Weidenauer L, Hany D, Wider D, Bernasconi L, Quadroni M, Collart M, Picard D. Translational reprogramming in response to accumulating stressors ensures critical threshold levels of Hsp90 for mammalian life. Nat Commun 2022; 13:6271. [PMID: 36270993 PMCID: PMC9587034 DOI: 10.1038/s41467-022-33916-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
The cytosolic molecular chaperone Hsp90 is essential for eukaryotic life. Although reduced Hsp90 levels correlate with aging, it was unknown whether eukaryotic cells and organisms can tune the basal Hsp90 levels to alleviate physiologically accumulated stress. We have investigated whether and how mice adapt to the deletion of three out of four alleles of the two genes encoding cytosolic Hsp90, with one Hsp90β allele being the only remaining one. While the vast majority of such mouse embryos die during gestation, survivors apparently manage to increase their Hsp90β protein to at least wild-type levels. Our studies reveal an internal ribosome entry site in the 5' untranslated region of the Hsp90β mRNA allowing translational reprogramming to compensate for the genetic loss of Hsp90 alleles and in response to stress. We find that the minimum amount of total Hsp90 required to support viability of mammalian cells and organisms is 50-70% of what is normally there. Those that fail to maintain a threshold level are subject to accelerated senescence, proteostatic collapse, and ultimately death. Therefore, considering that Hsp90 levels can be reduced ≥100-fold in the unicellular budding yeast, critical threshold levels of Hsp90 have markedly increased during eukaryotic evolution.
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Affiliation(s)
- Kaushik Bhattacharya
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Samarpan Maiti
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Szabolcs Zahoran
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Lorenz Weidenauer
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Dina Hany
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Diana Wider
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Lilia Bernasconi
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Martine Collart
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Didier Picard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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15
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Xiao L, Fan D, Qi H, Cong Y, Du Z. Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis. Cell Syst 2022; 13:615-630.e9. [PMID: 35882226 DOI: 10.1016/j.cels.2022.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/14/2022] [Accepted: 06/30/2022] [Indexed: 01/26/2023]
Abstract
Developmental processes are intrinsically robust so as to preserve a normal-like state in response to genetic and environmental fluctuations. However, the robustness and potential phenotypic plasticity of individual developing cells under genetic perturbations remain to be systematically evaluated. Using large-scale gene perturbation, live imaging, lineage tracing, and single-cell phenomics, we quantified the phenotypic landscape of C. elegans embryogenesis in >2,000 embryos following individual knockdown of over 750 conserved genes. We observed that cellular genetic systems are not sufficiently robust to single-gene perturbations across all cells; rather, gene knockdowns frequently induced cellular defects. Dynamic phenotypic analyses revealed many cellular defects to be transient, with cells exhibiting phenotypic plasticity that serves to alleviate, correct, and accommodate the defects. Moreover, potential developmentally related cell modules may buffer the phenotypic effects of individual cell position changes. Our findings reveal non-negligible contributions of cellular plasticity and multicellularity as compensatory strategies to increase developmental robustness.
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Affiliation(s)
- Long Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duchangjiang Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Qi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yulin Cong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Du
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Somogyvári M, Khatatneh S, Sőti C. Hsp90: From Cellular to Organismal Proteostasis. Cells 2022; 11:cells11162479. [PMID: 36010556 PMCID: PMC9406713 DOI: 10.3390/cells11162479] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Assuring a healthy proteome is indispensable for survival and organismal health. Proteome disbalance and the loss of the proteostasis buffer are hallmarks of various diseases. The essential molecular chaperone Hsp90 is a regulator of the heat shock response via HSF1 and a stabilizer of a plethora of signaling proteins. In this review, we summarize the role of Hsp90 in the cellular and organismal regulation of proteome maintenance.
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17
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Gera T, Jonas F, More R, Barkai N. Evolution of binding preferences among whole-genome duplicated transcription factors. eLife 2022; 11:73225. [PMID: 35404235 PMCID: PMC9000951 DOI: 10.7554/elife.73225] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/20/2022] [Indexed: 01/10/2023] Open
Abstract
Throughout evolution, new transcription factors (TFs) emerge by gene duplication, promoting growth and rewiring of transcriptional networks. How TF duplicates diverge was studied in a few cases only. To provide a genome-scale view, we considered the set of budding yeast TFs classified as whole-genome duplication (WGD)-retained paralogs (~35% of all specific TFs). Using high-resolution profiling, we find that ~60% of paralogs evolved differential binding preferences. We show that this divergence results primarily from variations outside the DNA-binding domains (DBDs), while DBD preferences remain largely conserved. Analysis of non-WGD orthologs revealed uneven splitting of ancestral preferences between duplicates, and the preferential acquiring of new targets by the least conserved paralog (biased neo/sub-functionalization). Interactions between paralogs were rare, and, when present, occurred through weak competition for DNA-binding or dependency between dimer-forming paralogs. We discuss the implications of our findings for the evolutionary design of transcriptional networks.
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Affiliation(s)
- Tamar Gera
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Roye More
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science
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18
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Kuzmin E, Taylor JS, Boone C. Retention of duplicated genes in evolution. Trends Genet 2022; 38:59-72. [PMID: 34294428 PMCID: PMC8678172 DOI: 10.1016/j.tig.2021.06.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/03/2023]
Abstract
Gene duplication is a prevalent phenomenon across the tree of life. The processes that lead to the retention of duplicated genes are not well understood. Functional genomics approaches in model organisms, such as yeast, provide useful tools to test the mechanisms underlying retention with functional redundancy and divergence of duplicated genes, including fates associated with neofunctionalization, subfunctionalization, back-up compensation, and dosage amplification. Duplicated genes may also be retained as a consequence of structural and functional entanglement. Advances in human gene editing have enabled the interrogation of duplicated genes in the human genome, providing new tools to evaluate the relative contributions of each of these factors to duplicate gene retention and the evolution of genome structure.
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Affiliation(s)
- Elena Kuzmin
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Centre, McGill University, 1160 Ave des Pins Ouest, Montreal, QC, Canada H3A 1A3.
| | - John S Taylor
- Department of Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, Canada V8W 2Y2
| | - Charles Boone
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1; RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan, 351-0198
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19
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Sands B, Yun S, Mendenhall AR. Introns control stochastic allele expression bias. Nat Commun 2021; 12:6527. [PMID: 34764277 PMCID: PMC8585970 DOI: 10.1038/s41467-021-26798-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Monoallelic expression (MAE) or extreme allele bias can account for incomplete penetrance, missing heritability and non-Mendelian diseases. In cancer, MAE is associated with shorter patient survival times and higher tumor grade. Prior studies showed that stochastic MAE is caused by stochastic epigenetic silencing, in a gene and tissue-specific manner. Here, we used C. elegans to study stochastic MAE in vivo. We found allele bias/MAE to be widespread within C. elegans tissues, presenting as a continuum from fully biallelic to MAE. We discovered that the presence of introns within alleles robustly decreases MAE. We determined that introns control MAE at distinct loci, in distinct cell types, with distinct promoters, and within distinct coding sequences, using a 5'-intron position-dependent mechanism. Bioinformatic analysis showed human intronless genes are significantly enriched for MAE. Our experimental evidence demonstrates a role for introns in regulating MAE, possibly explaining why some mutations within introns result in disease.
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Affiliation(s)
- Bryan Sands
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Soo Yun
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Alexander R. Mendenhall
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
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20
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Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo AF, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett SW, Kienberger H, Kleigrewe K, de Bono M, Wakelam MJO, Casanueva O. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biol 2021; 19:e3001431. [PMID: 34723964 PMCID: PMC8585009 DOI: 10.1371/journal.pbio.3001431] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 11/11/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane's phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal.
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Affiliation(s)
- Laetitia Chauve
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Francesca Hodge
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Sharlene Murdoch
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | | | | | | | | | - Greg West
- Babraham Institute, Cambridge, United Kingdom
| | | | | | - Cheryl Li
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | | | | | - Karin Kleigrewe
- Bavarian Centre for Biomolecular Mass Spectrometry, Freising, Germany
| | - Mario de Bono
- Institute of Science and Technology, Klosterneuburg, Austria
| | | | - Olivia Casanueva
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
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21
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Garge RK, Cha HJ, Lee C, Gollihar JD, Kachroo AH, Wallingford JB, Marcotte EM. Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast. Genetics 2021; 219:iyab101. [PMID: 34849907 PMCID: PMC8633126 DOI: 10.1093/genetics/iyab101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/15/2021] [Indexed: 12/20/2022] Open
Abstract
Thiabendazole (TBZ) is an FDA-approved benzimidazole widely used for its antifungal and antihelminthic properties. We showed previously that TBZ is also a potent vascular disrupting agent and inhibits angiogenesis at the tissue level by dissociating vascular endothelial cells in newly formed blood vessels. Here, we uncover TBZ's molecular target and mechanism of action. Using human cell culture, molecular modeling, and humanized yeast, we find that TBZ selectively targets only 1 of 9 human β-tubulin isotypes (TUBB8) to specifically disrupt endothelial cell microtubules. By leveraging epidemiological pesticide resistance data and mining chemical features of commercially used benzimidazoles, we discover that a broader class of benzimidazole compounds, in extensive use for 50 years, also potently disrupt immature blood vessels and inhibit angiogenesis. Thus, besides identifying the molecular mechanism of benzimidazole-mediated vascular disruption, this study presents evidence relevant to the widespread use of these compounds while offering potential new clinical applications.
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Affiliation(s)
- Riddhiman K Garge
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hye Ji Cha
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- US Army Research Laboratory—South, Austin, TX 78758, USA
| | - Aashiq H Kachroo
- The Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montreal, QC H4B 1R6, Canada
| | - John B Wallingford
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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22
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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23
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Koneru SL, Hintze M, Katsanos D, Barkoulas M. Cryptic genetic variation in a heat shock protein modifies the outcome of a mutation affecting epidermal stem cell development in C. elegans. Nat Commun 2021; 12:3263. [PMID: 34059684 PMCID: PMC8166903 DOI: 10.1038/s41467-021-23567-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
A fundamental question in medical genetics is how the genetic background modifies the phenotypic outcome of mutations. We address this question by focusing on the seam cells, which display stem cell properties in the epidermis of Caenorhabditis elegans. We demonstrate that a putative null mutation in the GATA transcription factor egl-18, which is involved in seam cell fate maintenance, is more tolerated in the CB4856 isolate from Hawaii than the lab reference strain N2 from Bristol. We identify multiple quantitative trait loci (QTLs) underlying the difference in phenotype expressivity between the two isolates. These QTLs reveal cryptic genetic variation that reinforces seam cell fate through potentiating Wnt signalling. Within one QTL region, a single amino acid deletion in the heat shock protein HSP-110 in CB4856 is sufficient to modify Wnt signalling and seam cell development, highlighting that natural variation in conserved heat shock proteins can shape phenotype expressivity. How the genetic background modifies the expression of mutations is a key question that is addressed in this study in the context of seam cell development in Caenorhabditis elegans isolates. One amino acid deletion in a conserved heat shock protein is sufficient to shape phenotype expressivity upon mutation of a GATA transcription factor.
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Affiliation(s)
- Sneha L Koneru
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Mark Hintze
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Dimitris Katsanos
- Department of Life Sciences, Imperial College, London, United Kingdom
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24
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Mendenhall AR, Martin GM, Kaeberlein M, Anderson RM. Cell-to-cell variation in gene expression and the aging process. GeroScience 2021; 43:181-196. [PMID: 33595768 PMCID: PMC8050212 DOI: 10.1007/s11357-021-00339-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
There is tremendous variation in biological traits, and much of it is not accounted for by variation in DNA sequence, including human diseases and lifespan. Emerging evidence points to differences in the execution of the genetic program as a key source of variation, be it stochastic variation or programmed variation. Here we discuss variation in gene expression as an intrinsic property and how it could contribute to variation in traits, including the rate of aging. The review is divided into sections describing the historical context and evidence to date for nongenetic variation, the different approaches that may be used to detect nongenetic variation, and recent findings showing that the amount of variation in gene expression can be both genetically programmed and epigenetically controlled. Finally, we present evidence that changes in cell-to-cell variation in gene expression emerge as part of the aging process and may be linked to disease vulnerability as a function of age. These emerging concepts are likely to be important across the spectrum of biomedical research and may well underpin what we understand as biological aging.
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Affiliation(s)
- Alexander R Mendenhall
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA.
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA.
| | - George M Martin
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Rozalyn M Anderson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin and Geriatric Research Education and Clinical Center, William S Middleton Memorial Veterans Hospital, Madison, WI, USA.
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25
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Gualtieri CT. Genomic Variation, Evolvability, and the Paradox of Mental Illness. Front Psychiatry 2021; 11:593233. [PMID: 33551865 PMCID: PMC7859268 DOI: 10.3389/fpsyt.2020.593233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.
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26
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Moreno-Ayala R, Olivares-Chauvet P, Schäfer R, Junker JP. Variability of an Early Developmental Cell Population Underlies Stochastic Laterality Defects. Cell Rep 2021; 34:108606. [PMID: 33440143 PMCID: PMC7809618 DOI: 10.1016/j.celrep.2020.108606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/28/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Embryonic development seemingly proceeds with almost perfect precision. However, it is largely unknown how much underlying microscopic variability is compatible with normal development. Here, we quantify embryo-to-embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We notice that the size of a sub-population of the endoderm, the dorsal forerunner cells (DFCs, which later form the left-right organizer), exhibits significantly more embryo-to-embryo variation than the rest of the endoderm. We find that, with incubation of the embryos at elevated temperature, the frequency of left-right laterality defects is increased drastically in embryos with a low number of DFCs. Furthermore, we observe that these fluctuations have a large stochastic component among fish of the same genetic background. Hence, a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be associated with maternal effects in the specification of the DFCs. High embryo-to-embryo variability of dorsal forerunner cell numbers Fluctuations of dorsal forerunner cells have a large stochastic component Embryos with fewer dorsal forerunner cells frequently develop laterality defects Variability of dorsal forerunner cell numbers is associated to maternal effects
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Affiliation(s)
- Roberto Moreno-Ayala
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Hannoversche Strasse 28, 10115 Berlin, Germany
| | - Pedro Olivares-Chauvet
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Hannoversche Strasse 28, 10115 Berlin, Germany
| | - Ronny Schäfer
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Hannoversche Strasse 28, 10115 Berlin, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Hannoversche Strasse 28, 10115 Berlin, Germany.
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27
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Houri-Zeevi L, Korem Kohanim Y, Antonova O, Rechavi O. Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans. Cell 2020; 182:1186-1197.e12. [PMID: 32841602 PMCID: PMC7479518 DOI: 10.1016/j.cell.2020.07.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/21/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023]
Abstract
Experiences trigger transgenerational small RNA-based responses in C. elegans nematodes. Dedicated machinery ensures that heritable effects are reset, but how the responses segregate in the population is unknown. We show that isogenic individuals differ dramatically in the persistence of transgenerational responses. By examining lineages of more than 20,000 worms, three principles emerge: (1) The silencing each mother initiates is distributed evenly among her descendants; heritable RNAi dissipates but is uniform in every generation. (2) Differences between lineages arise because the mothers that initiate heritable responses stochastically assume different "inheritance states" that determine the progeny's fate. (3) The likelihood that an RNAi response would continue to be inherited increases the more generations it lasts. The inheritance states are determined by HSF-1, which regulates silencing factors and, accordingly, small RNA levels. We found that, based on the parents' inheritance state, the descendants' developmental rate in response to stress can be predicted.
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Affiliation(s)
- Leah Houri-Zeevi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Yael Korem Kohanim
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Olga Antonova
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel.
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28
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Baugh LR, Day T. Nongenetic inheritance and multigenerational plasticity in the nematode C. elegans. eLife 2020; 9:e58498. [PMID: 32840479 PMCID: PMC7447421 DOI: 10.7554/elife.58498] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
A rapidly growing body of literature in several organisms suggests that environmentally-induced adaptive changes in phenotype can be transmitted across multiple generations. Although within-generation plasticity has been well documented, multigenerational plasticity represents a significant departure from conventional evolutionary thought. Studies of C. elegans have been particularly influential because this species exhibits extensive phenotypic plasticity, it is often essentially isogenic, and it has well-documented molecular and cellular mechanisms through which nongenetic inheritance occurs. However, while experimentalists are eager to claim that nongenetic modes of inheritance characterized in this and other model systems enhance fitness, many biologists remain skeptical given the extraordinary nature of this claim. We establish three criteria to evaluate how compelling the evidence for adaptive multigenerational plasticity is, and we use these criteria to critically examine putative cases of it in C. elegans. We conclude by suggesting potentially fruitful avenues for future research.
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Affiliation(s)
- L Ryan Baugh
- Department of Biology, Center for Genomics and Computational Biology, Duke UniversityDurhamUnited States
| | - Troy Day
- Departments of Mathematics and Statistics, Department of Biology, Queens UniversityKingstonCanada
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29
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Genome-wide DNA methylation analysis of KRAS mutant cell lines. Sci Rep 2020; 10:10149. [PMID: 32576853 PMCID: PMC7311523 DOI: 10.1038/s41598-020-66797-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/22/2020] [Indexed: 12/23/2022] Open
Abstract
Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 differentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in differentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream effector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer.
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30
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Jariani A, Vermeersch L, Cerulus B, Perez-Samper G, Voordeckers K, Van Brussel T, Thienpont B, Lambrechts D, Verstrepen KJ. A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast. eLife 2020; 9:e55320. [PMID: 32420869 PMCID: PMC7259953 DOI: 10.7554/elife.55320] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity of the state-of-the-art techniques that are available for mammalian cells. In this study, we report how 10x Genomics' droplet-based single-cell RNA sequencing technology can be modified to allow analysis of yeast cells. The protocol, which is based on in-droplet spheroplasting of the cells, yields an order-of-magnitude higher throughput in comparison to existing methods. After extensive validation of the method, we demonstrate its use by studying the dynamics of the response of isogenic yeast populations to a shift in carbon source, revealing the heterogeneity and underlying molecular processes during this shift. The method we describe opens new avenues for studies focusing on yeast cells, as well as other cells with a degradable cell wall.
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Affiliation(s)
- Abbas Jariani
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Lieselotte Vermeersch
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Bram Cerulus
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Gemma Perez-Samper
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Karin Voordeckers
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Thomas Van Brussel
- Laboratory for Translational Genetics, Department of Human Genetics, KU LeuvenLeuvenBelgium
- VIB Center for Cancer Biology, VIBLeuvenBelgium
| | - Bernard Thienpont
- Laboratory for Translational Genetics, Department of Human Genetics, KU LeuvenLeuvenBelgium
- VIB Center for Cancer Biology, VIBLeuvenBelgium
- Laboratory for Functional Epigenetics, Department of Genetics, KU LeuvenLeuvenBelgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU LeuvenLeuvenBelgium
- VIB Center for Cancer Biology, VIBLeuvenBelgium
| | - Kevin J Verstrepen
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
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31
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Li X, Zhao Z, Xu W, Fan R, Xiao L, Ma X, Du Z. Systems Properties and Spatiotemporal Regulation of Cell Position Variability during Embryogenesis. Cell Rep 2020; 26:313-321.e7. [PMID: 30625313 DOI: 10.1016/j.celrep.2018.12.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 11/06/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022] Open
Abstract
An intriguing question in developmental biology is how do developmental processes achieve high reproducibility among individuals? An in-depth analysis of information contained in phenotypic variability provides an important perspective to address this question. In this work, we present a quantitative and functional analysis of cell position variability during Caenorhabditis elegans embryogenesis. We find that cell position variability is highly deterministic and regulated by intrinsic and extrinsic mechanisms. Positional variability is determined by cell lineage identity and is coupled to diverse developmental properties of cells, including embryonic localization, cell contact, and left-right symmetry. Temporal dynamics of cell position variability are highly concordant, and fate specification contributes to a systems-wide reduction of variability that could provide a buffering strategy. Positional variability is stringently regulated throughout embryogenesis and cell-cell junctions function to restrict variability. Our results provide insight into systems properties and spatiotemporal control of cellular variability during development.
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Affiliation(s)
- Xiaoyu Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiguang Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weina Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuehua Ma
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuo Du
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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32
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Huang A, Rupprecht JF, Saunders TE. Embryonic geometry underlies phenotypic variation in decanalized conditions. eLife 2020; 9:e47380. [PMID: 32048988 PMCID: PMC7032927 DOI: 10.7554/elife.47380] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 02/11/2020] [Indexed: 11/13/2022] Open
Abstract
During development, many mutations cause increased variation in phenotypic outcomes, a phenomenon termed decanalization. Phenotypic discordance is often observed in the absence of genetic and environmental variations, but the mechanisms underlying such inter-individual phenotypic discordance remain elusive. Here, using the anterior-posterior (AP) patterning of the Drosophila embryo, we identified embryonic geometry as a key factor predetermining patterning outcomes under decanalizing mutations. With the wild-type AP patterning network, we found that AP patterning is robust to variations in embryonic geometry; segmentation gene expression remains reproducible even when the embryo aspect ratio is artificially reduced by more than twofold. In contrast, embryonic geometry is highly predictive of individual patterning defects under decanalized conditions of either increased bicoid (bcd) dosage or bcd knockout. We showed that the phenotypic discordance can be traced back to variations in the gap gene expression, which is rendered sensitive to the geometry of the embryo under mutations.
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Affiliation(s)
- Anqi Huang
- Mechanobiology Institute, National University of SingaporeSingaporeSingapore
| | - Jean-François Rupprecht
- Mechanobiology Institute, National University of SingaporeSingaporeSingapore
- CNRS and Turing Center for Living Systems, Centre de Physique Théorique, Aix-Marseille UniversitéMarseilleFrance
| | - Timothy E Saunders
- Mechanobiology Institute, National University of SingaporeSingaporeSingapore
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Institute of Molecular and Cell Biology, Proteos, A*StarSingaporeSingapore
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33
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Burnaevskiy N, Sands B, Yun S, Tedesco PM, Johnson TE, Kaeberlein M, Brent R, Mendenhall A. Chaperone biomarkers of lifespan and penetrance track the dosages of many other proteins. Nat Commun 2019; 10:5725. [PMID: 31844058 PMCID: PMC6914778 DOI: 10.1038/s41467-019-13664-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/11/2019] [Indexed: 12/27/2022] Open
Abstract
Many traits vary among isogenic individuals in homogeneous environments. In microbes, plants and animals, variation in the protein chaperone system affects many such traits. In the animal model C. elegans, the expression level of hsp-16.2 chaperone biomarkers correlates with or predicts the penetrance of mutations and lifespan after heat shock. But the physiological mechanisms causing cells to express different amounts of the biomarker were unknown. Here, we used an in vivo microscopy approach to dissect different contributions to cell-to-cell variation in hsp-16.2 expression in the intestines of young adult animals, which generate the most lifespan predicting signal. While we detected both cell autonomous intrinsic noise and signaling noise, we found both contributions were relatively unimportant. The major contributor to cell-to-cell variation in biomarker expression was general differences in protein dosage. The hsp-16.2 biomarker reveals states of high or low effective dosage for many genes.
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Affiliation(s)
| | - Bryan Sands
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Soo Yun
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Patricia M Tedesco
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Thomas E Johnson
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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34
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You ST, Jhou YT, Kao CF, Leu JY. Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering. PLoS Biol 2019; 17:e3000433. [PMID: 31613873 PMCID: PMC6814240 DOI: 10.1371/journal.pbio.3000433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/25/2019] [Accepted: 09/27/2019] [Indexed: 11/19/2022] Open
Abstract
Cell-to-cell heterogeneity within an isogenic population has been observed in prokaryotic and eukaryotic cells. Such heterogeneity often manifests at the level of individual protein abundance and may have evolutionary benefits, especially for organisms in fluctuating environments. Although general features and the origins of cellular noise have been revealed, details of the molecular pathways underlying noise regulation remain elusive. Here, we used experimental evolution of Saccharomyces cerevisiae to select for mutations that increase reporter protein noise. By combining bulk segregant analysis and CRISPR/Cas9-based reconstitution, we identified the methyltransferase Hmt1 as a general regulator of noise buffering. Hmt1 methylation activity is critical for the evolved phenotype, and we also show that two of the Hmt1 methylation targets can suppress noise. Hmt1 functions as an environmental sensor to adjust noise levels in response to environmental cues. Moreover, Hmt1-mediated noise buffering is conserved in an evolutionarily distant yeast species, suggesting broad significance of noise regulation. Experimental evolution in yeast reveals that the methyltransferase Hmt1 functions as a mediator connecting environmental stimuli to cellular noise; Hmt1-mediated noise buffering is conserved in an evolutionarily distant yeast.
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Affiliation(s)
- Shu-Ting You
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Jhou
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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35
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Zheng J, Payne JL, Wagner A. Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks. Science 2019; 365:347-353. [DOI: 10.1126/science.aax1837] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
Abstract
Cryptic genetic variation can facilitate adaptation in evolving populations. To elucidate the underlying genetic mechanisms, we used directed evolution in Escherichia coli to accumulate variation in populations of yellow fluorescent proteins and then evolved these proteins toward the new phenotype of green fluorescence. Populations with cryptic variation evolved adaptive genotypes with greater diversity and higher fitness than populations without cryptic variation, which converged on similar genotypes. Populations with cryptic variation accumulated neutral or deleterious mutations that break the constraints on the order in which adaptive mutations arise. In doing so, cryptic variation opens paths to adaptive genotypes, creates historical contingency, and reduces the predictability of evolution by allowing different replicate populations to climb different adaptive peaks and explore otherwise-inaccessible regions of an adaptive landscape.
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Affiliation(s)
- Jia Zheng
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
| | - Joshua L. Payne
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, NM, USA
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36
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Yevick HG, Miller PW, Dunkel J, Martin AC. Structural Redundancy in Supracellular Actomyosin Networks Enables Robust Tissue Folding. Dev Cell 2019; 50:586-598.e3. [PMID: 31353314 DOI: 10.1016/j.devcel.2019.06.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/08/2019] [Accepted: 06/21/2019] [Indexed: 12/31/2022]
Abstract
Tissue morphogenesis is strikingly robust. Yet, how tissues are sculpted under challenging conditions is unknown. Here, we combined network analysis, experimental perturbations, and computational modeling to determine how network connectivity between hundreds of contractile cells on the ventral side of the Drosophila embryo ensures robust tissue folding. We identified two network properties that mechanically promote robustness. First, redundant supracellular cytoskeletal network paths ensure global connectivity, even with network degradation. By forming many more connections than are required, morphogenesis is not disrupted by local network damage, analogous to the way redundancy guarantees the large-scale function of vasculature and transportation networks. Second, directional stiffening of edges oriented orthogonal to the folding axis promotes furrow formation at lower contractility levels. Structural redundancy and directional network stiffening ensure robust tissue folding with proper orientation.
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Affiliation(s)
- Hannah G Yevick
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Pearson W Miller
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Adam C Martin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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37
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Domingo J, Baeza-Centurion P, Lehner B. The Causes and Consequences of Genetic Interactions (Epistasis). Annu Rev Genomics Hum Genet 2019; 20:433-460. [PMID: 31082279 DOI: 10.1146/annurev-genom-083118-014857] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The same mutation can have different effects in different individuals. One important reason for this is that the outcome of a mutation can depend on the genetic context in which it occurs. This dependency is known as epistasis. In recent years, there has been a concerted effort to quantify the extent of pairwise and higher-order genetic interactions between mutations through deep mutagenesis of proteins and RNAs. This research has revealed two major components of epistasis: nonspecific genetic interactions caused by nonlinearities in genotype-to-phenotype maps, and specific interactions between particular mutations. Here, we provide an overview of our current understanding of the mechanisms causing epistasis at the molecular level, the consequences of genetic interactions for evolution and genetic prediction, and the applications of epistasis for understanding biology and determining macromolecular structures.
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Affiliation(s)
- Júlia Domingo
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , ,
| | - Pablo Baeza-Centurion
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , ,
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; , , .,Universitat Pompeu Fabra, 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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38
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Byrne JJ, Soh MS, Chandhok G, Vijayaraghavan T, Teoh JS, Crawford S, Cobham AE, Yapa NMB, Mirth CK, Neumann B. Disruption of mitochondrial dynamics affects behaviour and lifespan in Caenorhabditis elegans. Cell Mol Life Sci 2019; 76:1967-1985. [PMID: 30840087 PMCID: PMC6478650 DOI: 10.1007/s00018-019-03024-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 01/29/2023]
Abstract
Mitochondria are essential components of eukaryotic cells, carrying out critical physiological processes that include energy production and calcium buffering. Consequently, mitochondrial dysfunction is associated with a range of human diseases. Fundamental to their function is the ability to transition through fission and fusion states, which is regulated by several GTPases. Here, we have developed new methods for the non-subjective quantification of mitochondrial morphology in muscle and neuronal cells of Caenorhabditis elegans. Using these techniques, we uncover surprising tissue-specific differences in mitochondrial morphology when fusion or fission proteins are absent. From ultrastructural analysis, we reveal a novel role for the fusion protein FZO-1/mitofusin 2 in regulating the structure of the inner mitochondrial membrane. Moreover, we have determined the influence of the individual mitochondrial fission (DRP-1/DRP1) and fusion (FZO-1/mitofusin 1,2; EAT-3/OPA1) proteins on animal behaviour and lifespan. We show that loss of these mitochondrial fusion or fission regulators induced age-dependent and progressive deficits in animal movement, as well as in muscle and neuronal function. Our results reveal that disruption of fusion induces more profound defects than lack of fission on animal behaviour and tissue function, and imply that while fusion is required throughout life, fission is more important later in life likely to combat ageing-associated stressors. Furthermore, our data demonstrate that mitochondrial function is not strictly dependent on morphology, with no correlation found between morphological changes and behavioural defects. Surprisingly, we find that disruption of either mitochondrial fission or fusion significantly reduces median lifespan, but maximal lifespan is unchanged, demonstrating that mitochondrial dynamics play an important role in limiting variance in longevity across isogenic populations. Overall, our study provides important new insights into the central role of mitochondrial dynamics in maintaining organismal health.
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Affiliation(s)
- Joseph J Byrne
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Ming S Soh
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Gursimran Chandhok
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Tarika Vijayaraghavan
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Jean-Sébastien Teoh
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Simon Crawford
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Melbourne, VIC, 3800, Australia
| | - Ansa E Cobham
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Nethmi M B Yapa
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Christen K Mirth
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Brent Neumann
- Neuroscience Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, 3800, Australia.
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39
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Sanchez de Groot N, Torrent Burgas M, Ravarani CN, Trusina A, Ventura S, Babu MM. The fitness cost and benefit of phase-separated protein deposits. Mol Syst Biol 2019; 15:e8075. [PMID: 30962358 PMCID: PMC6452874 DOI: 10.15252/msb.20178075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane-less compartments for many cellular processes. What are the fitness costs and benefits of forming such deposits in different conditions? Using a model protein that phase-separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast. The environmental condition and the cellular demand for the protein function emerge as key determinants of fitness. Protein deposit formation can influence cell-to-cell variation in free protein abundance between individuals of a cell population (i.e., gene expression noise). This results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favoring survival of some individuals in certain environments. Thus, protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. The selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase-separated assemblies and may influence cell fitness.
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Affiliation(s)
- Natalia Sanchez de Groot
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK .,Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc Torrent Burgas
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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40
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Yatagai F, Honma M, Dohmae N, Ishioka N. Biological effects of space environmental factors: A possible interaction between space radiation and microgravity. LIFE SCIENCES IN SPACE RESEARCH 2019; 20:113-123. [PMID: 30797428 DOI: 10.1016/j.lssr.2018.10.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/27/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
In the mid-1980s, space experiments began to examine if microgravity could alter the biological effects of space radiation. In the late 1990s, repair of DNA strand breaks was reported to not be influenced by microgravity using the pre-irradiated cells, because the exposure doses of space radiation were few due to the short spaceflight. There were, however, conflicting reports depending on the biological endpoints used in various systems. While almost no attempts were made to assess the possibility that the microgravity effects could be altered by space radiation. This was probably due to the general understanding that microgravity plays a major role in space and works independently from space radiation. Recent ground-based simulation studies focusing on DNA oxidative damage and signal transduction suggested that combined effects of microgravity and space radiation might exist. These studies also implicated the importance of research focusing not only on chromosomal DNA but also on cytoplasm, especially mitochondria. Therefore, we propose a new model which accounts for the combined-effects through the window of cellular responses. In this model, the interactions between microgravity and space radiation might occur during the following cellular-responses; (A) damaging and signaling by ROS, (B) damage responses on DNA (repair, replication, transcription, etc.), and (C) expression of gene and protein (regulation by chromatin, epigenetic control, etc.).
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Affiliation(s)
- Fumio Yatagai
- Institute of Astronautical Research, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo-ku, Kanagawa 252-0022, Japan; Center for Sustainable Resource Science, The Institute of Physical and Chemical Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
| | - Masamitsu Honma
- Institute of Astronautical Research, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo-ku, Kanagawa 252-0022, Japan; Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Naoshi Dohmae
- Center for Sustainable Resource Science, The Institute of Physical and Chemical Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Noriaki Ishioka
- Institute of Astronautical Research, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo-ku, Kanagawa 252-0022, Japan; Department of Space and Astronautical Science, The Graduate University for Advanced Studies, 3-1-1 Yoshinodai, Chuo-ku, Kanagawa 252-0022, Japan
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41
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Dhar R, Missarova AM, Lehner B, Carey LB. Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation. eLife 2019; 8:38904. [PMID: 30638445 PMCID: PMC6366901 DOI: 10.7554/elife.38904] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/13/2019] [Indexed: 12/12/2022] Open
Abstract
Mutations frequently have outcomes that differ across individuals, even when these individuals are genetically identical and share a common environment. Moreover, individual microbial and mammalian cells can vary substantially in their proliferation rates, stress tolerance, and drug resistance, with important implications for the treatment of infections and cancer. To investigate the causes of cell-to-cell variation in proliferation, we used a high-throughput automated microscopy assay to quantify the impact of deleting >1500 genes in yeast. Mutations affecting mitochondria were particularly variable in their outcome. In both mutant and wild-type cells mitochondrial membrane potential - but not amount - varied substantially across individual cells and predicted cell-to-cell variation in proliferation, mutation outcome, stress tolerance, and resistance to a clinically used anti-fungal drug. These results suggest an important role for cell-to-cell variation in the state of an organelle in single cell phenotypic variation.
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Affiliation(s)
- Riddhiman Dhar
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Alsu M Missarova
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Lucas B Carey
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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42
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Mar JC. The rise of the distributions: why non-normality is important for understanding the transcriptome and beyond. Biophys Rev 2019; 11:89-94. [PMID: 30617454 PMCID: PMC6381358 DOI: 10.1007/s12551-018-0494-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/17/2018] [Indexed: 01/08/2023] Open
Abstract
The application of statistics has been instrumental in clarifying our understanding of the genome. While insights have been derived for almost all levels of genome function, most importantly, statistics has had the greatest impact on improving our knowledge of transcriptional regulation. But the drive to extract the most meaningful inferences from big data can often force us to overlook the fundamental role that statistics plays, and specifically, the basic assumptions that we make about big data. Normality is a statistical property that is often swept up into an assumption that we may or may not be consciously aware of making. This review highlights the inherent value of non-normal distributions to big data analysis by discussing use cases of non-normality that focus on gene expression data. Collectively, these examples help to motivate the premise of why at this stage, now more than ever, non-normality is important for learning about gene regulation, transcriptomics, and more.
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Affiliation(s)
- Jessica C Mar
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, QLD, Brisbane, 4072, Australia.
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43
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Wagih O, Galardini M, Busby BP, Memon D, Typas A, Beltrao P. A resource of variant effect predictions of single nucleotide variants in model organisms. Mol Syst Biol 2018; 14:e8430. [PMID: 30573687 PMCID: PMC6301329 DOI: 10.15252/msb.20188430] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/18/2022] Open
Abstract
The effect of single nucleotide variants (SNVs) in coding and noncoding regions is of great interest in genetics. Although many computational methods aim to elucidate the effects of SNVs on cellular mechanisms, it is not straightforward to comprehensively cover different molecular effects. To address this, we compiled and benchmarked sequence and structure-based variant effect predictors and we computed the impact of nearly all possible amino acid and nucleotide variants in the reference genomes of Homo sapiens, Saccharomyces cerevisiae and Escherichia coli Studied mechanisms include protein stability, interaction interfaces, post-translational modifications and transcription factor binding sites. We apply this resource to the study of natural and disease coding variants. We also show how variant effects can be aggregated to generate protein complex burden scores that uncover protein complex to phenotype associations based on a set of newly generated growth profiles of 93 sequenced S. cerevisiae strains in 43 conditions. This resource is available through mutfunc (www.mutfunc.com), a tool by which users can query precomputed predictions by providing amino acid or nucleotide-level variants.
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Affiliation(s)
- Omar Wagih
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Marco Galardini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Bede P Busby
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Danish Memon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
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44
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Lachowiec J, Mason GA, Schultz K, Queitsch C. Redundancy, Feedback, and Robustness in the Arabidopsis thaliana BZR/BEH Gene Family. Front Genet 2018; 9:523. [PMID: 30542366 PMCID: PMC6277886 DOI: 10.3389/fgene.2018.00523] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/17/2018] [Indexed: 11/19/2022] Open
Abstract
Organismal development is remarkably robust, tolerating stochastic errors to produce consistent, so-called canalized adult phenotypes. The mechanistic underpinnings of developmental robustness are poorly understood, but recent studies implicate certain features of genetic networks such as functional redundancy, connectivity, and feedback. Here, we examine the BZR/BEH gene family, whose function contributes to embryonic stem development in the plant Arabidopsis thaliana, to test current assumptions on functional redundancy and trait robustness. Our analyses of BZR/BEH gene mutants and mutant combinations revealed that functional redundancy among these gene family members is not necessary for trait robustness. Connectivity is another commonly cited determinant of robustness; however, we found no correlation between connectivity among gene family members or their connectivity with other transcription factors and effects on developmental robustness. Instead, our data suggest that BEH4, the earliest diverged family member, modulates developmental robustness. We present evidence indicating that regulatory cross-talk among gene family members is integrated by BEH4 to promote wild-type levels of developmental robustness. Further, the chaperone HSP90, a known determinant of developmental robustness, appears to act via BEH4 in maintaining robustness of embryonic stem length. In summary, we demonstrate that even among closely related transcription factors, trait robustness can arise through the activity of a single gene family member, challenging common assumptions about the molecular underpinnings of robustness.
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Affiliation(s)
- Jennifer Lachowiec
- Department of Genome Sciences, University of Washington, Seattle, WA, United States.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States
| | - G Alex Mason
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Karla Schultz
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
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45
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Santander N, Lizama C, Murgas L, Contreras S, Martin AJM, Molina P, Quiroz A, Rivera K, Salas-Pérez F, Godoy A, Rigotti A, Busso D. Transcriptional profiling of embryos lacking the lipoprotein receptor SR-B1 reveals a regulatory circuit governing a neurodevelopmental or metabolic decision during neural tube closure. BMC Genomics 2018; 19:731. [PMID: 30290792 PMCID: PMC6173885 DOI: 10.1186/s12864-018-5110-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022] Open
Abstract
Background The high-density lipoprotein receptor SR-B1 mediates cellular uptake of several lipid species, including cholesterol and vitamin E. During early mouse development, SR-B1 is located in the maternal-fetal interface, where it facilitates vitamin E transport towards the embryo. Consequently, mouse embryos lacking SR-B1 are vitamin E-deficient, and around half of them fail to close the neural tube and show cephalic neural tube defects (NTD). Here, we used transcriptomic profiling to identify the molecular determinants of this phenotypic difference between SR-B1 deficient embryos with normal morphology or with NTD. Results We used RNA-Seq to compare the transcriptomic profile of three groups of embryos retrieved from SR-B1 heterozygous intercrosses: wild-type E9.5 embryos (WT), embryos lacking SR-B1 that are morphologically normal, without NTD (KO-N) and SR-B1 deficient embryos with this defect (KO-NTD). We identified over 1000 differentially expressed genes: down-regulated genes in KO-NTD embryos were enriched for functions associated to neural development, while up-regulated genes in KO-NTD embryos were enriched for functions related to lipid metabolism. Feeding pregnant dams a vitamin E-enriched diet, which prevents NTD in SR-B1 KO embryos, resulted in mRNA levels for those differentially expressed genes that were more similar to KO-N than to KO-NTD embryos. We used gene regulatory network analysis to identify putative transcriptional regulators driving the different embryonic expression profiles, and identified a regulatory circuit controlled by the androgen receptor that may contribute to this dichotomous expression profile in SR-B1 embryos. Supporting this possibility, the expression level of the androgen receptor correlated strongly with the expression of several genes involved in neural development and lipid metabolism. Conclusions Our analysis shows that normal and defective embryos lacking SR-B1 have divergent expression profiles, explained by a defined set of transcription factors that may explain their divergent phenotype. We propose that distinct expression profiles may be relevant during early development to support embryonic nutrition and neural tube closure. Electronic supplementary material The online version of this article (10.1186/s12864-018-5110-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolás Santander
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Carlos Lizama
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Leandro Murgas
- Network Biology Laboratory, Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Sebastián Contreras
- Network Biology Laboratory, Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Alberto J M Martin
- Network Biology Laboratory, Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Paz Molina
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Alonso Quiroz
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Katherine Rivera
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Francisca Salas-Pérez
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile
| | - Alejandro Godoy
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Attilio Rigotti
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile.,Center of Molecular Nutrition and Chronic Diseases, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Dolores Busso
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Marcoleta 367, 83300024, Santiago, CP, Chile.
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46
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Kesselmeier M, Lorenzo Bermejo J. Robust logistic regression to narrow down the winner's curse for rare and recessive susceptibility variants. Brief Bioinform 2018; 18:962-972. [PMID: 27543791 DOI: 10.1093/bib/bbw074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 11/13/2022] Open
Abstract
Logistic regression is the most common technique used for genetic case-control association studies. A disadvantage of standard maximum likelihood estimators of the genotype relative risk (GRR) is their strong dependence on outlier subjects, for example, patients diagnosed at unusually young age. Robust methods are available to constrain outlier influence, but they are scarcely used in genetic studies. This article provides a non-intimidating introduction to robust logistic regression, and investigates its benefits and limitations in genetic association studies. We applied the bounded Huber and extended the R package 'robustbase' with the re-descending Hampel functions to down-weight outlier influence. Computer simulations were carried out to assess the type I error rate, mean squared error (MSE) and statistical power according to major characteristics of the genetic study and investigated markers. Simulations were complemented with the analysis of real data. Both standard and robust estimation controlled type I error rates. Standard logistic regression showed the highest power but standard GRR estimates also showed the largest bias and MSE, in particular for associated rare and recessive variants. For illustration, a recessive variant with a true GRR=6.32 and a minor allele frequency=0.05 investigated in a 1000 case/1000 control study by standard logistic regression resulted in power=0.60 and MSE=16.5. The corresponding figures for Huber-based estimation were power=0.51 and MSE=0.53. Overall, Hampel- and Huber-based GRR estimates did not differ much. Robust logistic regression may represent a valuable alternative to standard maximum likelihood estimation when the focus lies on risk prediction rather than identification of susceptibility variants.
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47
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Chen B, Feder ME, Kang L. Evolution of heat-shock protein expression underlying adaptive responses to environmental stress. Mol Ecol 2018; 27:3040-3054. [PMID: 29920826 DOI: 10.1111/mec.14769] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/03/2018] [Accepted: 06/07/2018] [Indexed: 12/27/2022]
Abstract
Heat-shock proteins (Hsps) and their cognates are primary mitigators of cell stress. With increasingly severe impacts of climate change and other human modifications of the biosphere, the ability of the heat-shock system to affect evolutionary fitness in environments outside the laboratory and to evolve in response is topic of growing importance. Since the last major reviews, several advances have occurred. First, demonstrations of the heat-shock response outside the laboratory now include many additional taxa and environments. Many of these demonstrations are only correlative, however. More importantly, technical advances in "omic" quantification of nucleic acids and proteins, genomewide association analysis, and manipulation of genes and their expression have enabled the field to move beyond correlation. Several consequent advances are already evident: The pathway from heat-shock gene expression to stress tolerance in nature can be extremely complex, mediated through multiple biological processes and systems, and even multiple species. The underlying genes are more numerous, diverse and variable than previously appreciated, especially with respect to their regulatory variation and epigenetic changes. The impacts and limitations (e.g., due to trade-offs) of natural selection on these genes have become more obvious and better established. At last, as evolutionary capacitors, Hsps may have distinctive impacts on the evolution of other genes and ecological consequences.
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Affiliation(s)
- Bing Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Martin E Feder
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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48
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Zabinsky RA, Mason GA, Queitsch C, Jarosz DF. It's not magic - Hsp90 and its effects on genetic and epigenetic variation. Semin Cell Dev Biol 2018; 88:21-35. [PMID: 29807130 DOI: 10.1016/j.semcdb.2018.05.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 04/15/2018] [Accepted: 05/15/2018] [Indexed: 10/14/2022]
Abstract
Canalization, or phenotypic robustness in the face of environmental and genetic perturbation, is an emergent property of living systems. Although this phenomenon has long been recognized, its molecular underpinnings have remained enigmatic until recently. Here, we review the contributions of the molecular chaperone Hsp90, a protein that facilitates the folding of many key regulators of growth and development, to canalization of phenotype - and de-canalization in times of stress - drawing on studies in eukaryotes as diverse as baker's yeast, mouse ear cress, and blind Mexican cavefish. Hsp90 is a hub of hubs that interacts with many so-called 'client proteins,' which affect virtually every aspect of cell signaling and physiology. As Hsp90 facilitates client folding and stability, it can epistatically suppress or enable the expression of genetic variants in its clients and other proteins that acquire client status through mutation. Hsp90's vast interaction network explains the breadth of its phenotypic reach, including Hsp90-dependent de novo mutations and epigenetic effects on gene regulation. Intrinsic links between environmental stress and Hsp90 function thus endow living systems with phenotypic plasticity in fluctuating environments. As environmental perturbations alter Hsp90 function, they also alter Hsp90's interaction with its client proteins, thereby re-wiring networks that determine the genotype-to-phenotype map. Ensuing de-canalization of phenotype creates phenotypic diversity that is not simply stochastic, but often has an underlying genetic basis. Thus, extreme phenotypes can be selected, and assimilated so that they no longer require environmental stress to manifest. In addition to acting on standing genetic variation, Hsp90 perturbation has also been linked to increased frequency of de novo variation and several epigenetic phenomena, all with the potential to generate heritable phenotypic change. Here, we aim to clarify and discuss the multiple means by which Hsp90 can affect phenotype and possibly evolutionary change, and identify their underlying common feature: at its core, Hsp90 interacts epistatically through its chaperone function with many other genes and their gene products. Its influence on phenotypic diversification is thus not magic but rather a fundamental property of genetics.
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Affiliation(s)
- Rebecca A Zabinsky
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford, CA, United States
| | | | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, United States.
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford, CA, United States; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States.
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49
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Stanta G, Bonin S. Overview on Clinical Relevance of Intra-Tumor Heterogeneity. Front Med (Lausanne) 2018; 5:85. [PMID: 29682505 PMCID: PMC5897590 DOI: 10.3389/fmed.2018.00085] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/19/2018] [Indexed: 12/12/2022] Open
Abstract
Today, clinical evaluation of tumor heterogeneity is an emergent issue to improve clinical oncology. In particular, intra-tumor heterogeneity (ITH) is closely related to cancer progression, resistance to therapy, and recurrences. It is interconnected with complex molecular mechanisms including spatial and temporal phenomena, which are often peculiar for every single patient. This review tries to describe all the types of ITH including morphohistological ITH, and at the molecular level clonal ITH derived from genomic instability and nonclonal ITH derived from microenvironment interaction. It is important to consider the different types of ITH as a whole for any patient to investigate on cancer progression, prognosis, and treatment opportunities. From a practical point of view, analytical methods that are widely accessible today, or will be in the near future, are evaluated to investigate the complex pattern of ITH in a reproducible way for a clinical application.
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Affiliation(s)
- Giorgio Stanta
- DSM, Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Serena Bonin
- DSM, Department of Medical Sciences, University of Trieste, Trieste, Italy
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Murray JI. Systems biology of embryonic development: Prospects for a complete understanding of the Caenorhabditis elegans embryo. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e314. [PMID: 29369536 DOI: 10.1002/wdev.314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/01/2017] [Accepted: 12/12/2017] [Indexed: 01/07/2023]
Abstract
The convergence of developmental biology and modern genomics tools brings the potential for a comprehensive understanding of developmental systems. This is especially true for the Caenorhabditis elegans embryo because its small size, invariant developmental lineage, and powerful genetic and genomic tools provide the prospect of a cellular resolution understanding of messenger RNA (mRNA) expression and regulation across the organism. We describe here how a systems biology framework might allow large-scale determination of the embryonic regulatory relationships encoded in the C. elegans genome. This framework consists of two broad steps: (a) defining the "parts list"-all genes expressed in all cells at each time during development and (b) iterative steps of computational modeling and refinement of these models by experimental perturbation. Substantial progress has been made towards defining the parts list through imaging methods such as large-scale green fluorescent protein (GFP) reporter analysis. Imaging results are now being augmented by high-resolution transcriptome methods such as single-cell RNA sequencing, and it is likely the complete expression patterns of all genes across the embryo will be known within the next few years. In contrast, the modeling and perturbation experiments performed so far have focused largely on individual cell types or genes, and improved methods will be needed to expand them to the full genome and organism. This emerging comprehensive map of embryonic expression and regulatory function will provide a powerful resource for developmental biologists, and would also allow scientists to ask questions not accessible without a comprehensive picture. This article is categorized under: Invertebrate Organogenesis > Worms Technologies > Analysis of the Transcriptome Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics.
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Affiliation(s)
- John Isaac Murray
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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