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Tower Z, Chang H. Technical Considerations for Detecting Protein-Protein Interactions Using Proximity Ligation Assay. J Proteome Res 2025; 24:2564-2568. [PMID: 40211936 DOI: 10.1021/acs.jproteome.4c00855] [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: 04/25/2025]
Abstract
Proximity ligation assay has been widely used to detect protein-protein interaction in cells and tissues. While with great sensitivity, its specificity was often neglected. Here, we report the existence of varying levels of false positives observed with this assay, most likely due to its high sensitivity. We also provide suggestions to minimize false positives for more accurate detection of protein-protein interactions, especially for membrane proteins. These suggestions include co-staining target proteins, using various negative controls and suitable antibodies, avoiding detergents if possible, and validating interactions with complementary methods.
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Affiliation(s)
- Zach Tower
- Department of Dermatology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Hao Chang
- Department of Dermatology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- William S. Middleton VA Medical Center, Madison, Wisconsin 53705, United States
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2
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Tower Z, Chang H. Improved method for detecting protein-protein interactions using proximity ligation assay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.01.610697. [PMID: 39282310 PMCID: PMC11398341 DOI: 10.1101/2024.09.01.610697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Proximity ligation assay has been widely used to detect protein-protein interaction in cells and tissues. While with great sensitivity, its specificity was often neglected. Here, we report the existence of varying levels of false positives observed with this assay and provide suggestions to minimize false positives for more accurate detection of protein-protein interactions, especially for membrane proteins.
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Affiliation(s)
- Zach Tower
- Department of Dermatology, University of Wisconsin-Madison, Madison, Wisconsin 53705
| | - Hao Chang
- Department of Dermatology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- William S. Middleton VA Medical Center, Madison, Wisconsin 53705
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3
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Ryan M, McDonough JA, Ward ME, Cookson MR, Skarnes WC, Merkle FT. Large structural variants in KOLF2.1J are unlikely to compromise neurological disease modeling. Cell Stem Cell 2024; 31:290-291. [PMID: 38458177 DOI: 10.1016/j.stem.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/22/2024] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Affiliation(s)
- Mallory Ryan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael E Ward
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark R Cookson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - William C Skarnes
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Florian T Merkle
- Institute of Metabolic Science, and Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0QQ, UK.
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4
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Ryan M, McDonough JA, Ward ME, Cookson MR, Skarnes WC, Merkle FT. Large structural variants in KOLF2.1J are unlikely to compromise neurological disease modelling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577739. [PMID: 38352495 PMCID: PMC10862770 DOI: 10.1101/2024.01.29.577739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Gracia-Diaz and colleagues analysed high-density DNA microarray and whole genome sequencing (WGS) data from the KOLF2.1J 'reference' human induced pluripotent stem cell (hiPSC) line1, and report the presence of five high-confidence heterozygous copy number variants (CNVs) at least 100kbp in length2. Since three of these CNVs span coding genes, some of which have been associated with neurodevelopmental disease, the authors raise the concern that these CNVs may compromise the utility of KOLF2.1J for neurological disease modelling. We appreciate their thorough analysis and thoughtful interpretation, and agree that potential users of this line should be made aware of all cases where KOLF2.1J differs from the reference genome. However, we believe that the benefits from the widespread use of KOLF2.1J outweigh the potential risks that might arise from the identified CNVs.
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Affiliation(s)
- Mallory Ryan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | | | - Michael E. Ward
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mark R. Cookson
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda MD, 20892, USA
| | | | - Florian T. Merkle
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, and Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0QQ, UK
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5
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Cetera M, Sharan R, Hayward-Lara G, Phillips B, Biswas A, Halley M, Beall E, vonHoldt B, Devenport D. Region-specific reversal of epidermal planar polarity in the rosette fancy mouse. Development 2023; 150:dev202078. [PMID: 37622728 PMCID: PMC10499026 DOI: 10.1242/dev.202078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
The planar cell polarity (PCP) pathway collectively orients cells with respect to a body axis. Hair follicles of the murine epidermis provide a striking readout of PCP activity in their uniform alignment across the skin. Here, we characterize, from the molecular to tissue-scale, PCP establishment in the rosette fancy mouse, a natural variant with posterior-specific whorls in its fur, to understand how epidermal polarity is coordinated across the tissue. We find that rosette hair follicles emerge with reversed orientations specifically in the posterior region, creating a mirror image of epidermal polarity. The rosette trait is associated with a missense mutation in the core PCP gene Fzd6, which alters a consensus site for N-linked glycosylation, inhibiting its membrane localization. Unexpectedly, the Fzd6 trafficking defect does not block asymmetric localization of the other PCP proteins. Rather, the normally uniform axis of PCP asymmetry rotates where the PCP-directed cell movements that orient follicles are reversed, suggesting the PCP axis rotates 180°. Collectively, our multiscale analysis of epidermal polarity reveals PCP patterning can be regionally decoupled to produce posterior whorls in the rosette fancy mouse.
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Affiliation(s)
- Maureen Cetera
- Department of Genetics, Cell Biology and Development, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Rishabh Sharan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | | | - Brooke Phillips
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Abhishek Biswas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Research Computing, Office of Information Technology, Princeton University, Princeton, NJ 08540, USA
| | - Madalene Halley
- Department of Genetics, Cell Biology and Development, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Evalyn Beall
- Department of Genetics, Cell Biology and Development, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
| | - Danelle Devenport
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
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Yudin NS, Larkin DM. Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds. Vavilovskii Zhurnal Genet Selektsii 2023; 27:463-470. [PMID: 37867610 PMCID: PMC10587008 DOI: 10.18699/vjgb-23-56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 10/24/2023] Open
Abstract
It is known that different species of animals, when living in the same environmental conditions, can form similar phenotypes. The study of the convergent evolution of several species under the influence of the same environmental factor makes it possible to identify common mechanisms of genetic adaptation. Local cattle and sheep breeds have been formed over thousands of years under the influence of domestication, as well as selection aimed at adaptation to the local environment and meeting human needs. Previously, we identified a number of candidate genes in genome regions potentially selected during domestication and adaptation to the climatic conditions of Russia, in local breeds of cattle and sheep using whole genome genotyping data. However, these data are of low resolution and do not reveal most nucleotide substitutions. The aim of the work was to create, using the whole genome sequencing data, a list of genes associated with domestication, selection and adaptation in Russian cattle and sheep breeds, as well as to identify candidate genes and metabolic pathways for selection for cold adaptation. We used our original data on the search for signatures of selection in the genomes of Russian cattle (Yakut, Kholmogory, Buryat, Wagyu) and sheep (Baikal, Tuva) breeds. We used the HapFLK, DCMS, FST and PBS methods to identify DNA regions with signatures of selection. The number of candidate genes in potentially selective regions was 946 in cattle and 151 in sheep. We showed that the studied Russian cattle and sheep breeds have at least 10 genes in common, apparently involved in the processes of adaptation/selection, including adaptation to a cold climate, including the ASTN2, PM20D1, TMEM176A, and GLIS1 genes. Based on the intersection with the list of selected genes in at least two Arctic/Antarctic mammal species, 20 and 8 genes, have been identified in cattle and sheep, respectively, that are potentially involved in cold adaptation. Among them, the most promising for further research are the ASPH, NCKAP5L, SERPINF1, and SND1 genes. Gene ontology analysis indicated the existence of possible common biochemical pathways for adaptation to cold in domestic and wild mammals associated with cytoskeleton disassembly and apoptosis.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
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Cetera M, Sharan R, Hayward-Lara G, Phillips B, Biswas A, Halley M, Beall E, vonHoldt B, Devenport D. Region-specific reversal of epidermal planar polarity in the fancy rosette mouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550849. [PMID: 37546950 PMCID: PMC10402159 DOI: 10.1101/2023.07.27.550849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The planar cell polarity (PCP) pathway collectively orients thousands of cells with respect to a body axis to direct cellular behaviors that are essential for embryonic morphogenesis. Hair follicles of the murine epidermis provide a striking readout of PCP activity in their uniform alignment along the entire skin surface. Here, we characterize, from the molecular to tissue-scale, PCP establishment in the rosette fancy mouse, a natural variant with posterior-specific whorls in its fur, to understand how epidermal polarity is coordinated across the tissue. We find that embryonic hair follicles of rosette mutants emerge with reversed orientations specifically in the posterior region, creating a mirror image of epidermal polarity. The rosette trait is associated with a missense mutation in the core PCP gene Fzd6 , which alters a consensus site for N-linked glycosylation and inhibits its membrane localization. Unexpectedly, this defect in Fzd6 trafficking, observed across the entire dorsal epidermis, does not interfere with the ability of other core PCP proteins to localize asymmetrically. Rather, the normally uniform axis of PCP asymmetry is disrupted and rotated in the posterior region such that polarity is reflected on either side of a transition zone. The result is a reversal of polarized cell movements that orient nascent follicles, specifically in the posterior of the embryo. Collectively, our multiscale analysis of epidermal polarity reveals PCP patterning can be regionally decoupled to produce the unique posterior whorls of the fancy rosette mouse. Summary Region-specific rotation of the Planar Cell Polarity axis reverses posterior hair follicles in the fancy rosette mouse.
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8
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Analysis of Copy Number Variation in the Whole Genome of Normal-Haired and Long-Haired Tianzhu White Yaks. Genes (Basel) 2022; 13:genes13122405. [PMID: 36553672 PMCID: PMC9777850 DOI: 10.3390/genes13122405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Long-haired individuals in the Tianzhu white yak population are a unique genetic resource, and have important landscape value. Copy number variation (CNV) is an important source of phenotypic variation in mammals. In this study, we used resequencing technology to detect the whole genome of 10 long-haired Tianzhu white yaks (LTWY) and 10 normal-haired Tianzhu white yaks (NTWY), and analyzed the differences of CNV in the genome of LTWYs and NTWYs. A total of 110268 CNVs were identified, 2006 CNVRs were defined, and the distribution map of these CNVRs on chromosomes was constructed. The comparison of LTWYs and NTWYs identified 80 differential CNVR-harbored genes, which were enriched in lipid metabolism, cell migration and other functions. Notably, some differential genes were identified as associated with hair growth and hair-follicle development (e.g., ASTN2, ATM, COL22A1, GK5, SLIT3, PM20D1, and SGCZ). In general, we present the first genome-wide analysis of CNV in LTWYs and NTWYs. Our results can provide new insights into the phenotypic variation of different hair lengths in Tianzhu white yaks.
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Cai Y, Lv W, Jiang Y, Li Q, Su P, Pang Y. Molecular evolution of the BRINP and ASTN genes and expression profles in response to pathogens and spinal cord injury repair in lamprey (Lethenteron reissneri). FISH & SHELLFISH IMMUNOLOGY 2022; 131:274-282. [PMID: 36228880 DOI: 10.1016/j.fsi.2022.09.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Bone morphogenic protein/retinoic acid inducible neural-specific proteins (BRINPs) and astrotactins (ASTNs) are two members of membrane attack complex/perforin-like (MACPF) superfamily proteins that present high expression in the growing and mature vertebrate neurons. Lamprey has a unique evolutionary status as a representative of the oldest jawless vertebrates, making it an ideal animal model for understanding vertebrate evolution. The evolutionary origins of BRINPs and ASTNs genes in vertebrates, however, have not been shown in lampreys. Here, BRINP and ASTN genes were found in lamprey genomes and the evolutionary relationships of them were investigated by phylogenetic analysis. Protein domains, motifs, genetic structure, and crystal structure analysis revealed that the features of BRINP and ASTN appear to be conserved in vertebrates. Genomic synteny analysis indicated that lamprey BRINP and ASTN neighbor genes differed dramatically from jawed vertebrate. Real-time quantitative results illustrated that the BRINP and ASTN genes family might take part in immune defence and spinal cord injury repair. This study not only enriches a better understanding of the evolution of the BRINP and ASTN genes but also offers a foundation for exploring their roles in the development of the vertebrate central nervous system (CNS).
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Affiliation(s)
- Yang Cai
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Wanrong Lv
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Ying Jiang
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Qingwei Li
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
| | - Peng Su
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
| | - Yue Pang
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
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10
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Simonson L, Oldham E, Chang H. Overactive Wnt5a signaling disrupts hair follicle polarity during mouse skin development. Development 2022; 149:dev200816. [PMID: 36305473 PMCID: PMC9845745 DOI: 10.1242/dev.200816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
The polarity of mouse hair follicles is controlled by the Frizzled (Fzd) receptors and other membrane planar cell polarity (PCP) proteins. Whether Wnt proteins can act as PCP ligands in the skin remains unknown. Here, we show that overexpression of Wnt5a in the posterior part of mouse embryos causes a local disruption of hair follicle orientation. The misoriented hair follicle phenotype in Wnt5a overexpressing mice can be rescued by a heterozygous loss of Fzd6, suggesting Wnt5a is likely to signal through Fzd6. Although the membrane distribution of PCP proteins seems unaffected by Wnt5a overexpression, transcriptional profiling analyses identify a set of genes as potential targets of the skin polarization program controlled by Wnt5a/Fzd6 signaling. Surprisingly, deletion of Wnt5a globally or in the posterior part of the mouse embryos does not affect hair follicle orientation. We show that many other Wnts are highly expressed in the developing skin. They can activate the Fzd6 signaling pathway in vitro and may act together with Wnt5a to regulate the Fzd6-mediated skin polarization. Our experiments demonstrate for the first time that Wnt5a can function as an orienting cue for mouse skin PCP.
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Affiliation(s)
- Laura Simonson
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ethan Oldham
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Hao Chang
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53705, USA
- William S. Middleton VA Medical Center, Madison, WI 53705, USA
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11
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Liu M, Yu C, Zhang Z, Song M, Sun X, Piálek J, Jacob J, Lu J, Cong L, Zhang H, Wang Y, Li G, Feng Z, Du Z, Wang M, Wan X, Wang D, Wang YL, Li H, Wang Z, Zhang B, Zhang Z. Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice. Genome Biol 2022; 23:203. [PMID: 36163035 PMCID: PMC9511766 DOI: 10.1186/s13059-022-02772-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studies using mouse models. However, the genetic mechanism of laboratory mouse domestication remains unknown due to lack of adequate genomic sequences of wild mice. Results We analyze the genetic relationships by whole-genome resequencing of 36 wild mice and 36 inbred strains. All classical inbred mice cluster together distinctly from wild and wild-derived inbred mice. Using nucleotide diversity analysis, Fst, and XP-CLR, we identify 339 positively selected genes that are closely associated with nervous system function. Approximately one third of these positively selected genes are highly expressed in brain tissues, and genetic mouse models of 125 genes in the positively selected genes exhibit abnormal behavioral or nervous system phenotypes. These positively selected genes show a higher ratio of differential expression between wild and classical inbred mice compared with all genes, especially in the hippocampus and frontal lobe. Using a mutant mouse model, we find that the SNP rs27900929 (T>C) in gene Astn2 significantly reduces the tameness of mice and modifies the ratio of the two Astn2 (a/b) isoforms. Conclusion Our study indicates that classical inbred mice experienced high selection pressure during domestication under laboratory conditions. The analysis shows the positively selected genes are closely associated with behavior and the nervous system in mice. Tameness may be related to the Astn2 mutation and regulated by the ratio of the two Astn2 (a/b) isoforms. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02772-1.
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Affiliation(s)
- Ming Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,International Society of Zoological Sciences, Beijing, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhichao Zhang
- Novogene Bioinformatics Institute, Beijing, China.,Glbizzia Biosciences, Beijing, China
| | - Mingjing Song
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiuping Sun
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
| | - Jaroslav Piálek
- House Mouse Group, Research Facility Studenec, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jens Jacob
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests / Institute for Epidemiology and Pathogen Diagnostics, Münster, Germany
| | - Jiqi Lu
- School of Life Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Lin Cong
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Hongmao Zhang
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Yong Wang
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Guoliang Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Feng
- Plant Protection Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Zhenglin Du
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Meng Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Xinru Wan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dawei Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan-Ling Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongjun Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zuoxin Wang
- Department of Psychology and Program in Neuroscience, Florida State University, Tallahassee, FL, 32306, USA
| | - Bing Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,International Society of Zoological Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
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12
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Jiang TX, Li A, Lin CM, Chiu C, Cho JH, Reid B, Zhao M, Chow RH, Widelitz RB, Chuong CM. Global feather orientations changed by electric current. iScience 2021; 24:102671. [PMID: 34179734 PMCID: PMC8214094 DOI: 10.1016/j.isci.2021.102671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/18/2021] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
During chicken skin development, each feather bud exhibits its own polarity, but a population of buds organizes with a collective global orientation. We used embryonic dorsal skin, with buds aligned parallel to the rostral-caudal body axis, to explore whether exogenous electric fields affect feather polarity. Interestingly, brief exogenous current exposure prior to visible bud formation later altered bud orientations. Applying electric pulses perpendicular to the body rostral-caudal axis realigned bud growth in a collective swirl, resembling an electric field pointing toward the anode. Perturbed buds show normal molecular expression and morphogenesis except for their altered orientation. Epithelial-mesenchymal recombination demonstrates the effects of exogenous electric fields are mediated through the epithelium. Small-molecule channel inhibitor screens show Ca2+ channels and PI3 Kinase are involved in controlling feather bud polarity. This work reveals the importance of bioelectricity in organ development and regeneration and provides an explant culture platform for experimentation.
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Affiliation(s)
- Ting-Xin Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Ángeles, CA 90033, USA
| | - Ang Li
- Department of Pathology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Ángeles, CA 90033, USA
| | - Chih-Min Lin
- Department of Pathology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Ángeles, CA 90033, USA
| | - Cathleen Chiu
- Department of Pathology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Ángeles, CA 90033, USA
| | - Jung-Hwa Cho
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Brian Reid
- Department of Ophthalmology & Vision Science, and Department of Dermatology, University of California, Davis, Sacramento, CA 95816, USA
| | - Min Zhao
- Department of Ophthalmology & Vision Science, and Department of Dermatology, University of California, Davis, Sacramento, CA 95816, USA
| | - Robert H. Chow
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Randall Bruce Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Ángeles, CA 90033, USA
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Ángeles, CA 90033, USA
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13
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Control of growth factor signalling by MACPF proteins. Biochem Soc Trans 2019; 47:801-810. [PMID: 31209154 DOI: 10.1042/bst20180179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/17/2019] [Accepted: 05/28/2019] [Indexed: 11/17/2022]
Abstract
Members of the membrane attack complex/perforin-like (MACPF) protein superfamily have long captured interest because of their unique ability to assemble into large oligomeric pores on the surfaces of cells. The best characterised of these act in vertebrate immunity where they function to deliver pro-apoptotic factors or induce the cytolysis and death of targeted cells. Less appreciated, however, is that rather than causing cell death, MACPF proteins have also evolved to control cellular signalling pathways and influence developmental programmes such as pattern formation and neurogenesis. Torso-like (Tsl) from the fruit fly Drosophila, for example, functions to localise the activity of a growth factor for patterning its embryonic termini. It remains unclear whether these developmental proteins employ an attenuated form of the classical MACPF lytic pore, or if they have evolved to function via alternative mechanisms of action. In this minireview, we examine the evidence that links pore-forming MACPF proteins to the control of growth factor and cytokine signalling. We will then attempt to reconcile how the MACPF domain may have been repurposed during evolution for developmental events rather than cell killing.
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14
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Yan H, Gao Y, Ding Q, Liu J, Li Y, Jin M, Xu H, Ma S, Wang X, Zeng W, Chen Y. Exosomal Micro RNAs Derived from Dermal Papilla Cells Mediate Hair Follicle Stem Cell Proliferation and Differentiation. Int J Biol Sci 2019; 15:1368-1382. [PMID: 31337968 PMCID: PMC6643152 DOI: 10.7150/ijbs.33233] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/24/2019] [Indexed: 12/17/2022] Open
Abstract
Recent studies have demonstrated that dermal papilla cell-derived exosomes (DPC-Exos) promote the anagen stage of hair follicle (HF) growth and delay the catagen stage. However, the roles of DPC-Exos in regulating hair follicle stem cell (HFSC) quiescence and activation remain unknown. Here, we found that HFSC differentiation was induced by co-culture with DPCs, and that DPC-Exos attached to the surface of HFSCs. Using micro RNA (miRNA) high-throughput sequencing, we identified 111 miRNAs that were significantly differentially expressed between DPC-Exos and DPCs, and the predicted target genes of the top 34 differentially expressed miRNAs indicated that DPC-Exos regulate HFSCs proliferation and differentiation via genes involved in cellular signal transduction, fatty acid expression regulation, and cellular communication. The overexpression of miR-22-5p indicated that it negatively regulates HFSC proliferation and LEF1 was revealed as the direct target gene of miR-22-5p. We therefore propose the miR-22-5p-LEF1 axis as a novel pathway regulating HFSC proliferation.
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Affiliation(s)
- Hailong Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Life Science Research Center, Yulin University, Yulin, China
| | - Ye Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- School of Medicine, Shanxi Datong University, Datong, China
| | - Qiang Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Miaohan Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Han Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Sen Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenxian Zeng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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15
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Lara P, Tellgren-Roth Å, Behesti H, Horn Z, Schiller N, Enquist K, Cammenberg M, Liljenström A, Hatten ME, von Heijne G, Nilsson I. Murine astrotactins 1 and 2 have a similar membrane topology and mature via endoproteolytic cleavage catalyzed by a signal peptidase. J Biol Chem 2019; 294:4538-4545. [PMID: 30696770 PMCID: PMC6433051 DOI: 10.1074/jbc.ra118.007093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/09/2019] [Indexed: 11/06/2022] Open
Abstract
Astrotactin 1 (Astn1) and Astn2 are membrane proteins that function in glial-guided migration, receptor trafficking, and synaptic plasticity in the brain as well as in planar polarity pathways in the skin. Here we used glycosylation mapping and protease protection approaches to map the topologies of mouse Astn1 and Astn2 in rough microsomal membranes and found that Astn2 has a cleaved N-terminal signal peptide, an N-terminal domain located in the lumen of the rough microsomal membranes (topologically equivalent to the extracellular surface in cells), two transmembrane helices, and a large C-terminal lumenal domain. We also found that Astn1 has the same topology as Astn2, but we did not observe any evidence of signal peptide cleavage in Astn1. Both Astn1 and Astn2 mature through endoproteolytic cleavage in the second transmembrane helix; importantly, we identified the endoprotease responsible for the maturation of Astn1 and Astn2 as the endoplasmic reticulum signal peptidase. Differences in the degree of Astn1 and Astn2 maturation possibly contribute to the higher levels of the C-terminal domain of Astn1 detected on neuronal membranes of the central nervous system. These differences may also explain the distinct cellular functions of Astn1 and Astn2, such as in membrane adhesion, receptor trafficking, and planar polarity signaling.
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Affiliation(s)
- Patricia Lara
- From the Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm, Sweden and
| | - Åsa Tellgren-Roth
- From the Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm, Sweden and
| | - Hourinaz Behesti
- the Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065
| | - Zachi Horn
- the Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065
| | - Nina Schiller
- From the Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm, Sweden and
| | - Karl Enquist
- From the Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm, Sweden and
| | - Malin Cammenberg
- From the Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm, Sweden and
| | - Amanda Liljenström
- From the Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm, Sweden and
| | - Mary E. Hatten
- the Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065
| | - Gunnar von Heijne
- From the Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm, Sweden and , To whom correspondence may be addressed:
Dept. of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691 Stockholm, Sweden. Tel.:
46-8-162590; E-mail:
| | - IngMarie Nilsson
- From the Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm, Sweden and , To whom correspondence may be addressed:
Dept. of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691 Stockholm, Sweden. Tel.:
46-8-162590; E-mail:
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16
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Dong B, Vold S, Olvera-Jaramillo C, Chang H. Functional redundancy of frizzled 3 and frizzled 6 in planar cell polarity control of mouse hair follicles. Development 2018; 145:dev168468. [PMID: 30237242 PMCID: PMC10682934 DOI: 10.1242/dev.168468] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
Abstract
The orientation of mouse hair follicles is controlled by the planar cell polarity (PCP) pathway. Mutations in PCP genes result in two categories of hair mis-orientation phenotype: randomly oriented and vertically oriented to the skin surface. Here, we demonstrate that the randomly oriented hair phenotype observed in frizzled 6 (Fzd6) mutants results from a partial loss of the polarity, due to the functional redundancy of another closely related frizzled gene, Fzd3 Double knockout of Fzd3 and Fzd6 globally, or only in the skin, led to vertically oriented hair follicles and a total loss of anterior-posterior polarity. Furthermore, we provide evidence that, contrary to the prevailing model, asymmetrical localization of the Fzd6 protein is not observed in skin epithelial cells. Through transcriptome analyses and in vitro studies, we show collagen triple helix repeat containing 1 (Cthrc1) to be a potential downstream effector of Fzd6, but not of Fzd3. Cthrc1 binds directly to the extracellular domains of Fzd3 and Fzd6 to enhance the Wnt/PCP signaling. These results suggest that Fzd3 and Fzd6 play a redundant role in controlling the polarity of developing skin, but through non-identical mechanisms.
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Affiliation(s)
- Bo Dong
- Department of Dermatology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Program in Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Samantha Vold
- Department of Dermatology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Hao Chang
- Department of Dermatology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Program in Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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17
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Ni T, Gilbert RJC. Repurposing a pore: highly conserved perforin-like proteins with alternative mechanisms. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160212. [PMID: 28630152 PMCID: PMC5483515 DOI: 10.1098/rstb.2016.0212] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2017] [Indexed: 12/02/2022] Open
Abstract
Pore-forming proteins play critical roles in pathogenic attack and immunological defence. The membrane attack complex/perforin (MACPF) group of homologues represents, with cholesterol-dependent cytolysins, the largest family of such proteins. In this review, we begin by describing briefly the structure of MACPF proteins, outlining their common mechanism of pore formation. We subsequently discuss some examples of MACPF proteins likely implicated in pore formation or other membrane-remodelling processes. Finally, we focus on astrotactin and bone morphogenetic protein and retinoic acid-induced neural-specific proteins, highly conserved MACPF family members involved in developmental processes, which have not been well studied to date or observed to form a pore-and which data suggest may act by alternative mechanisms.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Robert J C Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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18
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Cetera M, Leybova L, Woo FW, Deans M, Devenport D. Planar cell polarity-dependent and independent functions in the emergence of tissue-scale hair follicle patterns. Dev Biol 2017; 428:188-203. [PMID: 28599846 DOI: 10.1016/j.ydbio.2017.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/17/2017] [Accepted: 06/02/2017] [Indexed: 11/29/2022]
Abstract
Hair follicles of the mammalian epidermis display local order and global alignment, a complex pattern instructed by the core planar cell polarity (PCP) pathway. Here we address the contributions of core PCP genes, Van Gogh-like and Frizzled, to the establishment, local refinement, and global order of embryonic and postnatal hair follicles. We find that, similar to Fz6 mutants, the disordered hair patterns of Vangl2 mutants are refined over time and eventually corrected. In both mutants, we find that tissue-level reorientation occurs through locally coordinated follicle rotation at stereotyped locations. Strikingly, Vangl2 and Fz6 mutant follicles collectively rotate with opposing directionalities, suggesting that redundant core PCP signals contribute to their directed realignment. Consistently, global follicle alignment is not restored upon conditional ablation of both Vangl1 and Vangl2 genes. Instead, spatially distinct patterns of whorls and crosses emerge and persist even after a complete cycle of hair follicle regeneration. Thus, local refinement of hair follicles into higher order patterns can occur independently of the core PCP system, however, their global alignment with the body axes requires PCP function throughout morphogenesis, growth and regeneration.
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Affiliation(s)
- Maureen Cetera
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Liliya Leybova
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Frank W Woo
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael Deans
- Department of Surgery, Division of Otolaryngology, University of Utah School of Medicine, Salt Lake City, UT, USA; Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Danelle Devenport
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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19
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Chang H. Cleave but not leave: Astrotactin proteins in development and disease. IUBMB Life 2017; 69:572-577. [PMID: 28517363 DOI: 10.1002/iub.1641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/01/2017] [Accepted: 05/02/2017] [Indexed: 01/12/2023]
Abstract
Over the years, animal studies have identified astrotactins as important membrane proteins for glial-guided neuronal migration during central nervous system development and hair follicle polarity control during skin development. Biochemical studies have revealed intramembrane proteolysis as an important feature of astrotactins. The two fragments of astrotactins remain linked together by a disulfide bond after the proteolytic cleavage. In humans, mutations in astrotactin genes have also been linked to a wide range of diseases, including several developmental brain disorders, neurodegenerative diseases and cancer. In this review, I will summarize the current knowledge of the biological function of astrotactins in development, highlight the linkage between mutations in astrotactin genes and human disease and discuss several outstanding questions that remain unanswered. © 2017 IUBMB Life, 69(8):572-577, 2017.
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Affiliation(s)
- Hao Chang
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, USA
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20
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Berkowicz SR, Giousoh A, Bird PI. Neurodevelopmental MACPFs: The vertebrate astrotactins and BRINPs. Semin Cell Dev Biol 2017; 72:171-181. [PMID: 28506896 DOI: 10.1016/j.semcdb.2017.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 04/27/2017] [Accepted: 05/11/2017] [Indexed: 02/06/2023]
Abstract
Astrotactins (ASTNs) and Bone morphogenetic protein/retinoic acid inducible neural-specific proteins (BRINPs) are two groups of Membrane Attack Complex/Perforin (MACPF) superfamily proteins that show overlapping expression in the developing and mature vertebrate nervous system. ASTN(1-2) and BRINP(1-3) genes are found at conserved loci in humans that have been implicated in neurodevelopmental disorders (NDDs). Here we review the tissue distribution and cellular localization of these proteins, and discuss recent studies that provide insight into their structure and interactions. We highlight the genetic relationships and co-expression of Brinps and Astns; and review recent knock-out mouse phenotypes that indicate a possible overlap in protein function between ASTNs and BRINPs.
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Affiliation(s)
- Susan R Berkowicz
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, 3800, Australia.
| | - Aminah Giousoh
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, 3800, Australia
| | - Phillip I Bird
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, 3800, Australia
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21
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Chang H, Smallwood PM, Williams J, Nathans J. Intramembrane Proteolysis of Astrotactins. J Biol Chem 2017; 292:3506-3516. [PMID: 28100779 DOI: 10.1074/jbc.m116.768077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/14/2017] [Indexed: 11/06/2022] Open
Abstract
Astrotactins are vertebrate-specific membrane proteins implicated in neuron-glia interactions during central nervous system development and in hair follicle polarity during skin development. By studying epitope-tagged derivatives of mouse astrotactin-2 (Astn2) produced in transfected cells, we determined that the amino and carboxyl termini reside in the extracellular space and are initially linked by two transmembrane segments and a single cytoplasmic domain. We further show that Astn2 undergoes proteolytic cleavage in the second transmembrane domain (TM2) and that a disulfide bond holds the resulting two fragments together. Recombinant Astn1 also undergoes TM2 cleavage, as does Astn2 isolated from mouse cerebellum. Astn2 intramembrane proteolysis is insensitive to replacement of TM2 by the transmembrane domain of CD74 or by 21 alanines. However, replacement of TM2 by the transmembrane domain of CD4, the asialoglycoprotein receptor, or the transferrin receptor eliminates intramembrane proteolysis, as does leucine substitution of residues that overlap or are immediately upstream of the cleavage site. Replacement of the transmembrane domain of CD74 or the asialoglycoprotein receptor with Astn2 TM2 leads to the appearance of a carboxyl-terminal fragment consistent with intramembrane proteolysis. These experiments define a highly unusual transmembrane topology for the astrotactins, reveal intramembrane proteolysis as a feature of astrotactin maturation, and constrain the substrate sequences that are permissive for cleavage of one type 2 transmembrane segment.
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Affiliation(s)
- Hao Chang
- Departments of Molecular Biology and Genetics
| | | | | | - Jeremy Nathans
- Departments of Molecular Biology and Genetics; Neuroscience; Ophthalmology, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.
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22
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Ni T, Harlos K, Gilbert R. Structure of astrotactin-2: a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development. Open Biol 2016; 6:rsob.160053. [PMID: 27249642 PMCID: PMC4892435 DOI: 10.1098/rsob.160053] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/07/2016] [Indexed: 11/30/2022] Open
Abstract
The vertebrate-specific proteins astrotactin-1 and 2 (ASTN-1 and ASTN-2) are integral membrane perforin-like proteins known to play critical roles in neurodevelopment, while ASTN-2 has been linked to the planar cell polarity pathway in hair cells. Genetic variations associated with them are linked to a variety of neurodevelopmental disorders and other neurological pathologies, including an advanced onset of Alzheimer's disease. Here we present the structure of the majority endosomal region of ASTN-2, showing it to consist of a unique combination of polypeptide folds: a perforin-like domain, a minimal epidermal growth factor-like module, a unique form of fibronectin type III domain and an annexin-like domain. The perforin-like domain differs from that of other members of the membrane attack complex-perforin (MACPF) protein family in ways that suggest ASTN-2 does not form pores. Structural and biophysical data show that ASTN-2 (but not ASTN-1) binds inositol triphosphates, suggesting a mechanism for membrane recognition or secondary messenger regulation of its activity. The annexin-like domain is closest in fold to repeat three of human annexin V and similarly binds calcium, and yet shares no sequence homology with it. Overall, our structure provides the first atomic-resolution description of a MACPF protein involved in development, while highlighting distinctive features of ASTN-2 responsible for its activity.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Robert Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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