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Fronk AD, Manzanares MA, Zheng P, Geier A, Anderson K, Stanton S, Zumrut H, Gera S, Munch R, Frederick V, Dhingra P, Arun G, Akerman M. Development and validation of AI/ML derived splice-switching oligonucleotides. Mol Syst Biol 2024; 20:676-701. [PMID: 38664594 PMCID: PMC11148135 DOI: 10.1038/s44320-024-00034-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 06/05/2024] Open
Abstract
Splice-switching oligonucleotides (SSOs) are antisense compounds that act directly on pre-mRNA to modulate alternative splicing (AS). This study demonstrates the value that artificial intelligence/machine learning (AI/ML) provides for the identification of functional, verifiable, and therapeutic SSOs. We trained XGboost tree models using splicing factor (SF) pre-mRNA binding profiles and spliceosome assembly information to identify modulatory SSO binding sites on pre-mRNA. Using Shapley and out-of-bag analyses we also predicted the identity of specific SFs whose binding to pre-mRNA is blocked by SSOs. This step adds considerable transparency to AI/ML-driven drug discovery and informs biological insights useful in further validation steps. We applied this approach to previously established functional SSOs to retrospectively identify the SFs likely to regulate those events. We then took a prospective validation approach using a novel target in triple negative breast cancer (TNBC), NEDD4L exon 13 (NEDD4Le13). Targeting NEDD4Le13 with an AI/ML-designed SSO decreased the proliferative and migratory behavior of TNBC cells via downregulation of the TGFβ pathway. Overall, this study illustrates the ability of AI/ML to extract actionable insights from RNA-seq data.
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Affiliation(s)
| | | | - Paulina Zheng
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Adam Geier
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | | | | | - Hasan Zumrut
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Sakshi Gera
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Robin Munch
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | | | | | - Gayatri Arun
- Envisagenics, Inc., Long Island City, NY, 11101, USA
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Bossert JM, Mejias-Aponte CA, Saunders T, Altidor L, Emery M, Fredriksson I, Batista A, Claypool SM, Caldwell KE, Reiner DJ, Chow JJ, Foltz M, Kumar V, Seasholtz A, Hughes E, Filipiak W, Harvey BK, Richie CT, Vautier F, Gomez JL, Michaelides M, Kieffer BL, Watson SJ, Akil H, Shaham Y. Effect of Selective Lesions of Nucleus Accumbens µ-Opioid Receptor-Expressing Cells on Heroin Self-Administration in Male and Female Rats: A Study with Novel Oprm1-Cre Knock-in Rats. J Neurosci 2023; 43:1692-1713. [PMID: 36717230 PMCID: PMC10010456 DOI: 10.1523/jneurosci.2049-22.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/29/2022] [Accepted: 01/18/2023] [Indexed: 02/01/2023] Open
Abstract
The brain µ-opioid receptor (MOR) is critical for the analgesic, rewarding, and addictive effects of opioid drugs. However, in rat models of opioid-related behaviors, the circuit mechanisms of MOR-expressing cells are less known because of a lack of genetic tools to selectively manipulate them. We introduce a CRISPR-based Oprm1-Cre knock-in transgenic rat that provides cell type-specific genetic access to MOR-expressing cells. After performing anatomic and behavioral validation experiments, we used the Oprm1-Cre knock-in rats to study the involvement of NAc MOR-expressing cells in heroin self-administration in male and female rats. Using RNAscope, autoradiography, and FISH chain reaction (HCR-FISH), we found no differences in Oprm1 expression in NAc, dorsal striatum, and dorsal hippocampus, or MOR receptor density (except dorsal striatum) or function between Oprm1-Cre knock-in rats and wildtype littermates. HCR-FISH assay showed that iCre is highly coexpressed with Oprm1 (95%-98%). There were no genotype differences in pain responses, morphine analgesia and tolerance, heroin self-administration, and relapse-related behaviors. We used the Cre-dependent vector AAV1-EF1a-Flex-taCasp3-TEVP to lesion NAc MOR-expressing cells. We found that the lesions decreased acquisition of heroin self-administration in male Oprm1-Cre rats and had a stronger inhibitory effect on the effort to self-administer heroin in female Oprm1-Cre rats. The validation of an Oprm1-Cre knock-in rat enables new strategies for understanding the role of MOR-expressing cells in rat models of opioid addiction, pain-related behaviors, and other opioid-mediated functions. Our initial mechanistic study indicates that lesioning NAc MOR-expressing cells had different effects on heroin self-administration in male and female rats.SIGNIFICANCE STATEMENT The brain µ-opioid receptor (MOR) is critical for the analgesic, rewarding, and addictive effects of opioid drugs. However, in rat models of opioid-related behaviors, the circuit mechanisms of MOR-expressing cells are less known because of a lack of genetic tools to selectively manipulate them. We introduce a CRISPR-based Oprm1-Cre knock-in transgenic rat that provides cell type-specific genetic access to brain MOR-expressing cells. After performing anatomical and behavioral validation experiments, we used the Oprm1-Cre knock-in rats to show that lesioning NAc MOR-expressing cells had different effects on heroin self-administration in males and females. The new Oprm1-Cre rats can be used to study the role of brain MOR-expressing cells in animal models of opioid addiction, pain-related behaviors, and other opioid-mediated functions.
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Affiliation(s)
- Jennifer M Bossert
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Carlos A Mejias-Aponte
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | | | - Lindsay Altidor
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | | | - Ida Fredriksson
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Ashley Batista
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Sarah M Claypool
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Kiera E Caldwell
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - David J Reiner
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Jonathan J Chow
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | | | - Vivek Kumar
- University of Michigan, Ann Arbor, Michigan, 48104
| | | | | | | | - Brandon K Harvey
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Christopher T Richie
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Francois Vautier
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Juan L Gomez
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Michael Michaelides
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
| | - Brigitte L Kieffer
- University of Strasbourg-Institut National de la Santé et de la Recherche Médicale U1114, Strasbourg, France, 67084
| | | | - Huda Akil
- University of Michigan, Ann Arbor, Michigan, 48104
| | - Yavin Shaham
- Intramural Research Program, National Institute on Drug Abuse-National Institutes of Health, Baltimore, Maryland, 21224
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3
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Xue Y, Xie H, Wang Y, Feng S, Sun J, Huang J, Yang X. Novel and sensitive electrochemical/fluorescent dual-mode biosensing platform based on the cascaded cyclic amplification of enzyme-free DDSA and functional nucleic acids. Biosens Bioelectron 2022; 218:114762. [DOI: 10.1016/j.bios.2022.114762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/02/2022]
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Chen X, Peng Y, Xue H, Liu G, Wang N, Shao Z. MiR-21 regulating PVT1/PTEN/IL-17 axis towards the treatment of infectious diabetic wound healing by modified GO-derived biomaterial in mouse models. J Nanobiotechnology 2022; 20:309. [PMID: 35764963 PMCID: PMC9238182 DOI: 10.1186/s12951-022-01516-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/18/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Diabetic foot ulcer (DFU), persistent hyperglycemia and inflammation, together with impaired nutrient and oxygen deficiency, can present abnormal angiogenesis following tissue injury such that these tissues fail to heal properly. It is critical to design a new treatment method for DFU patients with a distinct biomechanism that is more effective than current treatment regimens. METHOD Graphene oxide (GO) was combined with a biocompatible polymer as a kind of modified GO-based hydrogel. The characterization of our biomaterial was measured in vitro. The repair efficiency of the biomaterial was evaluated in the mouse full-skin defect models. The key axis related to diabetic wound (DW) was identified and investigated using bioinformatics analyses and practical experiments. RESULT In the study, we found that our modified GO-based wound dressing material is a promising option for diabetic wound. Secondly, our biomaterial could enhance the secretion of small EVs (sEVs) with more miR-21 by adipose-derived mesenchymal stem cells (AD-MSCs). Thirdly, the PVT1/PTEN/IL-17 axis was found to be decreased to promote DFU wound healing by modifying miR-21 with the discovery of PVT1 as a critical LncRNA by bioinformatics analysis and tests. CONCLUSION These findings could aid in the development of clinical care strategies for DFU wounds.
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Affiliation(s)
- Xi Chen
- grid.33199.310000 0004 0368 7223Department of Orthopeadics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 Hubei China
| | - Yizhong Peng
- grid.33199.310000 0004 0368 7223Department of Orthopeadics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 Hubei China
| | - Hang Xue
- grid.33199.310000 0004 0368 7223Department of Orthopeadics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 Hubei China
| | - Guohui Liu
- grid.33199.310000 0004 0368 7223Department of Orthopeadics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 Hubei China
| | - Ning Wang
- grid.162110.50000 0000 9291 3229National Engineering Research Center of Fiber Optic Sensing Technology and Networks, Wuhan University of Technology, Wuhan, 430070 China
| | - Zengwu Shao
- grid.33199.310000 0004 0368 7223Department of Orthopeadics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 Hubei China
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5
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Koch P, Schmitt S, Heynisch A, Gumpinger A, Wüthrich I, Gysin M, Shcherbakov D, Hobbie SN, Panke S, Held M. Optimization of the antimicrobial peptide Bac7 by deep mutational scanning. BMC Biol 2022; 20:114. [PMID: 35578204 PMCID: PMC9112550 DOI: 10.1186/s12915-022-01304-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/30/2022] [Indexed: 11/24/2022] Open
Abstract
Background Intracellularly active antimicrobial peptides are promising candidates for the development of antibiotics for human applications. However, drug development using peptides is challenging as, owing to their large size, an enormous sequence space is spanned. We built a high-throughput platform that incorporates rapid investigation of the sequence-activity relationship of peptides and enables rational optimization of their antimicrobial activity. The platform is based on deep mutational scanning of DNA-encoded peptides and employs highly parallelized bacterial self-screening coupled to next-generation sequencing as a readout for their antimicrobial activity. As a target, we used Bac71-23, a 23 amino acid residues long variant of bactenecin-7, a potent translational inhibitor and one of the best researched proline-rich antimicrobial peptides. Results Using the platform, we simultaneously determined the antimicrobial activity of >600,000 Bac71-23 variants and explored their sequence-activity relationship. This dataset guided the design of a focused library of ~160,000 variants and the identification of a lead candidate Bac7PS. Bac7PS showed high activity against multidrug-resistant clinical isolates of E. coli, and its activity was less dependent on SbmA, a transporter commonly used by proline-rich antimicrobial peptides to reach the cytosol and then inhibit translation. Furthermore, Bac7PS displayed strong ribosomal inhibition and low toxicity against eukaryotic cells and demonstrated good efficacy in a murine septicemia model induced by E. coli. Conclusion We demonstrated that the presented platform can be used to establish the sequence-activity relationship of antimicrobial peptides, and showed its usefulness for hit-to-lead identification and optimization of antimicrobial drug candidates. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01304-4.
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Affiliation(s)
- Philipp Koch
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Steven Schmitt
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Alexander Heynisch
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Anja Gumpinger
- Machine Learning and Computational Biology, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Irene Wüthrich
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Marina Gysin
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Dimitri Shcherbakov
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Held
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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6
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Integrative structure determination reveals functional global flexibility for an ultra-multimodular arabinanase. Commun Biol 2022; 5:465. [PMID: 35577850 PMCID: PMC9110388 DOI: 10.1038/s42003-022-03054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 07/15/2021] [Indexed: 11/08/2022] Open
Abstract
AbnA is an extracellular GH43 α-L-arabinanase from Geobacillus stearothermophilus, a key bacterial enzyme in the degradation and utilization of arabinan. We present herein its full-length crystal structure, revealing the only ultra-multimodular architecture and the largest structure to be reported so far within the GH43 family. Additionally, the structure of AbnA appears to contain two domains belonging to new uncharacterized carbohydrate-binding module (CBM) families. Three crystallographic conformational states are determined for AbnA, and this conformational flexibility is thoroughly investigated further using the "integrative structure determination" approach, integrating molecular dynamics, metadynamics, normal mode analysis, small angle X-ray scattering, dynamic light scattering, cross-linking, and kinetic experiments to reveal large functional conformational changes for AbnA, involving up to ~100 Å movement in the relative positions of its domains. The integrative structure determination approach demonstrated here may apply also to the conformational study of other ultra-multimodular proteins of diverse functions and structures.
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7
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Vicencio J, Sánchez-Bolaños C, Moreno-Sánchez I, Brena D, Vejnar CE, Kukhtar D, Ruiz-López M, Cots-Ponjoan M, Rubio A, Melero NR, Crespo-Cuadrado J, Carolis C, Pérez-Pulido AJ, Giráldez AJ, Kleinstiver BP, Cerón J, Moreno-Mateos MA. Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes. Nat Commun 2022; 13:2601. [PMID: 35552388 PMCID: PMC9098488 DOI: 10.1038/s41467-022-30228-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 04/22/2022] [Indexed: 01/21/2023] Open
Abstract
The requirement for Cas nucleases to recognize a specific PAM is a major restriction for genome editing. SpCas9 variants SpG and SpRY, recognizing NGN and NRN PAMs, respectively, have contributed to increase the number of editable genomic sites in cell cultures and plants. However, their use has not been demonstrated in animals. Here we study the nuclease activity of SpG and SpRY by targeting 40 sites in zebrafish and C. elegans. Delivered as mRNA-gRNA or ribonucleoprotein (RNP) complexes, SpG and SpRY were able to induce mutations in vivo, albeit at a lower rate than SpCas9 in equivalent formulations. This lower activity was overcome by optimizing mRNA-gRNA or RNP concentration, leading to mutagenesis at regions inaccessible to SpCas9. We also found that the CRISPRscan algorithm could help to predict SpG and SpRY targets with high activity in vivo. Finally, we applied SpG and SpRY to generate knock-ins by homology-directed repair. Altogether, our results expand the CRISPR-Cas targeting genomic landscape in animals.
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Affiliation(s)
- Jeremy Vicencio
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Carlos Sánchez-Bolaños
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Ismael Moreno-Sánchez
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - David Brena
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Dmytro Kukhtar
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Miguel Ruiz-López
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Mariona Cots-Ponjoan
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Alejandro Rubio
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Natalia Rodrigo Melero
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Jesús Crespo-Cuadrado
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Carlo Carolis
- Biomolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Antonio J Pérez-Pulido
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Antonio J Giráldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Julián Cerón
- Modeling human diseases in C. elegans Group; Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
| | - Miguel A Moreno-Mateos
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain.
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain.
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Wingfield BD, De Vos L, Wilson AM, Duong TA, Vaghefi N, Botes A, Kharwar RN, Chand R, Poudel B, Aliyu H, Barbetti MJ, Chen S, de Maayer P, Liu F, Navathe S, Sinha S, Steenkamp ET, Suzuki H, Tshisekedi KA, van der Nest MA, Wingfield MJ. IMA Genome - F16 : Draft genome assemblies of Fusarium marasasianum, Huntiella abstrusa, two Immersiporthe knoxdaviesiana isolates, Macrophomina pseudophaseolina, Macrophomina phaseolina, Naganishia randhawae, and Pseudocercospora cruenta. IMA Fungus 2022; 13:3. [PMID: 35197126 PMCID: PMC8867778 DOI: 10.1186/s43008-022-00089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa.
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Andi M Wilson
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Australia
| | - Angela Botes
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Ravindra Nath Kharwar
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Ramesh Chand
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Barsha Poudel
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Australia
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Martin J Barbetti
- School of Agriculture and Environment and the UWA Institute of Agriculture, University of Western Australia, Perth, Australia
| | - ShuaiFei Chen
- China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang, Guangdong Province, China
| | - Pieter de Maayer
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - FeiFei Liu
- China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang, Guangdong Province, China
| | | | - Shagun Sinha
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Hiroyuki Suzuki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Kalonji A Tshisekedi
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Magriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
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9
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Choi H, Choi Y, Choi J, Lee AC, Yeom H, Hyun J, Ryu T, Kwon S. Purification of multiplex oligonucleotide libraries by synthesis and selection. Nat Biotechnol 2022; 40:47-53. [PMID: 34326548 DOI: 10.1038/s41587-021-00988-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023]
Abstract
Complex oligonucleotide (oligo) libraries are essential materials for diverse applications in synthetic biology, pharmaceutical production, nanotechnology and DNA-based data storage. However, the error rates in synthesizing complex oligo libraries can be substantial, leading to increment in cost and labor for the applications. As most synthesis errors arise from faulty insertions and deletions, we developed a length-based method with single-base resolution for purification of complex libraries containing oligos of identical or different lengths. Our method-purification of multiplex oligonucleotide libraries by synthesis and selection-can be performed either step-by-step manually or using a next-generation sequencer. When applied to a digital data-encoded library containing oligos of identical length, the method increased the purity of full-length oligos from 83% to 97%. We also show that libraries encoding the complementarity-determining region H3 with three different lengths (with an empirically achieved diversity >106) can be simultaneously purified in one pot, increasing the in-frame oligo fraction from 49.6% to 83.5%.
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Affiliation(s)
- Hansol Choi
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yeongjae Choi
- Nano Systems Institute, Seoul National University, Seoul, Republic of Korea.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Jaewon Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea.,Integrated Major in Innovative Medical Science, Seoul National University, Seoul, Republic of Korea
| | - Amos Chungwon Lee
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Huiran Yeom
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Jinwoo Hyun
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea. .,Nano Systems Institute, Seoul National University, Seoul, Republic of Korea. .,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea. .,Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea.
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10
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Bhandari N, Khare S, Walambe R, Kotecha K. Comparison of machine learning and deep learning techniques in promoter prediction across diverse species. PeerJ Comput Sci 2021; 7:e365. [PMID: 33817015 PMCID: PMC7959599 DOI: 10.7717/peerj-cs.365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are reported for the prediction of promoters. However, since all promoter sequences do not show explicit features, the prediction performance of these techniques is poor. Therefore, many machine learning and deep learning models have been proposed for promoter prediction. In this work, we studied methods for vector encoding and promoter classification using genome sequences of three distinct higher eukaryotes viz. yeast (Saccharomyces cerevisiae), A. thaliana (plant) and human (Homo sapiens). We compared one-hot vector encoding method with frequency-based tokenization (FBT) for data pre-processing on 1-D Convolutional Neural Network (CNN) model. We found that FBT gives a shorter input dimension reducing the training time without affecting the sensitivity and specificity of classification. We employed the deep learning techniques, mainly CNN and recurrent neural network with Long Short Term Memory (LSTM) and random forest (RF) classifier for promoter classification at k-mer sizes of 2, 4 and 8. We found CNN to be superior in classification of promoters from non-promoter sequences (binary classification) as well as species-specific classification of promoter sequences (multiclass classification). In summary, the contribution of this work lies in the use of synthetic shuffled negative dataset and frequency-based tokenization for pre-processing. This study provides a comprehensive and generic framework for classification tasks in genomic applications and can be extended to various classification problems.
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Affiliation(s)
- Nikita Bhandari
- Computer Science, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, MH, India
| | - Satyajeet Khare
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, MH, India
| | - Rahee Walambe
- Symbiosis Centre for Applied Artificial Intelligence, Symbiosis International (Deemed University), Pune, Maharashtra, India
- Electronics and Telecommunication Dept, Symbiosis Institute of Technology, Pune, Maharashtra, India
| | - Ketan Kotecha
- Computer Science, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, MH, India
- Symbiosis Centre for Applied Artificial Intelligence, Symbiosis International (Deemed University), Pune, Maharashtra, India
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11
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Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics. Sci Rep 2020; 10:18823. [PMID: 33139764 PMCID: PMC7606482 DOI: 10.1038/s41598-020-74883-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/21/2020] [Indexed: 01/27/2023] Open
Abstract
Mosquitoes are insects of medical importance due their role as vectors of different pathogens to humans. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquito species. Here we characterized the mitogenomes of mosquito species through low-coverage whole genome sequencing and data mining. A total of 37 draft mitogenomes of different species were assembled from which 16 are newly-sequenced species. We datamined additional 49 mosquito mitogenomes, and together with our 37 mitogenomes, we reconstructed the evolutionary history of 86 species including representatives from 15 genera and 7 tribes. Our results showed that most of the species clustered in clades with other members of their own genus with exception of Aedes genus which was paraphyletic. We confirmed the monophyletic status of the Mansoniini tribe including both Coquillettidia and Mansonia genus. The Aedeomyiini and Uranotaeniini were consistently recovered as basal to other tribes in the subfamily Culicinae, although the exact relationships among these tribes differed between analyses. These results demonstrate that low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge and hence generate basic fundamental information that will help in the understanding of the role of these species as pathogen vectors.
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12
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Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development. Sci Rep 2020; 10:16153. [PMID: 32999373 PMCID: PMC7527347 DOI: 10.1038/s41598-020-73146-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/10/2020] [Indexed: 01/08/2023] Open
Abstract
Mammalian IκB proteins (IκBs) exert their main function as negative regulators of NF-κB, a central signaling pathway controlling immunity and inflammation. An alternative chromatin role for IκBs has been shown to affect stemness and cell differentiation. However, the involvement of NF-κB in this function has not been excluded. NFKI-1 and IKB-1 are IκB homologs in Caenorhabditis elegans, which lacks NF-κB nuclear effectors. We found that nfki-1 and ikb-1 mutants display developmental defects that phenocopy mutations in Polycomb and UTX-1 histone demethylase, suggesting a role for C. elegans IκBs in chromatin regulation. Further supporting this possibility (1) we detected NFKI-1 in the nucleus of cells; (2) NFKI-1 and IKB-1 bind to histones and Polycomb proteins, (3) and associate with chromatin in vivo, and (4) mutations in nfki-1 and ikb-1 alter chromatin marks. Based on these results, we propose that ancestral IκB inhibitors modulate Polycomb activity at specific gene subsets with an impact on development.
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13
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de Maat V, Arredondo-Alonso S, Willems RJL, van Schaik W. Conditionally essential genes for survival during starvation in Enterococcus faecium E745. BMC Genomics 2020; 21:568. [PMID: 32811437 PMCID: PMC7437932 DOI: 10.1186/s12864-020-06984-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/12/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The nosocomial pathogen Enterococcus faecium can survive for prolonged periods of time on surfaces in the absence of nutrients. This trait is thought to contribute to the ability of E. faecium to spread among patients in hospitals. There is currently a lack of data on the mechanisms that are responsible for the ability of E. faecium to survive in the absence of nutrients. RESULTS We performed a high-throughput transposon mutant library screening (Tn-seq) to identify genes that have a role in long-term survival during incubation in phosphate-buffered saline (PBS) at 20 °C. A total of 24 genes were identified by Tn-seq to contribute to survival in PBS, with functions associated with the general stress response, DNA repair, metabolism, and membrane homeostasis. The gene which was quantitatively most important for survival in PBS was usp (locus tag: EfmE745_02439), which is predicted to encode a 17.4 kDa universal stress protein. After generating a targeted deletion mutant in usp, we were able to confirm that usp significantly contributes to survival in PBS and this defect was restored by in trans complementation. The usp gene is present in 99% of a set of 1644 E. faecium genomes that collectively span the diversity of the species. CONCLUSIONS We postulate that usp is a key determinant for the remarkable environmental robustness of E. faecium. Further mechanistic studies into usp and other genes identified in this study may shed further light on the mechanisms by which E. faecium can survive in the absence of nutrients for prolonged periods of time.
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Affiliation(s)
- Vincent de Maat
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Sergio Arredondo-Alonso
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands. .,Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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14
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Claverie S, Ouattara A, Hoareau M, Filloux D, Varsani A, Roumagnac P, Martin DP, Lett JM, Lefeuvre P. Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach. Sci Rep 2019; 9:12716. [PMID: 31481704 PMCID: PMC6722101 DOI: 10.1038/s41598-019-49134-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 08/20/2019] [Indexed: 01/22/2023] Open
Abstract
Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.
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Affiliation(s)
- Sohini Claverie
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.,Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, Saint-Pierre, 97410, France
| | - Alassane Ouattara
- INERA, 01 BP 476, Ouagadougou 01, Burkina Faso.,Laboratoire Biosciences, Université Joseph KI-ZERBO, 03 BP 7021, Ouagadougou 03, Burkina Faso
| | | | - Denis Filloux
- CIRAD, UMR BGPI, F-34398, Montpellier, France.,BGPI, Université de Montpellier, INRA, CIRAD, Montpellier SupAgro, F-34398, Montpellier, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA.,Structural Biology Research Unit, Departement of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, F-34398, Montpellier, France.,BGPI, Université de Montpellier, INRA, CIRAD, Montpellier SupAgro, F-34398, Montpellier, France
| | - Darren P Martin
- Computational Biology Division, Departement of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, South Africa
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15
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Abstract
Many studies have shown that the urinary tract harbours its own microbial community known as the urinary microbiota, which have been implicated in urinary tract disorders. This observation contradicts the long-held notion that urine is a sterile biofluid in the absence of acute infection of the urinary tract. In light of this new discovery, many basic questions that are crucial for understanding the role of the urinary microbiota in human health and disease remain unanswered. Given that the urinary microbiota is an emerging area of study, optimized techniques and protocols to identify microorganisms in the urinary tract are still being established. However, the low microbial biomass and close proximity to higher microbial biomass environments (for example, the vagina) present distinct methodological challenges for microbial community profiling of the urinary microbiota. A clear understanding of the unique technical considerations for obtaining and analysing low microbial biomass samples, as well the influence of key elements of experimental design and computational analysis on downstream interpretation, will improve our ability to interpret and compare results across methods and studies and is relevant for studies profiling the urinary microbiota and other sites of low microbial abundance.
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16
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Domingo-Prim J, Endara-Coll M, Bonath F, Jimeno S, Prados-Carvajal R, Friedländer MR, Huertas P, Visa N. EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks. Nat Commun 2019; 10:2135. [PMID: 31086179 PMCID: PMC6513946 DOI: 10.1038/s41467-019-10153-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
The exosome is a ribonucleolytic complex that plays important roles in RNA metabolism. Here we show that the exosome is necessary for the repair of DNA double-strand breaks (DSBs) in human cells and that RNA clearance is an essential step in homologous recombination. Transcription of DSB-flanking sequences results in the production of damage-induced long non-coding RNAs (dilncRNAs) that engage in DNA-RNA hybrid formation. Depletion of EXOSC10, an exosome catalytic subunit, leads to increased dilncRNA and DNA-RNA hybrid levels. Moreover, the targeting of the ssDNA-binding protein RPA to sites of DNA damage is impaired whereas DNA end resection is hyper-stimulated in EXOSC10-depleted cells. The DNA end resection deregulation is abolished by transcription inhibitors, and RNase H1 overexpression restores the RPA recruitment defect caused by EXOSC10 depletion, which suggests that RNA clearance of newly synthesized dilncRNAs is required for RPA recruitment, controlled DNA end resection and assembly of the homologous recombination machinery.
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Affiliation(s)
- Judit Domingo-Prim
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Martin Endara-Coll
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sonia Jimeno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Sevilla, Spain.,Departamento de Genética, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Rosario Prados-Carvajal
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Sevilla, Spain.,Departamento de Genética, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Sevilla, Spain.,Departamento de Genética, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
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17
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Ma J, Wang J, Ghoraie LS, Men X, Haibe-Kains B, Dai P. Network-based approach to identify principal isoforms among four cancer types. Mol Omics 2019; 15:117-129. [PMID: 30720033 DOI: 10.1039/c8mo00234g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein isoforms are structurally similar proteins produced by alternative splicing of a single gene or genes from the same family. Isoforms of a protein can perform the same, similar, or even opposite biological functions. A previous study identified principal isoforms of proteins based on the extent of interactions per isoform in a functional relationship network, focusing on data from normal tissues. Additionally, the expression levels of specific isoforms of various genes associated with tumorigenesis and prognosis are frequently altered in tumors compared with those in normal tissues. In this study, we aimed to identify higher degree isoforms (HDIs) of multi-isoform genes (MIGs) in cancer by applying a meta-analytical framework to calculate co-expression between each pair of isoforms in two large datasets of RNA-seq profiles from breast cancer, lung cancer, leukemia, and colon cancer cell lines. Then, we compared HDIs with isoforms identified by proteomic data and prognostic and predictive evidence in various cancers. In addition, we separately analyzed the associations between HDIs and non-HDIs (nHDIs) of the same genes according to transcript expression and drug responses in various cancer type cell lines. Collectively, these results indicated the complex properties of HDIs per gene identified by cancer type-based isoform-isoform co-expression networks and showed the potential of HDIs as novel therapeutic targets for cancer treatment.
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Affiliation(s)
- Jun Ma
- National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, P. R. China. and Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jenny Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laleh Soltan Ghoraie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Xin Men
- Microbiology Institute of Shaanxi, China and National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, P. R. China.
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, P. R. China.
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18
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Mylonas C, Tessarz P. Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells. Life Sci Alliance 2018; 1:e201800085. [PMID: 30456357 PMCID: PMC6238418 DOI: 10.26508/lsa.201800085] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 12/22/2022] Open
Abstract
Depletion of FACT in murine embryonic stem cells show mild changes on the nucleosomal landscape but widespread changes in the transcriptome, faster proliferation, and neuronal differentiation rates. The conserved and essential histone chaperone, facilitates chromatin transcription (FACT), reorganizes nucleosomes during DNA transcription, replication, and repair and ensures both efficient elongation of RNA Pol II and nucleosome integrity. In mammalian cells, FACT is a heterodimer, consisting of SSRP1 and SUPT16. Here, we show that in contrast to yeast, FACT accumulates at the transcription start site of genes reminiscent of RNA polymerase II profile. Depletion of FACT in mouse embryonic stem cells leads to deregulation of developmental and pro-proliferative genes concomitant with hyper-proliferation of mES cells. Using MNase-seq, Assay for Transposase-Accessible Chromatin sequencing, and nascent elongating transcript sequencing, we show that up-regulation of genes coincides with loss of nucleosomes upstream of the transcription start site and concomitant increase in antisense transcription, indicating that FACT impacts the promoter architecture to regulate the expression of these genes. Finally, we demonstrate a role for FACT in cell fate determination and show that FACT depletion primes embryonic stem cells for the neuronal lineage.
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Affiliation(s)
| | - Peter Tessarz
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing Associated Diseases, University of Cologne, Cologne, Germany
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19
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Cai H, Zhou C, Yang Q, Ai T, Huang Y, Lv Y, Geng J, Xiao D. Single-molecule investigation of human telomeric G-quadruplex interactions with Thioflavin T. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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20
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Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nat Commun 2017; 8:1814. [PMID: 29180750 PMCID: PMC5703836 DOI: 10.1038/s41467-017-02018-w] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 11/01/2017] [Indexed: 01/18/2023] Open
Abstract
Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such as Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae, which are frequently implicated in nosocomial infection and preterm infant gut colonization. Of the 15 K. pneumoniae strains detected in the study, four were detected in both infant gut and room samples. Time series experiments showed that nearly all strains associated with infant gut colonization can be detected in the room after, and often before, detection in the gut. Thus, we conclude that a component of premature infant gut colonization is the cycle of microbial exchange between the room and the occupant. It is thought that the hospital environment may contribute to infant microbiome development. Here, Brooks et al. present a genome-resolved metagenomic study of microbial genotypes from the infant gut and from neonatal intensive care unit rooms, showing that some strains are found in both infants and rooms.
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21
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An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue. Biol Proced Online 2017; 19:10. [PMID: 28855851 PMCID: PMC5576305 DOI: 10.1186/s12575-017-0059-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background Genomic loci associated with histone marks are typically analyzed by immunoprecipitation of the chromatin followed by quantitative-PCR (ChIP-qPCR) or high throughput sequencing (ChIP-seq). Chromatin can be either cross-linked (X-ChIP) or used in the native state (N-ChIP). Cross-linking of DNA and proteins helps stabilizing their interactions before analysis. Despite X-ChIP is the most commonly used method, muscle tissue fixation is known to be relatively inefficient. Moreover, no protocol described a simple and reliable preparation of skeletal muscle chromatin of sufficient quality for subsequent high-throughput sequencing. Here we aimed to set-up and compare both chromatin preparation methods for a genome-wide analysis of H3K27me3, a broad-peak histone mark, using chicken P. major muscle tissue. Results Fixed and unfixed chromatin were prepared from chicken muscle tissues (Pectoralis major). Chromatin fixation, shearing by sonication or digestion and immunoprecipitation performed equivalently. High-quality Illumina reads were obtained (q30 > 93%). The bioinformatic analysis of the data was performed using epic, a tool based on SICER, and MACS2. Forty millions of reads were analyzed for both X-ChIP-seq and N-ChIP-seq experiments. Surprisingly, H3K27me3 X-ChIP-seq analysis led to the identification of only 2000 enriched regions compared to about 15,000 regions identified in the case of N-ChIP-seq. N-ChIP-seq peaks were more consistent between replicates compared to X-ChIP-seq. Higher N-ChIP-seq enrichments were confirmed by ChIP-qPCR at the PAX5 and SOX2 loci known to be enriched for H3K27me3 in myotubes and at the loci of common regions of enrichment identified in this study. Conclusions Our findings suggest that the preparation of muscle chromatin for ChIP-seq in cross-linked conditions can compromise the systematic analysis of broad histone marks. Therefore, native chromatin preparation should be preferred to cross-linking when a ChIP experiment has to be performed on skeletal muscle tissue, particularly when a broad source signal is considered. Electronic supplementary material The online version of this article (doi:10.1186/s12575-017-0059-0) contains supplementary material, which is available to authorized users.
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22
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Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y. J Virol 2017; 91:JVI.00690-17. [PMID: 28592544 PMCID: PMC5533922 DOI: 10.1128/jvi.00690-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/28/2017] [Indexed: 11/20/2022] Open
Abstract
RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid).IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes.
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23
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Plumridge A, Meisburger SP, Pollack L. Visualizing single-stranded nucleic acids in solution. Nucleic Acids Res 2017; 45:e66. [PMID: 28034955 PMCID: PMC5435967 DOI: 10.1093/nar/gkw1297] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 02/06/2023] Open
Abstract
Single-stranded nucleic acids (ssNAs) are ubiquitous in many key cellular functions. Their flexibility limits both the number of high-resolution structures available, leaving only a small number of protein-ssNA crystal structures, while forcing solution investigations to report ensemble averages. A description of the conformational distributions of ssNAs is essential to more fully characterize biologically relevant interactions. We combine small angle X-ray scattering (SAXS) with ensemble-optimization methods (EOM) to dynamically build and refine sets of ssNA structures. By constructing candidate chains in representative dinucleotide steps and refining the models against SAXS data, a broad array of structures can be obtained to match varying solution conditions and strand sequences. In addition to the distribution of large scale structural parameters, this approach reveals, for the first time, intricate details of the phosphate backbone and underlying strand conformations. Such information on unperturbed strands will critically inform a detailed understanding of an array of problems including protein-ssNA binding, RNA folding and the polymer nature of NAs. In addition, this scheme, which couples EOM selection with an iteratively refining pool to give confidence in the underlying structures, is likely extendable to the study of other flexible systems.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | | | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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24
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Abstract
Protein-DNA binding plays a central role in gene regulation and by that in all processes in the living cell. Novel experimental and computational approaches facilitate better understanding of protein-DNA binding preferences via high-throughput measurement of protein binding to a large number of DNA sequences and inference of binding models from them. Here we review the state of the art in measuring protein-DNA binding in vitro, emphasizing the advantages and limitations of different technologies. In addition, we describe models for representing protein-DNA binding preferences and key computational approaches to learn those from high-throughput data. Using large experimental data sets, we test the performance of different models based on different measuring techniques. We conclude with pertinent open problems.
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Hurwitz AM, Huang W, Estes MK, Atmar RL, Palzkill T. Deep sequencing of phage-displayed peptide libraries reveals sequence motif that detects norovirus. Protein Eng Des Sel 2017; 30:129-139. [PMID: 28035012 PMCID: PMC5241761 DOI: 10.1093/protein/gzw074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 10/12/2016] [Accepted: 12/14/2016] [Indexed: 01/10/2023] Open
Abstract
Norovirus infections are the leading cause of non-bacterial gastroenteritis and result in about 21 million new cases and $2 billion in costs per year in the United States. Existing diagnostics have limited feasibility for point-of-care applications, so there is a clear need for more reliable, rapid, and simple-to-use diagnostic tools in order to contain outbreaks and prevent inappropriate treatments. In this study, a combination of phage display technology, deep sequencing and computational analysis was used to identify 12-mer peptides with specific binding to norovirus genotype GI.1 virus-like particles (VLPs). After biopanning, phage populations were sequenced and analyzed to identify a consensus peptide motif-YRSWXP. Two 12-mer peptides containing this sequence, NV-O-R5-3 and NV-O-R5-6, were further characterized to evaluate the motif's functional ability to detect VLPs and virus. Results indicated that these peptides effectively detect GI.1 VLPs in solid-phase peptide arrays, ELISAs and dot blots. Further, their specificity for the S-domain of the major capsid protein enables them to detect a wide range of GI and GII norovirus genotypes. Both peptides were able to detect virus in norovirus-positive clinical stool samples. Overall, the work reported here demonstrates the application of phage display coupled with next generation sequencing and computational analysis to uncover peptides with specific binding ability to a target protein for diagnostic applications. Further, the reagents characterized here can be integrated into existing diagnostic formats to detect clinically relevant genotypes of norovirus in stool.
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Affiliation(s)
- Amy M Hurwitz
- Interdepartmental Program in Translational Biology & Molecular Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Wanzhi Huang
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert L Atmar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Palzkill
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
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Tambunan USF, Parikesit AA, Nasution MAF, Hapsari A, Kerami D. Exposing the Molecular Screening Method of Indonesian Natural Products Derivate as Drug Candidates for Cervical Cancer. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2017; 16:1113-1127. [PMID: 29201098 PMCID: PMC5610765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The menace of cervical cancer has reached an alarming rate. There are more than 450.000 cases of cervical cancer yearly, with mortality rate of about 50%. This deadly cancer is caused by human papillomavirus (HPV), mainly subtypes 16 and 18. The pharmaceutical industry has produced drug for combating the virus, known as SAHA (suberoylanilide hydroxamic acid). It inhibits class II HDAC Homo sapiens (HDACi). The utilization of SAHA has some side effects, one of which is bone loss. Thus, searching for viable alternatives aside SAHA is inevitable. The objective of this research is to investigate the molecular interaction of selected Indonesian natural products with class II HDAC Homo sapiens. LigX tool in MOE 2008.10 was used as an instrument to investigate the molecular interaction. Then, computer-aided drug discovery and development (CADDD) approach involving molecular docking and dynamics methods was utilized to screen the natural products library. In the end, we found that herbaric acid could act as a potential drug candidate for cervical cancer.
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Affiliation(s)
- Usman Sumo Friend Tambunan
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Depok 16424, Indonesia. ,Corresponding author: E-mail:
| | - Arli Aditya Parikesit
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Depok 16424, Indonesia.
| | - Mochammad Arfin Fardiansyah Nasution
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Depok 16424, Indonesia.
| | - Amalia Hapsari
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Indonesia, Depok 16424, Indonesia.
| | - Djati Kerami
- Mathematics Computation Research Group, Department of Mathematics, Faculty of Mathematics and Natural Science, Universitas Indonesia, Depok 16424, Indonesia.
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Montiel-González MF, Vallecillo-Viejo IC, Rosenthal JJC. An efficient system for selectively altering genetic information within mRNAs. Nucleic Acids Res 2016; 44:e157. [PMID: 27557710 PMCID: PMC5137428 DOI: 10.1093/nar/gkw738] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 08/02/2016] [Accepted: 08/12/2016] [Indexed: 01/09/2023] Open
Abstract
Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encoded iteration of SDRE could target adenosines expressed in human cells, but not efficiently. Here we developed a reporter assay to quantify editing, and used it to improve our strategy. By enhancing the linkage between ADAR's catalytic domain and the guide RNA, and by introducing a mutation in the catalytic domain, the efficiency of converting a U A: G premature termination codon (PTC) to tryptophan (U G: G) was improved from ∼11 % to ∼70 %. Other PTCs were edited, but less efficiently. Numerous off-target edits were identified in the targeted mRNA, but not in randomly selected endogenous messages. Off-target edits could be eliminated by reducing the amount of guide RNA with a reduction in on-target editing. The catalytic rate of SDRE was compared with those for human ADARs on various substrates and found to be within an order of magnitude of most. These data underscore the promise of site-directed RNA editing as a therapeutic or experimental tool.
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Affiliation(s)
| | - Isabel C Vallecillo-Viejo
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00901, USA
- Department of Pharmacology, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA
| | - Joshua J C Rosenthal
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00901, USA
- The Marine Biological Laboratory, University of Chicago, Woods Hole, MA 02543, USA
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28
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Protein-RNA interactions: structural biology and computational modeling techniques. Biophys Rev 2016; 8:359-367. [PMID: 28510023 DOI: 10.1007/s12551-016-0223-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/20/2016] [Indexed: 12/30/2022] Open
Abstract
RNA-binding proteins are functionally diverse within cells, being involved in RNA-metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional and post-transcriptional levels. Much has been learnt about their interactions with RNAs through structure determination techniques and computational modeling. This review gives an overview of the structural data currently available for protein-RNA complexes, and discusses the technical issues facing structural biologists working to solve their structures. The review focuses on three techniques used to solve the 3-dimensional structure of protein-RNA complexes at atomic resolution, namely X-ray crystallography, solution nuclear magnetic resonance (NMR) and cryo-electron microscopy (cryo-EM). The review then focuses on the main computational modeling techniques that use these atomic resolution data: discussing the prediction of RNA-binding sites on unbound proteins, docking proteins, and RNAs, and modeling the molecular dynamics of the systems. In conclusion, the review looks at the future directions this field of research might take.
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Ghosh P, Mathew OK, Sowdhamini R. RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. BMC Bioinformatics 2016; 17:411. [PMID: 27717309 PMCID: PMC5054549 DOI: 10.1186/s12859-016-1289-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information. Results The web server employs Hidden Markov Model scan (hmmscan) to enable association to a back-end database of structural and sequence families. The database (HMMRBP) comprises of 437 HMMs of RBP families of known structure that have been generated using structure-based sequence alignments and 746 sequence-centric RBP family HMMs. The input protein sequence is associated with structural or sequence domain families, if structure or sequence signatures exist. In case of association of the protein with a family of known structures, output features like, multiple structure-based sequence alignment (MSSA) of the query with all others members of that family is provided. Further, cognate RNA partner(s) for that protein, Gene Ontology (GO) annotations, if any and a homology model of the protein can be obtained. The users can also browse through the database for details pertaining to each family, protein or RNA and their related information based on keyword search or RNA motif search. Conclusions RStrucFam is a web server that exploits structurally conserved features of RBPs, derived from known family members and imprinted in mathematical profiles, to predict putative RBPs from sequence information. Proteins that fail to associate with such structure-centric families are further queried against the sequence-centric RBP family HMMs in the HMMRBP database. Further, all other essential information pertaining to an RBP, like overall function annotations, are provided. The web server can be accessed at the following link: http://caps.ncbs.res.in/rstrucfam. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1289-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pritha Ghosh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, 560 065, India
| | - Oommen K Mathew
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, 560 065, India.,SASTRA University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, 560 065, India.
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30
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Tláskal V, Voříšková J, Baldrian P. Bacterial succession on decomposing leaf litter exhibits a specific occurrence pattern of cellulolytic taxa and potential decomposers of fungal mycelia. FEMS Microbiol Ecol 2016; 92:fiw177. [DOI: 10.1093/femsec/fiw177] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 11/13/2022] Open
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Catarino B, Hetherington AJ, Emms DM, Kelly S, Dolan L. The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Mol Biol Evol 2016; 33:2815-2819. [PMID: 27499132 DOI: 10.1093/molbev/msw155] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The colonization of the land by streptophytes and their subsequent radiation is a major event in Earth history. We report a stepwise increase in the number of transcription factor (TF) families and subfamilies in Archaeplastida before the colonization of the land. The subsequent increase in TF number on land was through duplication within existing TF families and subfamilies. Almost all subfamilies of the Homeodomain (HD) and basic Helix-Loop-Helix (bHLH) had evolved before the radiation of extant land plant lineages from a common ancestor. We demonstrate that the evolution of these TF families independently followed similar trends in both plants and metazoans; almost all extant HD and bHLH subfamilies were present in the first land plants and in the last common ancestor of bilaterians. These findings reveal that the majority of innovation in plant and metazoan TF families occurred in the Precambrian before the Phanerozoic radiation of land plants and metazoans.
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Affiliation(s)
- Bruno Catarino
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, United Kingdom
| | | | - David M Emms
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, United Kingdom
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Araújo GS, Lima LHC, Schneider S, Leal TP, da Silva APC, Vaz de Melo POS, Tarazona-Santos E, Scliar MO, Rodrigues MR. Integrating, summarizing and visualizing GWAS-hits and human diversity with DANCE (Disease-ANCEstry networks). Bioinformatics 2016; 32:1247-9. [PMID: 26673785 DOI: 10.1093/bioinformatics/btv708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/29/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The 1000 Genomes Project (1KGP) and thousands of Genome-Wide Association Studies (GWAS) performed during the last years have generated an enormous amount of information that needs to be integrated to better understand the genetic architecture of complex diseases in different populations. This integration is important in areas such as genetics, epidemiology, anthropology, as well as admixture mapping design and GWAS-replications. Network-based approaches that explore the genetic bases of human diseases and traits have not yet incorporated information on genetic diversity among human populations. RESULTS We propose Disease-ANCEstry networks (DANCE), a graph-based web tool that allows to integrate and visualize information on human complex phenotypes and their GWAS-hits, as well as their risk allele frequencies in different populations. DANCE provides an interactive way to explore the human SNP-Disease Network and its projection, a Disease-Disease Network. With these functionalities, DANCE fills a gap in our ability to handle and understand the knowledge generated by GWAS and 1KGP. We provide a number of case studies that show how DANCE can be used to explore the relationships between human complex diseases, their genetic bases and variability in different human populations. AVAILABILITY AND IMPLEMENTATION DANCE is freely available at http://ldgh.com.br/dance/ We recommend using DANCE with Mozilla Firefox, Safari, Chrome or Internet Explorer (v9 or v10). CONTACT gilderlanio@gmail.com or maira.r.rodrigues@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Silvana Schneider
- Department of Statistics, Federal University of Minas Gerais, Belo Horizonte, Brazil
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33
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Cass AA, Bahn JH, Lee JH, Greer C, Lin X, Kim Y, Hsiao YHE, Xiao X. Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets. Nucleic Acids Res 2016; 44:3253-63. [PMID: 26975654 PMCID: PMC4838385 DOI: 10.1093/nar/gkw164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/02/2016] [Indexed: 11/14/2022] Open
Abstract
In mammals, small RNAs are important players in post-transcriptional gene regulation. While their roles in mRNA destabilization and translational repression are well appreciated, their involvement in endonucleolytic cleavage of target RNAs is poorly understood. Very few microRNAs are known to guide RNA cleavage. Endogenous small interfering RNAs are expected to induce target cleavage, but their target genes remain largely unknown. We report a systematic study of small RNA-mediated endonucleolytic cleavage in mouse through integrative analysis of small RNA and degradome sequencing data without imposing any bias toward known small RNAs. Hundreds of small cleavage-inducing RNAs and their cognate target genes were identified, significantly expanding the repertoire of known small RNA-guided cleavage events. Strikingly, both small RNAs and their target sites demonstrated significant overlap with retrotransposons, providing evidence for the long-standing speculation that retrotransposable elements in mRNAs are leveraged as signals for gene targeting. Furthermore, our analysis showed that the RNA cleavage pathway is also present in human cells but affecting a different repertoire of retrotransposons. These results show that small RNA-guided cleavage is more widespread than previously appreciated. Their impact on retrotransposons in non-coding regions shed light on important aspects of mammalian gene regulation.
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Affiliation(s)
- Ashley A Cass
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jae-Hyung Lee
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Christopher Greer
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Xianzhi Lin
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Yong Kim
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA UCLA Broad Stem Cell Research Center, Los Angeles, CA, USA
| | - Yun-Hua Esther Hsiao
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
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Carvalho J, Ferreira J, Pereira P, Coutinho E, Guédin A, Nottelet P, Salgado GF, Mergny JL, Queiroz J, Sousa F, Cabrita EJ, Cruz C. Stabilization of novel immunoglobulin switch regions G-quadruplexes by naphthalene and quinoline-based ligands. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lewis SH, Salmela H, Obbard DJ. Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and Aubergine. Genome Biol Evol 2016; 8:507-18. [PMID: 26868596 PMCID: PMC4824172 DOI: 10.1093/gbe/evw018] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genetic studies of Drosophila melanogaster have provided a paradigm for RNA interference (RNAi) in arthropods, in which the microRNA and antiviral pathways are each mediated by a single Argonaute (Ago1 and Ago2) and germline suppression of transposable elements is mediated by a trio of Piwi-subfamily Argonaute proteins (Ago3, Aub, and Piwi). Without a suitable evolutionary context, deviations from this can be interpreted as derived or idiosyncratic. Here we analyze the evolution of Argonaute genes across the genomes and transcriptomes of 86 Dipteran species, showing that variation in copy number can occur rapidly, and that there is constant flux in some RNAi mechanisms. The lability of the RNAi pathways is illustrated by the divergence of Aub and Piwi (182-156 Ma), independent origins of multiple Piwi-family genes in Aedes mosquitoes (less than 25Ma), and the recent duplications of Ago2 and Ago3 in the tsetse fly Glossina morsitans. In each case the tissue specificity of these genes has altered, suggesting functional divergence or innovation, and consistent with the action of dynamic selection pressures across the Argonaute gene family. We find there are large differences in evolutionary rates and gene turnover between pathways, and that paralogs of Ago2, Ago3, and Piwi/Aub show contrasting rates of evolution after duplication. This suggests that Argonautes undergo frequent evolutionary expansions that facilitate functional divergence.
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Affiliation(s)
- Samuel H Lewis
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Present Address: Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH
| | - Heli Salmela
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Helsinki, Finland
| | - Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Centre for Immunity, Infection and Evolution, University of Edinburgh, United Kingdom
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A Versatile Procedure to Generate Genome-Wide Spatiotemporal Program of Replication in Yeast Species. Methods Mol Biol 2016; 1361:247-64. [PMID: 26483026 DOI: 10.1007/978-1-4939-3079-1_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Here, we describe a complete protocol, comprising both the experimental and the analytical procedures, that allows to generate genome-wide spatiotemporal program of replication and to find the location of chromosomally active replication origins in yeast. The first step consists on synchronizing a cell population by physical discrimination of G1 cells according to their sedimentation coefficient. G1 cells are then synchronously released into S-phase and time-point samples are regularly taken until they reach the G2 phase. Progression through the cell cycle is monitored by measuring DNA content variation by flow cytometry. DNA samples, covering the entire S-phase, are then extracted and analyzed using deep sequencing. The gradual change of DNA copy number is measured to determine the mean replication time along the genome. A simple method of peak calling allows to infer from the replication profile the location of replication origins along the chromosomes. Our protocol is versatile enough to be applied to virtually any yeast species of interest and generate its replication profile.
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Tek A, Korostelev AA, Flores SC. MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory. Nucleic Acids Res 2015; 44:95-105. [PMID: 26673695 PMCID: PMC4705676 DOI: 10.1093/nar/gkv1457] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 11/28/2015] [Indexed: 02/07/2023] Open
Abstract
Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use Chimera as an interactive graphical interface to control MMB. We show how this can be used for morphing of macromolecules that can be heterogeneous in biopolymer type, sequence, and chain count, accurately recapitulating structural intermediates. We use MMB-GUI to create a possible trajectory of EF-G mediated gate-passing translocation in the ribosome, with all-atom structures. This shows that the GUI makes modeling of large macromolecules accessible to a wide audience. The morph highlights similarities in tRNA conformational changes as tRNA translocates from A to P and from P to E sites and suggests that tRNA flexibility is critical for translocation completion.
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Affiliation(s)
- Alex Tek
- Cell and Molecular Biology Department, Uppsala University, Box 596, Uppsala 751 24, Sweden
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation St., Worcester, MA 01605, USA
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38
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Glick Y, Orenstein Y, Chen D, Avrahami D, Zor T, Shamir R, Gerber D. Integrated microfluidic approach for quantitative high-throughput measurements of transcription factor binding affinities. Nucleic Acids Res 2015; 44:e51. [PMID: 26635393 PMCID: PMC4824076 DOI: 10.1093/nar/gkv1327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 11/14/2015] [Indexed: 01/16/2023] Open
Abstract
Protein binding to DNA is a fundamental process in gene regulation. Methodologies such as ChIP-Seq and mapping of DNase I hypersensitive sites provide global information on this regulation in vivo In vitro methodologies provide valuable complementary information on protein-DNA specificities. However, current methods still do not measure absolute binding affinities. There is a real need for large-scale quantitative protein-DNA affinity measurements. We developed QPID, a microfluidic application for measuring protein-DNA affinities. A single run is equivalent to 4096 gel-shift experiments. Using QPID, we characterized the different affinities of ATF1, c-Jun, c-Fos and AP-1 to the CRE consensus motif and CRE half-site in two different genomic sequences on a single device. We discovered that binding of ATF1, but not of AP-1, to the CRE half-site is highly affected by its genomic context. This effect was highly correlated with ATF1 ChIP-seq and PBM experiments. Next, we characterized the affinities of ATF1 and ATF3 to 128 genomic CRE and CRE half-site sequences. Our affinity measurements explained that in vivo binding differences between ATF1 and ATF3 to CRE and CRE half-sites are partially mediated by differences in the minor groove width. We believe that QPID would become a central tool for quantitative characterization of biophysical aspects affecting protein-DNA binding.
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Affiliation(s)
- Yair Glick
- Mina and Evrard Goodman life science faculty, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Yaron Orenstein
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Dana Chen
- Mina and Evrard Goodman life science faculty, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Dorit Avrahami
- Mina and Evrard Goodman life science faculty, Bar Ilan University, Ramat-Gan, 5290002, Israel
| | - Tsaffrir Zor
- Department of Biochemistry & Molecular Biology, Life Sciences Institute, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Doron Gerber
- Mina and Evrard Goodman life science faculty, Bar Ilan University, Ramat-Gan, 5290002, Israel
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Yang P, Wang J, Qi Q. Prophage recombinases-mediated genome engineering in Lactobacillus plantarum. Microb Cell Fact 2015; 14:154. [PMID: 26438232 PMCID: PMC4595204 DOI: 10.1186/s12934-015-0344-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/18/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Lactobacillus plantarum is a food-grade microorganism with industrial and medical relevance belonging to the group of lactic acid bacteria (LAB). Traditional strategies for obtaining gene deletion variants in this organism are mainly vector-based double-crossover methods, which are inefficient and laborious. A feasible possibility to solve this problem is the recombineering, which greatly expands the possibilities for engineering DNA molecules in vivo in various organisms. RESULTS In this work, a double-stranded DNA (dsDNA) recombineering system was established in L. plantarum. An exonuclease encoded by lp_0642 and a potential host-nuclease inhibitor encoded by lp_0640 involved in dsDNA recombination were identified from a prophage P1 locus in L. plantarum WCFS1. These two proteins, combined with the previously characterized single strand annealing protein encoded by lp_0641, can perform homologous recombination between a heterologous dsDNA substrate and host genomic DNA. Based on this, we developed a method for marker-free genetic manipulation of the chromosome in L. plantarum. CONCLUSIONS This Lp_0640-41-42-mediated recombination allowed easy screening of mutants and could serve as an alternative to other genetic manipulation methods. We expect that this method can help for understanding the probiotic functionality and physiology of LAB.
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Affiliation(s)
- Peng Yang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China.
| | - Jing Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China.
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China.
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Pybus M, Luisi P, Dall'Olio GM, Uzkudun M, Laayouni H, Bertranpetit J, Engelken J. Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations. Bioinformatics 2015; 31:3946-52. [PMID: 26315912 DOI: 10.1093/bioinformatics/btv493] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/17/2015] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION Detecting positive selection in genomic regions is a recurrent topic in natural population genetic studies. However, there is little consistency among the regions detected in several genome-wide scans using different tests and/or populations. Furthermore, few methods address the challenge of classifying selective events according to specific features such as age, intensity or state (completeness). RESULTS We have developed a machine-learning classification framework that exploits the combined ability of some selection tests to uncover different polymorphism features expected under the hard sweep model, while controlling for population-specific demography. As a result, we achieve high sensitivity toward hard selective sweeps while adding insights about their completeness (whether a selected variant is fixed or not) and age of onset. Our method also determines the relevance of the individual methods implemented so far to detect positive selection under specific selective scenarios. We calibrated and applied the method to three reference human populations from The 1000 Genome Project to generate a genome-wide classification map of hard selective sweeps. This study improves detection of selective sweep by overcoming the classical selection versus no-selection classification strategy, and offers an explanation to the lack of consistency observed among selection tests when applied to real data. Very few signals were observed in the African population studied, while our method presents higher sensitivity in this population demography. AVAILABILITY AND IMPLEMENTATION The genome-wide results for three human populations from The 1000 Genomes Project and an R-package implementing the 'Hierarchical Boosting' framework are available at http://hsb.upf.edu/.
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Affiliation(s)
- Marc Pybus
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Pierre Luisi
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Giovanni Marco Dall'Olio
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain, Division of Cancer Studies, King's College of London, London SE1 1UL, UK and
| | - Manu Uzkudun
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain, Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra 8193, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Johannes Engelken
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Spain
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Sehnal D, Pravda L, Svobodová Vařeková R, Ionescu CM, Koča J. PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res 2015; 43:W383-8. [PMID: 26013810 PMCID: PMC4489247 DOI: 10.1093/nar/gkv561] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/17/2015] [Indexed: 01/10/2023] Open
Abstract
Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery.
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Affiliation(s)
- David Sehnal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Lukáš Pravda
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Radka Svobodová Vařeková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Crina-Maria Ionescu
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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Scaife MA, Nguyen GTDT, Rico J, Lambert D, Helliwell KE, Smith AG. Establishing Chlamydomonas reinhardtii as an industrial biotechnology host. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:532-546. [PMID: 25641561 PMCID: PMC4515103 DOI: 10.1111/tpj.12781] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 05/20/2023]
Abstract
Microalgae constitute a diverse group of eukaryotic unicellular organisms that are of interest for pure and applied research. Owing to their natural synthesis of value-added natural products microalgae are emerging as a source of sustainable chemical compounds, proteins and metabolites, including but not limited to those that could replace compounds currently made from fossil fuels. For the model microalga, Chlamydomonas reinhardtii, this has prompted a period of rapid development so that this organism is poised for exploitation as an industrial biotechnology platform. The question now is how best to achieve this? Highly advanced industrial biotechnology systems using bacteria and yeasts were established in a classical metabolic engineering manner over several decades. However, the advent of advanced molecular tools and the rise of synthetic biology provide an opportunity to expedite the development of C. reinhardtii as an industrial biotechnology platform, avoiding the process of incremental improvement. In this review we describe the current status of genetic manipulation of C. reinhardtii for metabolic engineering. We then introduce several concepts that underpin synthetic biology, and show how generic parts are identified and used in a standard manner to achieve predictable outputs. Based on this we suggest that the development of C. reinhardtii as an industrial biotechnology platform can be achieved more efficiently through adoption of a synthetic biology approach.
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Affiliation(s)
- Mark A Scaife
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
- *For correspondence (e-mails or )
| | - Ginnie TDT Nguyen
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Juan Rico
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Devinn Lambert
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Katherine E Helliwell
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
- *For correspondence (e-mails or )
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Peters GM, Skala LP, Plank TN, Oh H, Manjunatha Reddy GN, Marsh A, Brown SP, Raghavan SR, Davis JT. G4-Quartet·M+ Borate Hydrogels. J Am Chem Soc 2015; 137:5819-27. [DOI: 10.1021/jacs.5b02753] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Gretchen Marie Peters
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Luke P. Skala
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Taylor N. Plank
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Hyuntaek Oh
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - G. N. Manjunatha Reddy
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Andrew Marsh
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Steven P. Brown
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Srinivasa R. Raghavan
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Jeffery T. Davis
- Department of Chemistry & Biochemistry and ‡Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Department of Physics and #Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
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Zhang Z, Mei W, Wu X, Wang X, Wang B, Chen S. Synthesis and characterization of chiral ruthenium(II) complexes Λ /Δ-[Ru(bpy) 2(H 2iip)](ClO 4) 2 as stabilizers of c- myc G-quadruplex DNA. J COORD CHEM 2015; 68:1465-1475. [DOI: 10.1080/00958972.2015.1014352] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/12/2015] [Indexed: 02/01/2023]
Affiliation(s)
- Zhao Zhang
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Wenjie Mei
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Xiaohui Wu
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Xicheng Wang
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Baoguo Wang
- College of Public Health, Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Sidong Chen
- College of Public Health, Guangdong Pharmaceutical University, Guangzhou, PR China
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Zhang D, Iyer LM, Burroughs AM, Aravind L. Resilience of biochemical activity in protein domains in the face of structural divergence. Curr Opin Struct Biol 2014; 26:92-103. [PMID: 24952217 DOI: 10.1016/j.sbi.2014.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/20/2014] [Indexed: 01/07/2023]
Abstract
Recent studies point to the prevalence of the evolutionary phenomenon of drastic structural transformation of protein domains while continuing to preserve their basic biochemical function. These transformations span a wide spectrum, including simple domains incorporated into larger structural scaffolds, changes in the structural core, major active site shifts, topological rewiring and extensive structural transmogrifications. Proteins from biological conflict systems, such as toxin-antitoxin, restriction-modification, CRISPR/Cas, polymorphic toxin and secondary metabolism systems commonly display such transformations. These include endoDNases, metal-independent RNases, deaminases, ADP ribosyltransferases, immunity proteins, kinases and E1-like enzymes. In eukaryotes such transformations are seen in domains involved in chromatin-related peptide recognition and protein/DNA-modification. Intense selective pressures from 'arms-race'-like situations in conflict and macromolecular modification systems could favor drastic structural divergence while preserving function.
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Affiliation(s)
- Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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