1
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Monroy-Eklund A, Taylor C, Weidmann CA, Burch C, Laederach A. Structural analysis of MALAT1 long noncoding RNA in cells and in evolution. RNA 2023; 29:691-704. [PMID: 36792358 PMCID: PMC10159000 DOI: 10.1261/rna.079388.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/02/2023] [Indexed: 05/06/2023]
Abstract
Although not canonically polyadenylated, the long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) is stabilized by a highly conserved 76-nt triple helix structure on its 3' end. The entire MALAT1 transcript is over 8000 nt long in humans. The strongest structural conservation signal in MALAT1 (as measured by covariation of base pairs) is in the triple helix structure. Primary sequence analysis of covariation alone does not reveal the degree of structural conservation of the entire full-length transcript, however. Furthermore, RNA structure is often context dependent; RNA binding proteins that are differentially expressed in different cell types may alter structure. We investigate here the in-cell and cell-free structures of the full-length human and green monkey (Chlorocebus sabaeus) MALAT1 transcripts in multiple tissue-derived cell lines using SHAPE chemical probing. Our data reveal levels of uniform structural conservation in different cell lines, in cells and cell-free, and even between species, despite significant differences in primary sequence. The uniformity of the structural conservation across the entire transcript suggests that, despite seeing covariation signals only in the triple helix junction of the lncRNA, the rest of the transcript's structure is remarkably conserved, at least in primates and across multiple cell types and conditions.
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Affiliation(s)
- Anais Monroy-Eklund
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Colin Taylor
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Chase A Weidmann
- Department of Biological Chemistry, University of Michigan Medical School, Center for RNA Biomedicine, Rogel Cancer Center, Ann Arbor, Michigan 48109, USA
| | - Christina Burch
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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2
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Banijamali E, Baronti L, Becker W, Sajkowska-Kozielewicz JJ, Huang T, Palka C, Kosek D, Sweetapple L, Müller J, Stone MD, Andersson ER, Petzold K. RNA:RNA interaction in ternary complexes resolved by chemical probing. RNA 2023; 29:317-329. [PMID: 36617673 PMCID: PMC9945442 DOI: 10.1261/rna.079190.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
RNA regulation can be performed by a second targeting RNA molecule, such as in the microRNA regulation mechanism. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) probes the structure of RNA molecules and can resolve RNA:protein interactions, but RNA:RNA interactions have not yet been addressed with this technique. Here, we apply SHAPE to investigate RNA-mediated binding processes in RNA:RNA and RNA:RNA-RBP complexes. We use RNA:RNA binding by SHAPE (RABS) to investigate microRNA-34a (miR-34a) binding its mRNA target, the silent information regulator 1 (mSIRT1), both with and without the Argonaute protein, constituting the RNA-induced silencing complex (RISC). We show that the seed of the mRNA target must be bound to the microRNA loaded into RISC to enable further binding of the compensatory region by RISC, while the naked miR-34a is able to bind the compensatory region without seed interaction. The method presented here provides complementary structural evidence for the commonly performed luciferase-assay-based evaluation of microRNA binding-site efficiency and specificity on the mRNA target site and could therefore be used in conjunction with it. The method can be applied to any nucleic acid-mediated RNA- or RBP-binding process, such as splicing, antisense RNA binding, or regulation by RISC, providing important insight into the targeted RNA structure.
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Affiliation(s)
- Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Lorenzo Baronti
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Walter Becker
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | | | - Ting Huang
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Christina Palka
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - David Kosek
- Department of Cell and Molecular Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Lara Sweetapple
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Juliane Müller
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa
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3
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Holmquist CE, He W, Meganck RM, Marzluff WF. Knockouts of TUT7 and 3'hExo show that they cooperate in histone mRNA maintenance and degradation. RNA 2022; 28:1519-1533. [PMID: 36041871 PMCID: PMC9745837 DOI: 10.1261/rna.079233.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/12/2022] [Indexed: 05/18/2023]
Abstract
Metazoan histone mRNAs are the only cellular eukaryotic mRNAs that are not polyadenylated, ending instead in a conserved stem-loop. SLBP is bound to the 3' end of histone mRNAs and is required for translation of histone mRNA. The expression of histone mRNAs is tightly cell-cycle regulated. A major regulatory step is rapid degradation of histone mRNA at the end of S-phase or when DNA synthesis is inhibited in S-phase. 3'hExo, a 3' to 5' exonuclease, binds to the SLBP/SL complex and trims histone mRNA to 3 nt after the stem-loop. Together with a terminal uridyl transferase, 3'hExo maintains the length of the histone mRNA during S-phase. 3'hExo is essential for initiating histone mRNA degradation on polyribosomes, initiating degradation into the 3' side of the stem-loop. There is extensive uridylation of degradation intermediates in the 3' side of the stem when histone mRNA is degraded. Here, we knocked out TUT7 and 3'hExo and we show that both modification of histone mRNA during S-phase and degradation of histone mRNA involve the interaction of 3'hExo, and a specific TUTase, TENT3B (TUT7, ZCCHC6). Knockout of 3'hExo prevents the initiation of 3' to 5' degradation, stabilizing histone mRNA, whereas knockout of TUT7 prevents uridylation of the mRNA degradation intermediates, slowing the rate of degradation. In synchronized 3'hExo KO cells, histone mRNA degradation is delayed, but the histone mRNA is degraded prior to mitosis by a different pathway.
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Affiliation(s)
- Chris E Holmquist
- Division of Medicinal Chemistry and Chemical Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Integrated Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Wenxia He
- Integrated Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Rita M Meganck
- Integrated Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - William F Marzluff
- Integrated Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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4
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Yu T, Biasini A, Cecchini K, Saflund M, Mou H, Arif A, Eghbali A, de Rooij D, Weng Z, Zamore PD, Ozata DM. A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals. RNA 2022; 29:rna.079472.122. [PMID: 36241367 PMCID: PMC9808571 DOI: 10.1261/rna.079472.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
In male mice, the transcription factor A MYB initiates the transcription of pachytene piRNA genes during meiosis. Here, we report that A MYB activates the transcription factor Tcfl5 produced in pachytene spermatocytes. Subsequently, A MYB and TCFL5 reciprocally reinforce their own transcription to establish a positive feedback circuit that triggers pachytene piRNA production. TCFL5 regulates the expression of genes required for piRNA maturation and promotes transcription of evolutionarily young pachytene piRNA genes, whereas A-MYB activates the transcription of older pachytene piRNA genes. Intriguingly, pachytene piRNAs from TCFL5-dependent young loci initiates the production of piRNAs from A-MYB-dependent older loci ensuring the self-propagation of pachytene piRNAs. A MYB and TCFL5 act via a set of incoherent feedforward loops that drive regulation of gene expression by pachytene piRNAs during spermatogenesis. This regulatory architecture is conserved in rhesus macaque, suggesting that it was present in the last common ancestor of placental mammals.
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Affiliation(s)
| | | | | | | | | | - Amena Arif
- University of Massachusetts Medical School
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5
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Ruggieri AA, Livraghi L, Lewis JJ, Evans E, Cicconardi F, Hebberecht L, Ortiz-Ruiz Y, Montgomery SH, Ghezzi A, Rodriguez-Martinez JA, Jiggins CD, McMillan WO, Counterman BA, Papa R, Van Belleghem SM. A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility. Genome Res 2022; 32:1862-1875. [PMID: 36109150 PMCID: PMC9712634 DOI: 10.1101/gr.276839.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/13/2022] [Indexed: 01/16/2023]
Abstract
Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how much these SVs vary within populations and between closely related species, nor their significance in evolution. To address these questions, we characterized the evolution of indel SVs using genome assemblies of three closely related Heliconius butterfly species. Over the relatively short evolutionary timescales investigated, up to 18.0% of the genome was composed of indels between two haplotypes of an individual Heliconius charithonia butterfly and up to 62.7% included lineage-specific SVs between the genomes of the most distant species (11 Mya). Lineage-specific sequences were mostly characterized as transposable elements (TEs) inserted at random throughout the genome and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potential cis-regulatory function, we found that out of the 31,066 identified differences in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for sites with significant resemblance to several transcription factor binding sites with known function in neuron development in Drosophila We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural genome evolution that were previously overlooked in comparative genomic studies and suggest a high potential for structural variation to serve as raw material for adaptive evolution.
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Affiliation(s)
- Angelo A Ruggieri
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
| | - Luca Livraghi
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Smithsonian Tropical Research Institute, Apartado 0843-03092 Panamá, Panama
| | - James J Lewis
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Elizabeth Evans
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
| | - Francesco Cicconardi
- School of Biological Sciences, Bristol University, Bristol BS8 1QU, United Kingdom
| | - Laura Hebberecht
- School of Biological Sciences, Bristol University, Bristol BS8 1QU, United Kingdom
| | - Yadira Ortiz-Ruiz
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan 00926, Puerto Rico
| | - Stephen H Montgomery
- School of Biological Sciences, Bristol University, Bristol BS8 1QU, United Kingdom
| | - Alfredo Ghezzi
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado 0843-03092 Panamá, Panama
| | - Brian A Counterman
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan 00926, Puerto Rico
| | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
- Ecology, Evolution and Conservation Biology, Biology Department, KU Leuven, 3000 Leuven, Belgium
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6
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Fan W, Eklund E, Sherman RM, Liu H, Pitts S, Ford B, Rajeshkumar NV, Laiho M. Widespread genetic heterogeneity of human ribosomal RNA genes. RNA 2022; 28:478-492. [PMID: 35110373 PMCID: PMC8925967 DOI: 10.1261/rna.078925.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/28/2021] [Indexed: 05/28/2023]
Abstract
Polymorphism drives survival under stress and provides adaptability. Genetic polymorphism of ribosomal RNA (rRNA) genes derives from internal repeat variation of this multicopy gene, and from interindividual variation. A considerable amount of rRNA sequence heterogeneity has been proposed but has been challenging to estimate given the scarcity of accurate reference sequences. We identified four rDNA copies on chromosome 21 (GRCh38) with 99% similarity to recently introduced reference sequence KY962518.1. We customized a GATK bioinformatics pipeline using the four rDNA loci, spanning a total 145 kb, for variant calling and used high-coverage whole-genome sequencing (WGS) data from the 1000 Genomes Project to analyze variants in 2504 individuals from 26 populations. We identified a total of 3791 variant positions. The variants positioned nonrandomly on the rRNA gene. Invariant regions included the promoter, early 5' ETS, most of 18S, 5.8S, ITS1, and large areas of the intragenic spacer. A total of 470 variant positions were observed on 28S rRNA. The majority of the 28S rRNA variants were located on highly flexible human-expanded rRNA helical folds ES7L and ES27L, suggesting that these represent positions of diversity and are potentially under continuous evolution. Several variants were validated based on RNA-seq analyses. Population analyses showed remarkable ancestry-linked genetic variance and the presence of both high penetrance and frequent variants in the 5' ETS, ITS2, and 28S regions segregating according to the continental populations. These findings provide a genetic view of rRNA gene array heterogeneity and raise the need to functionally assess how the 28S rRNA variants affect ribosome functions.
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Affiliation(s)
- Wenjun Fan
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Eetu Eklund
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Rachel M Sherman
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Hester Liu
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Stephanie Pitts
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Brittany Ford
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - N V Rajeshkumar
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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7
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Jin B, Capra JA, Benchek P, Wheeler N, Naj AC, Hamilton-Nelson KL, Farrell JJ, Leung YY, Kunkle B, Vadarajan B, Schellenberg GD, Mayeux R, Wang LS, Farrer LA, Pericak-Vance MA, Martin ER, Haines JL, Crawford DC, Bush WS. An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns. Genome Res 2022; 32:778-790. [PMID: 35210353 PMCID: PMC8997344 DOI: 10.1101/gr.276069.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022]
Abstract
More than 90% of genetic variants are rare in most modern sequencing studies, such as the Alzheimer's Disease Sequencing Project (ADSP) whole-exome sequencing (WES) data. Furthermore, 54% of the rare variants in ADSP WES are singletons. However, both single variant and unit-based tests are limited in their statistical power to detect an association between rare variants and phenotypes. To best use missense rare variants and investigate their biological effect, we examine their association with phenotypes in the context of protein structures. We developed a protein structure-based approach, protein optimized kernel evaluation of missense nucleotides (POKEMON), which evaluates rare missense variants based on their spatial distribution within a protein rather than their allele frequency. The hypothesis behind this test is that the three-dimensional spatial distribution of variants within a protein structure provides functional context to power an association test. POKEMON identified three candidate genes (TREM2, SORL1, and EXOC3L4) and another suggestive gene from the ADSP WES data. For TREM2 and SORL1, two known Alzheimer's disease (AD) genes, the signal from the spatial cluster is stable even if we exclude known AD risk variants, indicating the presence of additional low-frequency risk variants within these genes. EXOC3L4 is a novel AD risk gene that has a cluster of variants primarily shared by case subjects around the Sec6 domain. This cluster is also validated in an independent replication data set and a validation data set with a larger sample size.
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Affiliation(s)
- Bowen Jin
- Graduate Program in Systems Biology and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - John A Capra
- The Bakar Computational Health Sciences Institute, Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA
| | - Penelope Benchek
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Nicholas Wheeler
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Adam C Naj
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kara L Hamilton-Nelson
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Brian Kunkle
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Badri Vadarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University, New York, New York 10032, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University, New York, New York 10032, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Eden R Martin
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Dana C Crawford
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
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8
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Martin AM, Cassirer EF, Waits LP, Plowright RK, Cross PC, Andrews KR. Genomic association with pathogen carriage in bighorn sheep ( Ovis canadensis). Ecol Evol 2021; 11:2488-2502. [PMID: 33767816 PMCID: PMC7981200 DOI: 10.1002/ece3.7159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/03/2022] Open
Abstract
Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population-level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well-studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family-based genome-wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome-wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP-based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.
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Affiliation(s)
- Alynn M. Martin
- United States Geological SurveyNorthern Rocky Mountain Science CenterBozemanMTUSA
| | | | | | - Raina K. Plowright
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Paul C. Cross
- United States Geological SurveyNorthern Rocky Mountain Science CenterBozemanMTUSA
| | - Kimberly R. Andrews
- Institute for Bioinformatics and Evolutionary Studies (IBEST)University of IdahoMoscowIDUSA
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9
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Souza LAC, Cooper SG, Worker CJ, Thakore P, Feng Earley Y. Use of chlorisondamine to assess the neurogenic contribution to blood pressure in mice: An evaluation of method. Physiol Rep 2021; 9:e14753. [PMID: 33587331 PMCID: PMC7883841 DOI: 10.14814/phy2.14753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 11/24/2022] Open
Abstract
Chlorisondamine (CSD) has been used to assess the neurogenic contribution to blood pressure (BP) and vasomotor sympathetic tone in animal models. It is assumed that the reduction in BP following CSD administration is associated to decreases in cardiac output (CO) and peripheral resistance, reflecting cardiac and vasomotor sympathetic tone, respectively. Surprisingly, this has not been characterized experimentally in mice, despite the extensive use of this animal model in cardiovascular research. We hypothesize that a specific dose of CSD can selectively block the sympathetic vasomotor tone. To test this hypothesis, we evaluated the effects of different doses of CSD (intraperitoneal) on BP and heart rate (HR) using telemetry, and on CO using echocardiography. BP and HR in normotensive C57Bl/6J mice reduced to a similar extent by all CSD doses tested (1-6 mg/kg). CSD at 6 mg/kg also reduced CO without affecting left ventricular stroke volume or fractional shortening. On the other hand, lower doses of CSD (1 and 2 mg/kg) produced significantly larger BP and HR reductions in DOCA-salt-induced hypertensive mice, indicating a greater neurogenic BP response. In addition, all doses of CSD reduced CO in hypertensive mice. Our data suggest that the BP response to CSD in mice likely reflects reduced CO and vasomotor sympathetic tone. We conclude that CSD can be used to assess the neurogenic contribution to BP in mice but may not be appropriate for specifically estimating vasomotor sympathetic tone.
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Affiliation(s)
- Lucas AC. Souza
- Departments of Pharmacology and Physiology & Cell BiologySchool of MedicineUniversity of Nevada, RenoRenoNVUSA
- Center for Molecular and Cellular Signaling in the Cardiovascular SystemUniversity of Nevada, RenoRenoNVUSA
| | - Silvana G. Cooper
- Departments of Pharmacology and Physiology & Cell BiologySchool of MedicineUniversity of Nevada, RenoRenoNVUSA
- Center for Molecular and Cellular Signaling in the Cardiovascular SystemUniversity of Nevada, RenoRenoNVUSA
| | - Caleb J. Worker
- Departments of Pharmacology and Physiology & Cell BiologySchool of MedicineUniversity of Nevada, RenoRenoNVUSA
- Center for Molecular and Cellular Signaling in the Cardiovascular SystemUniversity of Nevada, RenoRenoNVUSA
| | - Pratish Thakore
- Departments of Pharmacology and Physiology & Cell BiologySchool of MedicineUniversity of Nevada, RenoRenoNVUSA
- Center for Molecular and Cellular Signaling in the Cardiovascular SystemUniversity of Nevada, RenoRenoNVUSA
| | - Yumei Feng Earley
- Departments of Pharmacology and Physiology & Cell BiologySchool of MedicineUniversity of Nevada, RenoRenoNVUSA
- Center for Molecular and Cellular Signaling in the Cardiovascular SystemUniversity of Nevada, RenoRenoNVUSA
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10
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Skinner A, Yang C, Hincks K, Wang H, Resendiz MJE. Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8-oxo-7,8-dihydropurine, and 8-bromopurine analogues within A-form duplexes of RNA. Biopolymers 2020; 111:e23410. [PMID: 33216981 PMCID: PMC7780609 DOI: 10.1002/bip.23410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/30/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022]
Abstract
Inosine is an important RNA modification, furthermore RNA oxidation has gained interest due, in part, to its potential role in the development/progression of disease as well as on its impact on RNA structure and function. In this report we established the base pairing abilities of purine nucleobases G, I, A, as well as their corresponding, 8-oxo-7,8-dihydropurine (common products of oxidation at the C8-position of purines), and 8-bromopurine (as probes to explore conformational changes), derivatives, namely 8-oxoG, 8-oxoI, 8-oxoA, 8-BrG, and 8-BrI. Dodecamers of RNA were obtained using standard phosphoramidite chemistry via solid-phase synthesis, and used as models to establish the impact that each of these nucleobases have on the thermal stability of duplexes, when base pairing to canonical and noncanonical nucleobases. Thermal stabilities were obtained from thermal denaturation transition (Tm ) measurements, via circular dichroism (CD). The results were then rationalized using models of base pairs between two monomers, via density functional theory (DFT), that allowed us to better understand potential contributions from H-bonding patterns arising from distinct conformations. Overall, some of the important results indicate that: (a) an anti-I:syn-A base pair provides thermal stability, due to the absence of the exocyclic amine; (b) 8-oxoG base pairs like U, and does not induce destabilization within the duplex when compared to the pyrimidine ring; (c) a U:G wobble-pair is only stabilized by G; and (d) 8-oxoA displays an inherited base pairing promiscuity in this sequence context. Gaining a better understanding of how this oxidatively generated lesions potentially base pair with other nucleobases will be useful to predict various biological outcomes, as well as in the design of biomaterials and/or nucleotide derivatives with biological potential.
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Affiliation(s)
- Austin Skinner
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Chou‐Hsun Yang
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Kazuki Hincks
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Haobin Wang
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
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11
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Ren L, You T, Li Q, Chen G, Liu Z, Zhao X, Wang Y, Wang L, Wu Y, Tang C, Zhu L. Molecular docking-assisted screening reveals tannic acid as a natural protein disulphide isomerase inhibitor with antiplatelet and antithrombotic activities. J Cell Mol Med 2020; 24:14257-14269. [PMID: 33128352 PMCID: PMC7753999 DOI: 10.1111/jcmm.16043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
Protein disulphide isomerase (PDI) promotes platelet activation and constitutes a novel antithrombotic target. In this study, we reported that a PDI‐binding plant polyphenol, tannic acid (TA), inhibits PDI activity, platelet activation and thrombus formation. Molecular docking using plant polyphenols from dietary sources with cardiovascular benefits revealed TA as the most potent binding molecule with PDI active centre. Surface plasmon resonance demonstrated that TA bound PDI with high affinity. Using Di‐eosin‐glutathione disulphide fluorescence assay and PDI assay kit, we showed that TA inhibited PDI activity. In isolated platelets, TA inhibited platelet aggregation stimulated by either GPVI or ITAM pathway agonists. Flow cytometry showed that TA inhibited thrombin‐ or CRP‐stimulated platelet activation, as reflected by reduced granule secretion and integrin activation. TA also reduced platelet spreading on immobilized fibrinogen and platelet adhesion under flow conditions. In a laser‐induced vascular injury mouse model, intraperitoneal injection of TA significantly decreased the size of cremaster arteriole thrombi. No prolongation of mouse jugular vein and tail‐bleeding time was observed after TA administration. Therefore, we identified TA from natural polyphenols as a novel inhibitor of PDI function. TA inhibits platelet activation and thrombus formation, suggesting it as a potential antithrombotic agent.
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Affiliation(s)
- Lijie Ren
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
- National Clinical Research Center for Hematologic Diseasesthe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Tao You
- Jiangsu Institute of HematologyKey Laboratory of Thrombosis and Hemostasis of Ministry of HealthThe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Department of CardiologyThe Second Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Qing Li
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
| | - Guona Chen
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
| | - Ziting Liu
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
| | - Xuefei Zhao
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
| | - Yinyan Wang
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
| | - Lei Wang
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
| | - Yi Wu
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
- National Clinical Research Center for Hematologic Diseasesthe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chaojun Tang
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
- National Clinical Research Center for Hematologic Diseasesthe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Li Zhu
- Cyrus Tang Hematology CenterCollaborative Innovation Center of HematologySuzhou Key Laboratory of Thrombosis and Vascular DiseasesState Key Laboratory of Radiation Medicine and ProtectionSoochow UniversitySuzhouChina
- National Clinical Research Center for Hematologic Diseasesthe First Affiliated Hospital of Soochow UniversitySuzhouChina
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12
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Schwer B, Sanchez AM, Shuman S. Inactivation of fission yeast Erh1 de-represses pho1 expression: evidence that Erh1 is a negative regulator of prt lncRNA termination. RNA 2020; 26:1334-1344. [PMID: 32546512 PMCID: PMC7491324 DOI: 10.1261/rna.076463.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/01/2020] [Indexed: 05/08/2023]
Abstract
Fission yeast Erh1 exists in a complex with RNA-binding protein Mmi1. Deletion of erh1 up-regulates the phosphate homeostasis gene pho1, which is normally repressed by transcription in cis of a 5' flanking prt lncRNA. Here we present evidence that de-repression of pho1 by erh1Δ is achieved through precocious 3'-processing/termination of prt lncRNA synthesis, to wit: (i) erh1Δ does not affect the activity of the prt or pho1 promoters per se; (ii) de-repression by erh1Δ depends on CPF (cleavage and polyadenylation factor) subunits Ctf1, Dis2, Ssu72, Swd22, and Ppn1 and on termination factor Rhn1; (iii) de-repression requires synthesis by the Asp1 IPP kinase of inositol 1-pyrophosphates (1-IPPs); (iv) de-repression is effaced by mutating Thr4 of the RNA polymerase II CTD to alanine; and (v) erh1Δ exerts an additive effect on pho1 de-repression in combination with mutating CTD Ser7 to alanine and with deletion of the IPP pyrophosphatase Aps1. These findings point to Erh1 as an antagonist of lncRNA termination in the prt-pho1 axis. In contrast, in mmi1Δ cells there is a reduction in pho1 mRNA and increase in the formation of a prt-pho1 read-through transcript, consistent with Mmi1 being an agonist of prt termination. We envision that Erh1 acts as a brake on Mmi1's ability to promote CPF-dependent termination during prt lncRNA synthesis. Consistent with this idea, erh1Δ de-repression of pho1 was eliminated by mutating the Mmi1-binding sites in the prt lncRNA.
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Affiliation(s)
- Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Ana M Sanchez
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
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Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res 2020; 30:1291-1305. [PMID: 32801147 PMCID: PMC7545148 DOI: 10.1101/gr.263566.120] [Citation(s) in RCA: 292] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced Pacific Biosciences (PacBio) HiFi sequencing technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human genomes sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy and allele recovery compared to the current state of the art. On the effectively haploid CHM13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy of 99.999% (QV50), surpassing recent assemblies of high-coverage, ultralong Oxford Nanopore Technologies (ONT) reads in terms of both accuracy and continuity. This HiCanu assembly correctly resolves 337 out of 341 validation BACs sampled from known segmental duplications and provides the first preliminary assemblies of nine complete human centromeric regions. Although gaps and errors still remain within the most challenging regions of the genome, these results represent a significant advance toward the complete assembly of human genomes.
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Affiliation(s)
- Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Robert Grothe
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
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14
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Turbeville HR, Johnson AC, Garrett MR, Dent EL, Sasser JM. Nitric oxide and oxidative stress pathways do not contribute to sex differences in renal injury and function in Dahl SS/Jr rats. Physiol Rep 2020; 8:e14440. [PMID: 32652814 PMCID: PMC7354091 DOI: 10.14814/phy2.14440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/13/2022] Open
Abstract
The burden of hypertension in the United States is increasing and yields significant morbidity and mortality, and sex differences in hypertension are widely recognized. Reduced nitric oxide (NO) bioavailability and increased oxidative stress are known to contribute to the pathogenesis of hypertensive renal injury, and but their contributions to sex differences in injury progression of are undefined. Our purpose was to test the hypothesis that male hypertensive rats have accelerated renal injury compared to females and to determine the contributions of the nitric oxide pathway and oxidative stress in these differences. Male and female Dahl SS/Jr rats, a model that spontaneously develops hypertension with age, were allowed to age on a 0.3% NaCl diet until 3 or 6 months of age, at which points blood pressure was measured and plasma, tissue, and urine were collected. While no significant sex differences in blood pressure were present at either time point, renal injury measured by urine protein excretion was more severe (male = 44.9 ± 6; female = 15±3 mg/day/100 g bw, p = .0001), and renal function was reduced (male = 0.48 ± 0.02; female = 0.7 ± 0.03 ml min-1 g-1 kw, p = .001) in males compared to females with age. Both male and female rats exhibited reduced nitric oxide metabolites (3 months: male = 0.65 ± 0.1; female = 0.74 ± 0.3; 6 months: male = 0.16 ± 0.1; female = 0.41 ± 0.1 ml min-1 g-1 kw, p, age = 0.02, p, sex = 0.3). Levels of urinary TBARS were similar (3 months: male = 20±1.5; female = 23±1.8; 6 months: male = 26±4.8; female = 23±4.7µM day g-1 kw, p, age = 0.4, p, sex = 0.9), extracellular superoxide dismutase (EC SOD) mRNA was greater in females (3 months: male = 0.35 ± 0.03; female = 1.4 ± 0.2; 6 months: male = 0.4 ± 0.05; female = 1.3 ± 0.1 normalized counts, p, age = 0.7, p, sex < 0.0001), but EC SOD protein expression was not different (3 months: male = 0.01 ± 0.002; female = 0.01 ± 0.002; 6 months: male = 0.02 ± 0.004; female = 0.01 ± 0.002 relative density, p, age = 0.2, p, sex = 0.8). These data support the presence of significant sex differences in renal injury and function in the Dahl S rat and identify a need for further study into the mechanisms involved.
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Affiliation(s)
- Hannah R. Turbeville
- Department of Pharmacology and ToxicologyUniversity of Mississippi Medical CenterJacksonMSUSA
| | - Ashley C. Johnson
- Department of Pharmacology and ToxicologyUniversity of Mississippi Medical CenterJacksonMSUSA
| | - Michael R. Garrett
- Department of Pharmacology and ToxicologyUniversity of Mississippi Medical CenterJacksonMSUSA
| | - Elena L. Dent
- Department Physiology and BiophysicsUniversity of Mississippi Medical CenterJacksonMSUSA
| | - Jennifer M. Sasser
- Department of Pharmacology and ToxicologyUniversity of Mississippi Medical CenterJacksonMSUSA
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15
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Di Pauli von Treuheim T, Torre OM, Mosley GE, Nasser P, Iatridis JC. Measuring the neutral zone of spinal motion segments: Comparison of multiple analysis methods to quantify spinal instability. JOR Spine 2020; 3:e1088. [PMID: 32613163 PMCID: PMC7323462 DOI: 10.1002/jsp2.1088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/26/2020] [Accepted: 03/22/2020] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Neutral zone (NZ) parameters in spinal biomechanics studies are sensitive to spinal instability, disc degeneration, and repair. Multiple methods in the literature quantify NZ, yet no consensus exists on applicability and comparability of methods. This study compares five different NZ quantification methods using two different load-deflection profiles. METHODS Rat caudal and lumbar motion segments were tested in axial rotation to generate load-deflection curves with profiles exhibiting prominent distinction between elastic and NZ regions (ie, triphasic) and profiles that did not (ie, viscoelastic). NZ was quantified using five methods: trilinear, double sigmoid (DS), zero load, stiffness threshold (ST), and extrapolated elastic zone. Absolute agreement and consistency of NZ parameters were assessed using intraclass correlation (ICC), Bland-Altman analyses, and analysis of variance. RESULTS For triphasic profiles, NZ magnitude exhibited high consistency (methods correlate but differ in absolute values), and only some methods exhibited agreement. For viscoelastic profiles, NZ magnitude showed limited consistency and no absolute agreement. NZ stiffness had high agreement and consistency across most methods and profiles. For triphasic profiles, the linear NZ regions for all methods were not well-described by a linear fit yet for viscoelastic profiles all methods characterized a linear NZ region. CONCLUSION This NZ comparison study showed surprisingly limited agreement and consistency among NZ parameters with approximately 5% to 100% difference depending on the method and load-deflection profile. Nevertheless, the DS and ST methods appeared to be most comparable. We conclude that most NZ quantification methods cannot be applied interchangeably, highlighting a need to clearly state NZ calculation methods. Future studies are required to identify which methods are most sensitive to disc degeneration and repair in order to identify a "best" method.
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Affiliation(s)
| | - Olivia M. Torre
- Leni & Peter W. May Department of OrthopaedicsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Grace E. Mosley
- Leni & Peter W. May Department of OrthopaedicsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Philip Nasser
- Leni & Peter W. May Department of OrthopaedicsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - James C. Iatridis
- Leni & Peter W. May Department of OrthopaedicsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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16
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Gurumurthy CB, O'Brien AR, Quadros RM, Adams J, Alcaide P, Ayabe S, Ballard J, Batra SK, Beauchamp MC, Becker KA, Bernas G, Brough D, Carrillo-Salinas F, Chan W, Chen H, Dawson R, DeMambro V, D'Hont J, Dibb KM, Eudy JD, Gan L, Gao J, Gonzales A, Guntur AR, Guo H, Harms DW, Harrington A, Hentges KE, Humphreys N, Imai S, Ishii H, Iwama M, Jonasch E, Karolak M, Keavney B, Khin NC, Konno M, Kotani Y, Kunihiro Y, Lakshmanan I, Larochelle C, Lawrence CB, Li L, Lindner V, Liu XD, Lopez-Castejon G, Loudon A, Lowe J, Jerome-Majewska LA, Matsusaka T, Miura H, Miyasaka Y, Morpurgo B, Motyl K, Nabeshima YI, Nakade K, Nakashiba T, Nakashima K, Obata Y, Ogiwara S, Ouellet M, Oxburgh L, Piltz S, Pinz I, Ponnusamy MP, Ray D, Redder RJ, Rosen CJ, Ross N, Ruhe MT, Ryzhova L, Salvador AM, Alam SS, Sedlacek R, Sharma K, Smith C, Staes K, Starrs L, Sugiyama F, Takahashi S, Tanaka T, Trafford AW, Uno Y, Vanhoutte L, Vanrockeghem F, Willis BJ, Wright CS, Yamauchi Y, Yi X, Yoshimi K, Zhang X, Zhang Y, Ohtsuka M, Das S, Garry DJ, Hochepied T, Thomas P, Parker-Thornburg J, Adamson AD, Yoshiki A, Schmouth JF, Golovko A, Thompson WR, Lloyd KCK, Wood JA, Cowan M, Mashimo T, Mizuno S, Zhu H, Kasparek P, Liaw L, Miano JM, Burgio G. Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation. Genome Biol 2019; 20:171. [PMID: 31446895 PMCID: PMC6709553 DOI: 10.1186/s13059-019-1776-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/27/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND CRISPR-Cas9 gene-editing technology has facilitated the generation of knockout mice, providing an alternative to cumbersome and time-consuming traditional embryonic stem cell-based methods. An earlier study reported up to 16% efficiency in generating conditional knockout (cKO or floxed) alleles by microinjection of 2 single guide RNAs (sgRNA) and 2 single-stranded oligonucleotides as donors (referred herein as "two-donor floxing" method). RESULTS We re-evaluate the two-donor method from a consortium of 20 laboratories across the world. The dataset constitutes 56 genetic loci, 17,887 zygotes, and 1718 live-born mice, of which only 15 (0.87%) mice contain cKO alleles. We subject the dataset to statistical analyses and a machine learning algorithm, which reveals that none of the factors analyzed was predictive for the success of this method. We test some of the newer methods that use one-donor DNA on 18 loci for which the two-donor approach failed to produce cKO alleles. We find that the one-donor methods are 10- to 20-fold more efficient than the two-donor approach. CONCLUSION We propose that the two-donor method lacks efficiency because it relies on two simultaneous recombination events in cis, an outcome that is dwarfed by pervasive accompanying undesired editing events. The methods that use one-donor DNA are fairly efficient as they rely on only one recombination event, and the probability of correct insertion of the donor cassette without unanticipated mutational events is much higher. Therefore, one-donor methods offer higher efficiencies for the routine generation of cKO animal models.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Aidan R O'Brien
- Transformational Bioinformatics, Health and Biosecurity Business Unit, CSIRO, North Ryde, Australia
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - John Adams
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Pilar Alcaide
- Department of Immunology, Tufts University School of Medicine, Boston, USA
| | - Shinya Ayabe
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Johnathan Ballard
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Marie-Claude Beauchamp
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Kathleen A Becker
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Guillaume Bernas
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | | | - Wesley Chan
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Hanying Chen
- School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Ruby Dawson
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Victoria DeMambro
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Jinke D'Hont
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Katharine M Dibb
- Unit of Cardiac Physiology, School of Medical Sciences, Manchester Academic Health Science Center, University of Manchester, Manchester, UK
| | - James D Eudy
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, USA
| | - Lin Gan
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jing Gao
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Amy Gonzales
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Anyonya R Guntur
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Huiping Guo
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Donald W Harms
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne Harrington
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Neil Humphreys
- Transgenic Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shiho Imai
- Department of Basic Medicine, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Japan
| | - Mizuho Iwama
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Eric Jonasch
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle Karolak
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Nay-Chi Khin
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuko Kotani
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yayoi Kunihiro
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Catherine Larochelle
- Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Catherine B Lawrence
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Lin Li
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Volkhard Lindner
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Xian-De Liu
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gloria Lopez-Castejon
- Manchester Collaborative Centre for Inflammation Research (MCCIR), School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Andrew Loudon
- Centre for Biological Timing, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jenna Lowe
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Loydie A Jerome-Majewska
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Taiji Matsusaka
- Department of Basic Medicine, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hiromi Miura
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Yoshiki Miyasaka
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Benjamin Morpurgo
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Katherine Motyl
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Yo-Ichi Nabeshima
- Laboratory of Molecular Life Science, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | - Koji Nakade
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - Kenichi Nakashima
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yuichi Obata
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Sanae Ogiwara
- Department of Laboratory Animal Science, Support Center for Medical Research and Education, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Mariette Ouellet
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Leif Oxburgh
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
- Basic and Clinical Research, The Rogosin Institute, New York, USA
| | - Sandra Piltz
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Ilka Pinz
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - David Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX37LE, UK
| | - Ronald J Redder
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, USA
| | - Clifford J Rosen
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Nikki Ross
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Mark T Ruhe
- Mouse Biology Program, University of California, Davis, USA
| | - Larisa Ryzhova
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Ane M Salvador
- Department of Immunology, Tufts University School of Medicine, Boston, USA
| | - Sabrina Shameen Alam
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Karan Sharma
- College of Osteopathic Medicine, Marian University, Indianapolis, IN, 46222, USA
| | - Chad Smith
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katrien Staes
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Lora Starrs
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Tomohiro Tanaka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Andrew W Trafford
- Unit of Cardiac Physiology, School of Medical Sciences, Manchester Academic Health Science Center, University of Manchester, Manchester, UK
| | - Yoshihiro Uno
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Leen Vanhoutte
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Frederique Vanrockeghem
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Christian S Wright
- School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA
| | - Yuko Yamauchi
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Xin Yi
- School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA
| | - Kazuto Yoshimi
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Xuesong Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Zhang
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Masato Ohtsuka
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Satyabrata Das
- Lillehei Heart Institute Regenerative Medicine and Sciences Program, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Garry
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, USA
| | - Tino Hochepied
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Paul Thomas
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | | | - Antony D Adamson
- Transgenic Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Atsushi Yoshiki
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Jean-Francois Schmouth
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Andrei Golovko
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - William R Thompson
- School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, USA
| | - Joshua A Wood
- Mouse Biology Program, University of California, Davis, USA
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), Montreal, Canada
| | - Tomoji Mashimo
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Hao Zhu
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lucy Liaw
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Joseph M Miano
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia.
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Schertzer MD, Thulson E, Braceros KCA, Lee DM, Hinkle ER, Murphy RM, Kim SO, Vitucci ECM, Calabrese JM. A piggyBac-based toolkit for inducible genome editing in mammalian cells. RNA 2019; 25:1047-1058. [PMID: 31101683 PMCID: PMC6633203 DOI: 10.1261/rna.068932.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 05/15/2019] [Indexed: 05/30/2023]
Abstract
We describe the development and application of a novel series of vectors that facilitate CRISPR-Cas9-mediated genome editing in mammalian cells, which we call CRISPR-Bac. CRISPR-Bac leverages the piggyBac transposon to randomly insert CRISPR-Cas9 components into mammalian genomes. In CRISPR-Bac, a single piggyBac cargo vector containing a doxycycline-inducible Cas9 or catalytically dead Cas9 (dCas9) variant and a gene conferring resistance to Hygromycin B is cotransfected with a plasmid expressing the piggyBac transposase. A second cargo vector, expressing a single-guide RNA (sgRNA) of interest, the reverse-tetracycline TransActivator (rtTA), and a gene conferring resistance to G418, is also cotransfected. Subsequent selection on Hygromycin B and G418 generates polyclonal cell populations that stably express Cas9, rtTA, and the sgRNA(s) of interest. We show that CRISPR-Bac can be used to knock down proteins of interest, to create targeted genetic deletions with high efficiency, and to activate or repress transcription of protein-coding genes and an imprinted long noncoding RNA. The ratio of sgRNA-to-Cas9-to-transposase can be adjusted in transfections to alter the average number of cargo insertions into the genome. sgRNAs targeting multiple genes can be inserted in a single transfection. CRISPR-Bac is a versatile platform for genome editing that simplifies the generation of mammalian cells that stably express the CRISPR-Cas9 machinery.
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Affiliation(s)
- Megan D Schertzer
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Eliza Thulson
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Keean C A Braceros
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - David M Lee
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Emma R Hinkle
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Ryan M Murphy
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Susan O Kim
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Eva C M Vitucci
- Curriculum in Toxicology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- U.S. Environmental Protection Agency, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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18
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Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC. The accessible chromatin landscape of the murine hippocampus at single-cell resolution. Genome Res 2019; 29:857-869. [PMID: 30936163 PMCID: PMC6499306 DOI: 10.1101/gr.243725.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 03/21/2019] [Indexed: 11/29/2022]
Abstract
Here we present a comprehensive map of the accessible chromatin landscape of the mouse hippocampus at single-cell resolution. Substantial advances of this work include the optimization of a single-cell combinatorial indexing assay for transposase accessible chromatin (sci-ATAC-seq); a software suite, scitools, for the rapid processing and visualization of single-cell combinatorial indexing data sets; and a valuable resource of hippocampal regulatory networks at single-cell resolution. We used sci-ATAC-seq to produce 2346 high-quality single-cell chromatin accessibility maps with a mean unique read count per cell of 29,201 from both fresh and frozen hippocampi, observing little difference in accessibility patterns between the preparations. By using this data set, we identified eight distinct major clusters of cells representing both neuronal and nonneuronal cell types and characterized the driving regulatory factors and differentially accessible loci that define each cluster. Within pyramidal neurons, we identified four major clusters, including CA1 and CA3 neurons, and three additional subclusters. We then applied a recently described coaccessibility framework, Cicero, which identified 146,818 links between promoters and putative distal regulatory DNA. Identified coaccessibility networks showed cell-type specificity, shedding light on key dynamic loci that reconfigure to specify hippocampal cell lineages. Lastly, we performed an additional sci-ATAC-seq preparation from cultured hippocampal neurons (899 high-quality cells, 43,532 mean unique reads) that revealed substantial alterations in their epigenetic landscape compared with nuclei from hippocampal tissue. This data set and accompanying analysis tools provide a new resource that can guide subsequent studies of the hippocampus.
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Affiliation(s)
- John R Sinnamon
- The Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kristof A Torkenczy
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Michael W Linhoff
- The Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Sarah A Vitak
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Ryan M Mulqueen
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Hannah A Pliner
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | | | - Gail Mandel
- The Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Center for Early Detection Advanced Research, Oregon Health and Science University, Portland, Oregon 97239, USA
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19
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Atilho RM, Perkins KR, Breaker RR. Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity. RNA 2019; 25:23-34. [PMID: 30287481 PMCID: PMC6298564 DOI: 10.1261/rna.067975.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/02/2018] [Indexed: 05/10/2023]
Abstract
Many bacteria use flavin mononucleotide (FMN) riboswitches to control the expression of genes responsible for the biosynthesis and transport of this enzyme cofactor or its precursor, riboflavin. Rare variants of FMN riboswitches found in strains of Clostridium difficile and some other bacteria typically control the expression of proteins annotated as transporters, including multidrug efflux pumps. These RNAs no longer recognize FMN, and differ from the original riboswitch consensus sequence at nucleotide positions normally involved in binding of the ribityl and phosphate moieties of the cofactor. Representatives of one of the two variant subtypes were found to bind the FMN precursor riboflavin and the FMN degradation products lumiflavin and lumichrome. Although the biologically relevant ligand sensed by these variant FMN riboswitches remains uncertain, our findings suggest that many strains of C. difficile might use rare riboswitches to sense flavin degradation products and activate transporters for their detoxification.
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Affiliation(s)
- Ruben M Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Kevin R Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
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20
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Sinha D, Matz LM, Cameron TA, De Lay NR. Poly(A) polymerase is required for RyhB sRNA stability and function in Escherichia coli. RNA 2018; 24:1496-1511. [PMID: 30061117 PMCID: PMC6191717 DOI: 10.1261/rna.067181.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/24/2018] [Indexed: 05/05/2023]
Abstract
Small regulatory RNAs (sRNAs) are an important class of bacterial post-transcriptional regulators that control numerous physiological processes, including stress responses. In Gram-negative bacteria including Escherichia coli, the RNA chaperone Hfq binds many sRNAs and facilitates pairing to target transcripts, resulting in changes in mRNA transcription, translation, or stability. Here, we report that poly(A) polymerase (PAP I), which promotes RNA degradation by exoribonucleases through the addition of poly(A) tails, has a crucial role in the regulation of gene expression by Hfq-dependent sRNAs. Specifically, we show that deletion of pcnB, encoding PAP I, paradoxically resulted in an increased turnover of certain Hfq-dependent sRNAs, including RyhB. RyhB instability in the pcnB deletion strain was suppressed by mutations in hfq or ryhB that disrupt pairing of RyhB with target RNAs, by mutations in the 3' external transcribed spacer of the glyW-cysT-leuZ transcript (3'ETSLeuZ) involved in pairing with RyhB, or an internal deletion in rne, which encodes the endoribonuclease RNase E. Finally, the reduced stability of RyhB in the pcnB deletion strain resulted in impaired regulation of some of its target mRNAs, specifically sodB and sdhCDAB. Altogether our data support a model where PAP I plays a critical role in ensuring the efficient decay of the 3'ETSLeuZ In the absence of PAP I, the 3'ETSLeuZ transcripts accumulate, bind Hfq, and pair with RyhB, resulting in its depletion via RNase E-mediated decay. This ultimately leads to a defect in RyhB function in a PAP I deficient strain.
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Affiliation(s)
- Dhriti Sinha
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Lisa M Matz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Nicholas R De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas 77030, USA
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21
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Song X, Beck CR, Du R, Campbell IM, Coban-Akdemir Z, Gu S, Breman AM, Stankiewicz P, Ira G, Shaw CA, Lupski JR. Predicting human genes susceptible to genomic instability associated with Alu/ Alu-mediated rearrangements. Genome Res 2018; 28:1228-1242. [PMID: 29907612 PMCID: PMC6071635 DOI: 10.1101/gr.229401.117] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 06/06/2018] [Indexed: 12/14/2022]
Abstract
Alu elements, the short interspersed element numbering more than 1 million copies per human genome, can mediate the formation of copy number variants (CNVs) between substrate pairs. These Alu/Alu-mediated rearrangements (AAMRs) can result in pathogenic variants that cause diseases. To investigate the impact of AAMR on gene variation and human health, we first characterized Alus that are involved in mediating CNVs (CNV-Alus) and observed that these Alus tend to be evolutionarily younger. We then computationally generated, with the assistance of a supercomputer, a test data set consisting of 78 million Alu pairs and predicted ∼18% of them are potentially susceptible to AAMR. We further determined the relative risk of AAMR in 12,074 OMIM genes using the count of predicted CNV-Alu pairs and experimentally validated the predictions with 89 samples selected by correlating predicted hotspots with a database of CNVs identified by clinical chromosomal microarrays (CMAs) on the genomes of approximately 54,000 subjects. We fine-mapped 47 duplications, 40 deletions, and two complex rearrangements and examined a total of 52 breakpoint junctions of simple CNVs. Overall, 94% of the candidate breakpoints were at least partially Alu mediated. We successfully predicted all (100%) of Alu pairs that mediated deletions (n = 21) and achieved an 87% positive predictive value overall when including AAMR-generated deletions and duplications. We provided a tool, AluAluCNVpredictor, for assessing AAMR hotspots and their role in human disease. These results demonstrate the utility of our predictive model and provide insights into the genomic features and molecular mechanisms underlying AAMR.
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Affiliation(s)
- Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Baylor Genetics, Houston, Texas 77021, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Baylor Genetics, Houston, Texas 77021, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Baylor Genetics, Houston, Texas 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Hospital, Houston, Texas 77030, USA
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