1
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Ott RK, Williams IH, Armstrong AR. Improved whole-mount immunofluorescence protocol for consistent and robust labeling of adult Drosophila melanogaster adipose tissue. Biol Open 2024; 13:bio060491. [PMID: 39041865 DOI: 10.1242/bio.060491] [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: 04/18/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024] Open
Abstract
Energy storage and endocrine functions of the Drosophila fat body make it an excellent model for elucidating mechanisms that underlie physiological and pathophysiological organismal metabolism. Combined with Drosophila's robust genetic and immunofluorescence microscopy toolkits, studies of Drosophila fat body function are ripe for cell biological analysis. Unlike the larval fat body, which is easily removed as a single, cohesive sheet of tissue, isolating intact adult fat body proves to be more challenging, thus hindering consistent immunofluorescence labeling even within a single piece of adipose tissue. Here, we describe an improved approach to handling Drosophila abdomens that ensures full access of the adult fat body to solutions generally used in immunofluorescence labeling protocols. In addition, we assess the quality of fluorescence reporter expression and antibody immunoreactivity in response to variations in fixative type, fixation incubation time, and detergent used for cellular permeabilization. Overall, we provide several recommendations for steps in a whole-mount staining protocol that results in consistent and robust immunofluorescence labeling of the adult Drosophila fat body.
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Affiliation(s)
- Rachael K Ott
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29072, USA
| | - Isaiah H Williams
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29072, USA
| | - Alissa R Armstrong
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29072, USA
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2
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der Heyden KAV, Gibbon VE, Mpolokeng KS. A South African case study on anatomical embalming for human body donation programmes with toxicological considerations. Ann Anat 2024; 255:152296. [PMID: 38925274 DOI: 10.1016/j.aanat.2024.152296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Body embalming, a practice with deep historical roots across various cultures, forms the backbone of contemporary human body donation educational programmes. In this study, we explored current embalming practices within six South African human anatomical dissection programmes, focusing on the use and volumes of key chemicals-formalin, phenol, and alcohol-and their associated health risks and potential toxicity. We measured and compared aspects of embalming practices such as the duration of body preservation and the annual intake of bodies. Variations in embalming practices and chemical ratios across different South African universities were found. However, the consistent use of formalin, phenol and alcohol were observed across all six programmes. Formaldehyde concentrations used in South African dissection programmes were within the generally acceptable international range. Regarding arterial embalming, South African dissection programmes showed widespread adherence to international embalming practices, with one programme using a substantially lower concentration of formalin. The dual nature of formaldehyde as both an effective preservative and a recognised carcinogen was underscored in relation to human health regarding chemical toxicity. Phenol, like formaldehyde, was consistently used as it is important for the inhibition of bacterial and fungal growth. Alcohol was also consistently used, but there was much greater variation in its volume across South African institutions. Our data showed a slight positive relationship between storage duration and the volumes of formalin and phenol in human embalming fluid. South African regulators enforce stricter exposure limits than those set by the World Health Organisation and various European agencies. While South African institutions operate within internationally acceptable ranges of chemical use that both maximise preservation and minimise toxicity, we acknowledge that these data are preliminary. Further investigation is encouraged to ensure embalming practices effectively protect all those involved and support the educational goals of human anatomical dissection programmes in South Africa.
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Affiliation(s)
- Kirsten Alexandria van der Heyden
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Victoria Elaine Gibbon
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kentse Sana Mpolokeng
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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3
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Ye R, Zhao H, Wang X, Xue Y. Technological advancements in deciphering RNA-RNA interactions. Mol Cell 2024:S1097-2765(24)00543-4. [PMID: 39047724 DOI: 10.1016/j.molcel.2024.06.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/11/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
RNA-RNA interactions (RRIs) can dictate RNA molecules to form intricate higher-order structures and bind their RNA substrates in diverse biological processes. To elucidate the function, binding specificity, and regulatory mechanisms of various RNA molecules, especially the vast repertoire of non-coding RNAs, advanced technologies and methods that globally map RRIs are extremely valuable. In the past decades, many state-of-the-art technologies have been developed for this purpose. This review focuses on those high-throughput technologies for the global mapping of RRIs. We summarize the key concepts and the pros and cons of different technologies. In addition, we highlight the novel biological insights uncovered by these RRI mapping methods and discuss the future challenges for appreciating the crucial roles of RRIs in gene regulation across bacteria, viruses, archaea, and mammals.
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Affiliation(s)
- Rong Ye
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailian Zhao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Wang
- State Key Laboratory of Female Fertility Promotion, Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yuanchao Xue
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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4
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Platon IV, Ghiorghita CA, Lazar MM, Aprotosoaie AC, Gradinaru AC, Nacu I, Verestiuc L, Nicolescu A, Ciocarlan N, Dinu MV. Highly Compressible, Superabsorbent, and Biocompatible Hybrid Cryogel Constructs Comprising Functionalized Chitosan and St. John's Wort Extract. Biomacromolecules 2024. [PMID: 38990059 DOI: 10.1021/acs.biomac.4c00496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Biobased porous hydrogels enriched with phytocompounds-rich herbal extracts have aroused great interest in recent years, especially in healthcare. In this study, new macroporous hybrid cryogel constructs comprising thiourea-containing chitosan (CSTU) derivative and a Hypericum perforatum L. extract (HYPE), commonly known as St John's wort, were prepared by a facile one-pot ice-templating strategy. Benefiting from the strong interactions between the functional groups of the CSTU matrix and those of polyphenols in HYPE, the hybrid cryogels possess excellent liquid absorption capacity, mechanical resilience, antioxidant performance, and a broad spectrum of antibacterial activity simultaneously. Thus, owing to their design, the hybrid constructs exhibit an interconnected porous architecture with the ability to absorb over 33 and 136 times their dry weight, respectively, when contacted with a phosphate buffer solution (pH 7.4) and an acidic aqueous solution (pH 2). These cryogel constructs have extremely high compressive strengths ranging from 839 to 1045 kPa and withstand elevated strains of over 70% without developing fractures. Moreover, the water-swollen hybrid cryogels with the highest HYPE content revealed a complete and instant shape recovery after uniaxial compression. The incorporation of HYPE into CSTU cryogels enabled substantial improvement in scavenging reactive oxygen species and an expanded antibacterial spectrum toward multiple pathogens, including Gram-positive bacteria (Staphylococcus aureus and Staphylococcus epidermidis), Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa), and fungi (Candida albicans). Cell viability experiments demonstrated the cytocompatibility of the 3D cryogel constructs, which did not induce changes in the fibroblast morphology. This work showcases a simple and effective strategy to immobilize HYPE extracts on CSTU 3D networks, allowing the development of novel multifunctional platforms with promising potential in hemostasis, wound dressing, and dermal regeneration scaffolds.
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Affiliation(s)
- Ioana-Victoria Platon
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41A, Iasi 700487, Romania
| | | | - Maria Marinela Lazar
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41A, Iasi 700487, Romania
| | - Ana Clara Aprotosoaie
- Faculty of Pharmacy, "Grigore T. Popa" University of Medicine and Pharmacy, Universitatii Street 16, Iasi 700115, Romania
| | - Adina Catinca Gradinaru
- Faculty of Pharmacy, "Grigore T. Popa" University of Medicine and Pharmacy, Universitatii Street 16, Iasi 700115, Romania
| | - Isabella Nacu
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41A, Iasi 700487, Romania
- Faculty of Medical Bioengineering, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi 700115, Romania
| | - Liliana Verestiuc
- Faculty of Medical Bioengineering, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi 700115, Romania
| | - Alina Nicolescu
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41A, Iasi 700487, Romania
| | - Nina Ciocarlan
- Botanical Garden, Academy of Sciences of Moldova, Padurii Street 18, Chisinau 2002, Republic of Moldova
| | - Maria Valentina Dinu
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41A, Iasi 700487, Romania
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5
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Hu S, Liu Y, Zhang Q, Bai J, Xu C. A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Mol Syst Biol 2024; 20:799-824. [PMID: 38745107 PMCID: PMC11220090 DOI: 10.1038/s44320-024-00038-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription factor (TF) residence on chromatin translates into quantitative transcriptional or structural outcomes on genome. Commonly used formaldehyde crosslinking fixes TF-DNA interactions cumulatively and compromises the measured occupancy level. Here we mapped the occupancy level of global or individual zinc finger TFs like CTCF and MAZ, in the form of highly resolved footprints, on native chromatin. By incorporating reinforcing perturbation conditions, we established S-score, a quantitative metric to proxy the continuum of CTCF or MAZ retention across different motifs on native chromatin. The native chromatin-retained CTCF sites harbor sequence features within CTCF motifs better explained by S-score than the metrics obtained from other crosslinking or native assays. CTCF retention on native chromatin correlates with local SUMOylation level, and anti-correlates with transcriptional activity. The S-score successfully delineates the otherwise-masked differential stability of chromatin structures mediated by CTCF, or by MAZ independent of CTCF. Overall, our study established a paradigm continuum of TF retention across binding sites on native chromatin, explaining the dynamic genome organization.
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Affiliation(s)
- Siling Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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6
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Zhou C, Wagner S, Liang FS. Induced proximity labeling and editing for epigenetic research. Cell Chem Biol 2024; 31:1118-1131. [PMID: 38866004 PMCID: PMC11193966 DOI: 10.1016/j.chembiol.2024.05.005] [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: 04/05/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
Epigenetic regulation plays a pivotal role in various biological and disease processes. Two key lines of investigation have been pursued that aim to unravel endogenous epigenetic events at particular genes (probing) and artificially manipulate the epigenetic landscape (editing). The concept of induced proximity has inspired the development of powerful tools for epigenetic research. Induced proximity strategies involve bringing molecular effectors into spatial proximity with specific genomic regions to achieve the probing or manipulation of local epigenetic environments with increased proximity. In this review, we detail the development of induced proximity methods and applications in shedding light on the intricacies of epigenetic regulation.
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Affiliation(s)
- Chenwei Zhou
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Sarah Wagner
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA.
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7
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Gignac PM, Valdez D, Morhardt AC, Lynch LM. Buffered Lugol's Iodine Preserves DNA Fragment Lengths. Integr Org Biol 2024; 6:obae017. [PMID: 38887427 PMCID: PMC11182668 DOI: 10.1093/iob/obae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/05/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Museum collections play a pivotal role in the advancement of biological science by preserving phenotypic and genotypic history and variation. Recently, contrast-enhanced X-ray computed tomography (CT) has aided these advances by allowing improved visualization of internal soft tissues. However, vouchered specimens could be at risk if staining techniques are destructive. For instance, the pH of unbuffered Lugol's iodine (I2KI) may be low enough to damage deoxyribonucleic acid (DNA). The extent of this risk is unknown due to a lack of rigorous evaluation of DNA quality between control and experimental samples. Here, we used formalin-fixed mice to document DNA concentrations and fragment lengths in nonstained, ethanol-preserved controls and 3 iodine-based staining preparations: (1) 1.25% weight-by-volume (wt/vol.) alcoholic iodine (I2E); (2) 3.75% wt/vol. I2KI; and (3) 3.75% wt/vol. buffered I2KI. We tested a null hypothesis of no significant difference in DNA concentrations and fragment lengths between control and treatment samples. We found that DNA concentration decreases because of staining-potentially an effect of measuring intact double-stranded DNA only. Fragment lengths, however, were significantly higher for buffered I2KI and control samples, which were not, themselves, significantly different. Our results implicate buffered I2KI as the appropriate choice for contrast-enhanced CT imaging of museum wet collections to safely maximize their potential for understanding genetic and phenotypic diversity.
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Affiliation(s)
- P M Gignac
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - D Valdez
- Department of Anatomy, Midwestern University, Glendale, AZ 85308, USA
| | - A C Morhardt
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - L M Lynch
- Department of Anatomy, Midwestern University, Glendale, AZ 85308, USA
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8
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Mohammadi MA, Alizadeh AM, Mousavi M, Hashempour-Baltork F, Kooki S, Shadan MR, Hosseini SM, McClements DJ. Advances and applications of crosslinked electrospun biomacromolecular nanofibers. Int J Biol Macromol 2024; 271:132743. [PMID: 38821308 DOI: 10.1016/j.ijbiomac.2024.132743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Electrospinning is a technology for fabricating ultrafine fibers from natural or synthetic polymers that have novel or enhanced functional properties. These fibers have found applications in a diverse range of fields, including the food, medicine, cosmetics, agriculture, and chemical industries. However, the tendency for electrospun nanofibers to dissociate when exposed to certain environmental conditions limits many of their practical applications. The structural integrity and functional attributes of these nanofibers can be improved using physical and/or chemical crosslinking methods. This review article discusses the formation of polymeric nanofibers using electrospinning and then describes how different crosslinking methods can be used to enhance their mechanical, thermal, and biological attributes. Methods for optimizing the crosslinking reactions are discussed, including proper selection of crosslinker type and reaction conditions. Then, food, medical, and separation applications of crosslinked electrospun fibers are assessed, including in bone and skin tissue engineering, wound healing, drug delivery, air filtration, water filtration, oil removal, food packaging, food preservation, and bioactive delivery. Finally, areas where future research are needed are highlighted, as well as possible future applications of crosslinked nanofibers.
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Affiliation(s)
- Masoud Aman Mohammadi
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Adel Mirza Alizadeh
- Department of Food Safety and Hygiene, School of Public Health, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Malihe Mousavi
- Department of Nutrition, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fataneh Hashempour-Baltork
- Halal Research Center of IRI, Iran Food and Drug Administration, Ministry of Health and Medical Education, Tehran, Iran.
| | - Safa Kooki
- Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mohammad Reza Shadan
- Clinical Immunology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyede Marzieh Hosseini
- Department of Food Technology, Faculty of Nutrition Science and Food Technology, Nutritional, and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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9
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Benedict B, Kristensen SM, Duxin JP. What are the DNA lesions underlying formaldehyde toxicity? DNA Repair (Amst) 2024; 138:103667. [PMID: 38554505 DOI: 10.1016/j.dnarep.2024.103667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/01/2024]
Abstract
Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.
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Affiliation(s)
- Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Stella Munkholm Kristensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark.
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10
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Gómez Acuña LI, Flyamer I, Boyle S, Friman ET, Bickmore WA. Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity. PLoS Genet 2024; 20:e1011277. [PMID: 38781242 DOI: 10.1371/journal.pgen.1011277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 06/05/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
How enhancers regulate their target genes in the context of 3D chromatin organization is extensively studied and models which do not require direct enhancer-promoter contact have recently emerged. Here, we use the activation of estrogen receptor-dependent enhancers in a breast cancer cell line to study enhancer-promoter communication at two loci. This allows high temporal resolution tracking of molecular events from hormone stimulation to efficient gene activation. We examine how both enhancer-promoter spatial proximity assayed by DNA fluorescence in situ hybridization, and contact frequencies resulting from chromatin in situ fragmentation and proximity ligation, change dynamically during enhancer-driven gene activation. These orthogonal methods produce seemingly paradoxical results: upon enhancer activation enhancer-promoter contact frequencies increase while spatial proximity decreases. We explore this apparent discrepancy using different estrogen receptor ligands and transcription inhibitors. Our data demonstrate that enhancer-promoter contact frequencies are transcription independent whereas altered enhancer-promoter proximity depends on transcription. Our results emphasize that the relationship between contact frequencies and physical distance in the nucleus, especially over short genomic distances, is not always a simple one.
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Affiliation(s)
- Luciana I Gómez Acuña
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Ilya Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
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11
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Gizardin-Fredon H, Santo PE, Chagot ME, Charpentier B, Bandeiras TM, Manival X, Hernandez-Alba O, Cianférani S. Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions. Nat Commun 2024; 15:3516. [PMID: 38664367 PMCID: PMC11045720 DOI: 10.1038/s41467-024-47732-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Chemical cross-linking reactions (XL) are an important strategy for studying protein-protein interactions (PPIs), including low abundant sub-complexes, in structural biology. However, choosing XL reagents and conditions is laborious and mostly limited to analysis of protein assemblies that can be resolved using SDS-PAGE. To overcome these limitations, we develop here a denaturing mass photometry (dMP) method for fast, reliable and user-friendly optimization and monitoring of chemical XL reactions. The dMP is a robust 2-step protocol that ensures 95% of irreversible denaturation within only 5 min. We show that dMP provides accurate mass identification across a broad mass range (30 kDa-5 MDa) along with direct label-free relative quantification of all coexisting XL species (sub-complexes and aggregates). We compare dMP with SDS-PAGE and observe that, unlike the benchmark, dMP is time-efficient (3 min/triplicate), requires significantly less material (20-100×) and affords single molecule sensitivity. To illustrate its utility for routine structural biology applications, we show that dMP affords screening of 20 XL conditions in 1 h, accurately identifying and quantifying all coexisting species. Taken together, we anticipate that dMP will have an impact on ability to structurally characterize more PPIs and macromolecular assemblies, expected final complexes but also sub-complexes that form en route.
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Affiliation(s)
- Hugo Gizardin-Fredon
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | | | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France.
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France.
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12
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Thompson SD, Pichika R, Lieber RL, Lavasani M. Extracting high-quality RNA from formaldehyde-fixed naturally aged neuromusculoskeletal tissues. Biotechniques 2024; 76:153-160. [PMID: 38334498 PMCID: PMC10988388 DOI: 10.2144/btn-2023-0092] [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: 09/12/2023] [Accepted: 12/22/2023] [Indexed: 02/10/2024] Open
Abstract
Modern approaches to discovering molecular mechanisms and validating treatments for age-related neuromusculoskeletal dysfunction typically rely on high-throughput transcriptome analysis. Previously harvested and fixed tissues offer an incredible reservoir of untapped molecular information. However, obtaining RNA from such formaldehyde-fixed neuromusculoskeletal tissues, especially fibrotic aged tissues, is technically challenging and often results in RNA degradation, chemical modification and yield reduction, prohibiting further analysis. Therefore, we developed a protocol to extract high-quality RNA from formaldehyde-fixed brain, cartilage, muscle and peripheral nerve isolated from naturally aged mice. Isolated RNA produced reliable gene expression data comparable to fresh and flash-frozen tissues and was sensitive enough to detect age-related changes, making our protocol valuable to researchers in the field of aging.
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Affiliation(s)
- Seth D Thompson
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Graduate Program, Northwestern University, Chicago, IL 60611, USA
| | - Rajeswari Pichika
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Edward Hines Jr VA Medical Center, Maywood, IL 60153, USA
| | - Richard L Lieber
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Edward Hines Jr VA Medical Center, Maywood, IL 60153, USA
| | - Mitra Lavasani
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Graduate Program, Northwestern University, Chicago, IL 60611, USA
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13
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Peng Q, Weerapana E. Profiling nuclear cysteine ligandability and effects on nuclear localization using proximity labeling-coupled chemoproteomics. Cell Chem Biol 2024; 31:550-564.e9. [PMID: 38086369 PMCID: PMC10960692 DOI: 10.1016/j.chembiol.2023.11.010] [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: 08/03/2023] [Revised: 10/11/2023] [Accepted: 11/17/2023] [Indexed: 03/24/2024]
Abstract
The nucleus controls cell growth and division through coordinated interactions between nuclear proteins and chromatin. Mutations that impair nuclear protein association with chromatin are implicated in numerous diseases. Covalent ligands are a promising strategy to pharmacologically target nuclear proteins, such as transcription factors, which lack ordered small-molecule binding pockets. To identify nuclear cysteines that are susceptible to covalent liganding, we couple proximity labeling (PL), using a histone H3.3-TurboID (His-TID) construct, with chemoproteomics. Using covalent scout fragments, KB02 and KB05, we identified ligandable cysteines on proteins involved in spindle assembly, DNA repair, and transcriptional regulation, such as Cys101 of histone acetyltransferase 1 (HAT1). Furthermore, we show that covalent fragments can affect the abundance, localization, and chromatin association of nuclear proteins. Notably, the Parkinson disease protein 7 (PARK7) showed increased nuclear localization and chromatin association upon KB02 modification at Cys106. Together, this platform provides insights into targeting nuclear cysteines with covalent ligands.
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Affiliation(s)
- Qianni Peng
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
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14
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King A, Zhao Y, Lazar A, Capron M, Thiruvur N, Liu X. Methods comparison of two-dimensional gel electrophoresis for host cell protein characterization. Biotechnol Prog 2024:e3452. [PMID: 38494896 DOI: 10.1002/btpr.3452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/19/2024] [Indexed: 03/19/2024]
Abstract
Two-dimensional electrophoresis (2DE) is a gel-based protein separation method based on size and charge which is commonly used for the characterization of host cell proteins (HCPs) during drug development in biotech and pharmaceutical companies. HCPs are a heterogenous mixture of proteins produced by host cells during a biologics drug manufacturing process. Different gel electrophoresis methods including traditional 2D SDS-PAGE with silver and SYPRO Ruby fluorescent dye staining as well as two-dimensional difference gel electrophoresis (2D-DIGE) were compared for their relative abilities to characterize HCPs. SYPRO Ruby was shown to be more sensitive than silver stain in the traditional 2D gels both with and without product protein present. Silver stain also displayed a significant preference for staining acidic proteins over basic ones while SYPRO Ruby was more consistent in imaging proteins across different isoelectric points. The non-traditional method of 2D-DIGE provides high resolution and reproducibility when comparing samples with similar protein profiles but was limited in imaging HCP spots due to its narrow dynamic range. Overall, 2DE is a powerful tool to separate and characterize HCPs and is optimized by choosing the best stain or method for each specific application. Using a combination of two or more different 2DE staining methods, when possible, provides the most comprehensive coverage to support the characterization of a complex mixture like HCPs. However, in instances where only one staining method can be used, SYPRO Ruby is shown to be the more reliable, more sensitive, and easier to use traditional staining method for most HCP-based applications.
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Affiliation(s)
- Abigail King
- Department of Analytical Development, Mural Oncology, Inc., Waltham, Massachusetts, USA
| | - Yiwei Zhao
- Department of Analytical Development, Mural Oncology, Inc., Waltham, Massachusetts, USA
| | - Alexandru Lazar
- Department of Analytical Development, Mural Oncology, Inc., Waltham, Massachusetts, USA
| | - Margeaux Capron
- Department of Analytical Development, Mural Oncology, Inc., Waltham, Massachusetts, USA
| | - Niranjan Thiruvur
- Department of Analytical Development, Mural Oncology, Inc., Waltham, Massachusetts, USA
| | - Xinrong Liu
- Department of Analytical Development, Mural Oncology, Inc., Waltham, Massachusetts, USA
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15
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Datta S, Patel M, Sathyaseelan C, Ghosh C, Mudgal A, Patel D, Rathinavelan T, Singh U. G-quadruplex landscape and its regulation revealed by a new antibody capture method. Oncotarget 2024; 15:175-198. [PMID: 38484151 PMCID: PMC10939474 DOI: 10.18632/oncotarget.28564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
Our understanding of DNA G-quadruplexes (G4s) from in vitro studies has been complemented by genome-wide G4 landscapes from cultured cells. Conventionally, the formation of G4s is accepted to depend on G-repeats such that they form tetrads. However, genome-wide G4s characterized through high-throughput sequencing suggest that these structures form at a large number of regions with no such canonical G4-forming signatures. Many G4-binding proteins have been described with no evidence for any protein that binds to and stabilizes G4s. It remains unknown what fraction of G4s formed in human cells are protein-bound. The G4-chromatin immunoprecipitation (G4-ChIP) method hitherto employed to describe G4 landscapes preferentially reports G4s that get crosslinked to proteins in their proximity. Our current understanding of the G4 landscape is biased against representation of G4s which escape crosslinking as they are not stabilized by protein-binding and presumably transient. We report a protocol that captures G4s from the cells efficiently without any bias as well as eliminates the detection of G4s formed artifactually on crosslinked sheared chromatin post-fixation. We discover that G4s form sparingly at SINEs. An application of this method shows that depletion of a repeat-binding protein CGGBP1 enhances net G4 capture at CGGBP1-dependent CTCF-binding sites and regions of sharp interstrand G/C-skew transitions. Thus, we present an improved method for G4 landscape determination and by applying it we show that sequence property-specific constraints of the nuclear environment mitigate G4 formation.
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Affiliation(s)
- Subhamoy Datta
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Manthan Patel
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Chakkarai Sathyaseelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi Campus, Telangana 502285, India
| | - Chandrama Ghosh
- Azrieli Faculty of Medicine, Bar-Ilan University, Henrietta Szold 8A, Safed 1311502, Israel
| | - Akanksha Mudgal
- Department of Biopharmacy, Medical University of Lublin, Lublin 20059, Poland
| | - Divyesh Patel
- Research Programs Unit, Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Biomedicum, Helsinki 00290, Finland
| | | | - Umashankar Singh
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
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16
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Cai S, Tang H, Li B, Shao Y, Zhang D, Zheng H, Qiao T, Chu X, He G, Xue XS, Chen G. Formaldehyde-Mediated Hydride Liberation of Alkylamines for Intermolecular Reactions in Hexafluoroisopropanol. J Am Chem Soc 2024; 146:5952-5963. [PMID: 38408428 DOI: 10.1021/jacs.3c12215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The ability of alkylamines to spontaneously liberate hydride ions is typically restrained, except under specific intramolecular reaction settings. Herein, we demonstrate that this reactivity can be unlocked through simple treatment with formaldehyde in hexafluoroisopropanol (HFIP) solvent, thereby enabling various intermolecular hydride transfer reactions of alkylamines under mild conditions. Besides transformations of small molecules, these reactions enable unique late-stage modification of complex peptides. Mechanistic investigations uncover that the key to these intermolecular hydride transfer processes lies in the accommodating conformation of solvent-mediated macrocyclic transition states, where the aggregates of HFIP molecules act as dexterous proton shuttles. Importantly, negative hyperconjugation between the lone electron pair of nitrogen and the antibonding orbital of amine's α C-H bond plays a critical role in the C-H activation, promoting its hydride liberation.
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Affiliation(s)
- Shaokun Cai
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yingbo Shao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Danqi Zhang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hanliang Zheng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Tianjiao Qiao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao-Song Xue
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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17
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Víšková P, Ištvánková E, Ryneš J, Džatko Š, Loja T, Živković ML, Rigo R, El-Khoury R, Serrano-Chacón I, Damha MJ, González C, Mergny JL, Foldynová-Trantírková S, Trantírek L. In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells. Nat Commun 2024; 15:1992. [PMID: 38443388 PMCID: PMC10914786 DOI: 10.1038/s41467-024-46221-y] [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: 09/10/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single-stranded, cytosine-rich genomic regions with regulatory roles. Chromatin, protein interactions, and intracellular properties seem to govern iM formation at sites with i-motif formation propensity (iMFPS) in human cells, yet their specific contributions remain unclear. Using in-cell NMR with oligonucleotide iMFPS models, we monitor iM-associated structural equilibria in asynchronous and cell cycle-synchronized HeLa cells at 37 °C. Our findings show that iMFPS displaying pHT < 7 under reference in vitro conditions occur predominantly in unfolded states in cells, while those with pHT > 7 appear as a mix of folded and unfolded states depending on the cell cycle phase. Comparing these results with previous data obtained using an iM-specific antibody (iMab) reveals that cell cycle-dependent iM formation has a dual origin, and iM formation concerns only a tiny fraction (possibly 1%) of genomic sites with iM formation propensity. We propose a comprehensive model aligning observations from iMab and in-cell NMR and enabling the identification of iMFPS capable of adopting iM structures under physiological conditions in living human cells. Our results suggest that many iMFPS may have biological roles linked to their unfolded states.
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Affiliation(s)
- Pavlína Víšková
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Eva Ištvánková
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Jan Ryneš
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Šimon Džatko
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- Centre for Advanced Materials Application, Slovak Academy of Sciences, 845 11, Bratislava, Slovakia
| | - Tomáš Loja
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Martina Lenarčič Živković
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000, Ljubljana, Slovenia
| | - Riccardo Rigo
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
- Pharmaceutical and Pharmacological Sciences Department, University of Padova, 35131, Padova, Italy
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, QC, H3A0B8, Canada
| | - Israel Serrano-Chacón
- Instituto de Química Física 'Blas Cabrera', CSIC, C/Serrano 119, 28006, Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC, H3A0B8, Canada
| | - Carlos González
- Instituto de Química Física 'Blas Cabrera', CSIC, C/Serrano 119, 28006, Madrid, Spain
| | - Jean-Louis Mergny
- Institute of Biophysics, Czech Academy of Sciences, Brno, 612 00, Czech Republic
- Laboratoire d'Optique & Biosciences, Institut Polytechnique de Paris, Inserm, CNRS, Ecole Polytechnique, Palaiseau, 91120, France
| | - Silvie Foldynová-Trantírková
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.
- Institute of Biophysics, Czech Academy of Sciences, Brno, 612 00, Czech Republic.
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.
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18
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Jaiswal M, Tran TT, Guo J, Zhou M, Kundu S, Guo Z, Fanucci GE. Spin-labeling Insights into How Chemical Fixation Impacts Glycan Organization on Cells. APPLIED MAGNETIC RESONANCE 2024; 55:317-333. [PMID: 38469359 PMCID: PMC10927023 DOI: 10.1007/s00723-023-01624-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 03/13/2024]
Abstract
As new methods to interrogate glycan organization on cells develop, it is important to have a molecular level understanding of how chemical fixation can impact results and interpretations. Site-directed spin labeling technologies are well suited to study how the spin label mobility is impacted by local environmental conditions, such as those imposed by cross-linking effects of paraformaldehyde cell fixation methods. Here, we utilize three different azide-containing sugars for metabolic glycan engineering with HeLa cells to incorporate azido glycans that are modified with a DBCO-based nitroxide moiety via click reaction. Continuous wave X-band electron paramagnetic resonance spectroscopy is employed to characterize how the chronological sequence of chemical fixation and spin labeling impacts the local mobility and accessibility of the nitroxide-labeled glycans in the glycocalyx of HeLa cells. Results demonstrate that chemical fixation with paraformaldehyde can alter local glycan mobility and care should be taken in the analysis of data in any study where chemical fixation and cellular labeling occur.
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Affiliation(s)
- Mohit Jaiswal
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Trang T Tran
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Jiatong Guo
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Mingwei Zhou
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Sayan Kundu
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
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19
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Stortz M, Presman DM, Levi V. Transcriptional condensates: a blessing or a curse for gene regulation? Commun Biol 2024; 7:187. [PMID: 38365945 PMCID: PMC10873363 DOI: 10.1038/s42003-024-05892-5] [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: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Whether phase-separation is involved in the organization of the transcriptional machinery and if it aids or inhibits the transcriptional process is a matter of intense debate. In this Mini Review, we will cover the current knowledge regarding the role of transcriptional condensates on gene expression regulation. We will summarize the latest discoveries on the relationship between condensate formation, genome organization, and transcriptional activity, focusing on the strengths and weaknesses of the experimental approaches used to interrogate these aspects of transcription in living cells. Finally, we will discuss the challenges for future research.
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Grants
- PICT 2020-00818 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT-2018-1921 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT 2019-0397 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- 20020190100101BA University of Buenos Aires | Secretaría de Ciencia y Técnica, Universidad de Buenos Aires (Secretaría de Ciencia y Técnica de la Universidad de Buenos Aires)
- 2022-11220210100212CO Consejo Nacional de Investigaciones Científicas y Técnicas (National Scientific and Technical Research Council)
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Affiliation(s)
- Martin Stortz
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EGA, Argentina.
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
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20
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Zhang S, Zhang W, Xiao S, Zhang Y, Chen D, Liu X, Wu Y. Efficacy of enzyme‑induced collagen crosslinking on porcine cornea. Exp Ther Med 2024; 27:87. [PMID: 38274339 PMCID: PMC10809311 DOI: 10.3892/etm.2024.12377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 11/22/2023] [Indexed: 01/27/2024] Open
Abstract
The purpose of the present study was to investigate the effect of a new crosslinking (CXL) method, induced by enzymes, on porcine corneas. Corneal strip (10x3 mm) pairs obtained from 60 fresh porcine eyes were harvested and divided into four groups, Groups A-D. Each pair of corneal strips was incised from the central part of the same cornea; one was incubated in transglutaminase (Tgase) solution (microbial Tgase 2 produced by tissue engineering) and the other remained untreated as a control. CXL strips of Groups A-D were incubated with 2, 1, 0.5 and 0.25 U/ml Tgase solution, respectively at 37˚C for 30 min. After that, tensile strain measurements were performed for all strips. One cornea from each group was chosen randomly for hematoxylin and eosin, and Masson staining to identify histological morphology changes. The elastic modulus of treated corneas of Groups A-D were 6.56±2.93, 4.72±1.29, 5.24±2.13 and 3.48±1.60 MPa (mean ± SD), respectively at a strain of 20%, and had a 66, 43, 36 and -6% increase compared with those of their control strips. Compared with the control strips, the elastic modulus of the treated strips significantly increased in Groups A-C. The central corneal thickness of the treated corneas in Groups A-D were 1.54±0.14, 1.41±0.15, 1.47±0.11 and 1.43±0.13 µm, respectively; however, there was not a statistically significant difference compared with the control group. No reduction in corneal transparency was observed, and no obvious abnormalities were found in corneal morphology. CXL mediated by enzymes can lead to a notable enhancement in the biomechanical characteristics of the cornea while maintaining its structural integrity. Enzyme-induced CXL could be a new generation CXL method for strengthening the cornea.
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Affiliation(s)
- Shijie Zhang
- Department of Ophthalmology, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Wenbo Zhang
- Department of Ophthalmology, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Shiyu Xiao
- Department of Ophthalmology, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Yanzhen Zhang
- Department of Ophthalmology, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Duo Chen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Sciences and Medical Engineering, Beihang University, Beijing 100191, P.R. China
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing 100083, P.R. China
| | - Xiaoyu Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Sciences and Medical Engineering, Beihang University, Beijing 100191, P.R. China
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing 100083, P.R. China
| | - Yuan Wu
- Department of Ophthalmology, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
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21
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Bernauer H, Maier J, Bannert N, Ivanusic D. tANCHOR cell-based ELISA approach as a surrogate for antigen-coated plates to monitor specific IgG directed to the SARS-CoV-2 receptor-binding domain. Biol Methods Protoc 2024; 9:bpae001. [PMID: 38332985 PMCID: PMC10850845 DOI: 10.1093/biomethods/bpae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
Enzyme-linked immunosorbent assay (ELISA) systems use plates coated with peptides or expressed and purified proteins to monitor immunoglobulins derived from patient serum. However, there is currently no easy, flexible, and fast adaptive ELISA-based system for testing antibodies directed against new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. In this study, we utilized the tANCHOR protein display system that provides a cell surface decorated with the receptor-binding domain (RBD) to monitor specific antibodies derived from SARS-CoV-2 convalescent and vaccinated individuals directed against it. To test sera from vaccinees or convalescent individuals, only the RBD coding sequence needs to be cloned in the tANCHOR vector system and transfected into HeLa cells. Time-consuming protein expression, isolation, and purification followed by coating assay plates are not necessary. With this technique, the immune evasion of new SARS-CoV-2 variants from current vaccination regimes can be examined quickly and reliably.
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Affiliation(s)
| | - Josef Maier
- ATG:biosynthetics GmbH, 79249 Merzhausen, Germany
| | - Norbert Bannert
- Sexually Transmitted Bacterial Pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
| | - Daniel Ivanusic
- Sexually Transmitted Bacterial Pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
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22
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Budaeva N, Agne S, Ribeiro PA, Straube N, Preick M, Hofreiter M. Wide-spread dispersal in a deep-sea brooding polychaete: the role of natural history collections in assessing the distribution in quill worms (Onuphidae, Annelida). Front Zool 2024; 21:1. [PMID: 38233869 PMCID: PMC10795374 DOI: 10.1186/s12983-023-00520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Modern integrative taxonomy-based annelid species descriptions are detailed combining morphological data and, since the last decades, also molecular information. Historic species descriptions are often comparatively brief lacking such detail. Adoptions of species names from western literature in the past led to the assumption of cosmopolitan ranges for many species, which, in many cases, were later found to include cryptic or pseudocryptic lineages with subtle morphological differences. Natural history collections and databases can aid in assessing the geographic ranges of species but depend on correct species identification. Obtaining DNA sequence information from wet-collection museum specimens of marine annelids is often impeded by the use of formaldehyde and/or long-term storage in ethanol resulting in DNA degradation and cross-linking. RESULTS The application of ancient DNA extraction methodology in combination with single-stranded DNA library preparation and target gene capture resulted in successful sequencing of a 110-year-old collection specimen of quill worms. Furthermore, a 40-year-old specimen of quill worms was successfully sequenced using a standard extraction protocol for modern samples, PCR and Sanger sequencing. Our study presents the first molecular analysis of Hyalinoecia species including the previously known species Hyalinoecia robusta, H. tubicloa, H. artifex, and H. longibranchiata, and a potentially undescribed species from equatorial western Africa morphologically indistinguishable from H. tubicola. The study also investigates the distribution of these five Hyalinoecia species. Reassessing the distribution of H. robusta reveals a geographical range covering both the Atlantic and the Indian Oceans as indicated by molecular data obtained from recent and historical specimens. CONCLUSION Our results represent an example of a very wide geographical distribution of a brooding deep-sea annelid with a complex reproduction strategy and seemingly very limited dispersal capacity of its offspring, and highlights the importance of molecular information from museum specimens for integrative annelid taxonomy and biogeography.
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Affiliation(s)
- Nataliya Budaeva
- Department of Natural History, University Museum of Bergen, University of Bergen, Allégaten 41, 5007, Bergen, Norway.
| | - Stefanie Agne
- Evolutionary Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Pedro A Ribeiro
- Department of Biological Sciences and Centre for Deep-Sea Research, University of Bergen, Thormøhlens Gate 53B, 5006, Bergen, Norway
| | - Nicolas Straube
- Department of Natural History, University Museum of Bergen, University of Bergen, Allégaten 41, 5007, Bergen, Norway
| | - Michaela Preick
- Evolutionary Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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23
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Gilbert BR, Luthey-Schulten Z. Replicating Chromosomes in Whole-Cell Models of Bacteria. Methods Mol Biol 2024; 2819:625-653. [PMID: 39028527 DOI: 10.1007/978-1-0716-3930-6_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication of genetic material. In a recent study, we presented a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics. This approach was used to investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell cycle. To achieve cell-scale chromosome structures that are realistic, we modeled the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. Additionally, the polymer interacts with ribosomes distributed according to cryo-electron tomograms of Syn3A. The polymer model was further augmented by computational models of loop extrusion by structural maintenance of chromosomes (SMC) protein complexes and topoisomerase action, and the modeling and analysis of multi-fork replication states.
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Affiliation(s)
- Benjamin R Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NSF Science and Technology Center for Quantitative Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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24
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Hayek H, Gross L, Alghoul F, Martin F, Eriani G, Allmang C. Immunoprecipitation Methods to Isolate Messenger Ribonucleoprotein Complexes (mRNP). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:1-15. [PMID: 38507196 DOI: 10.1007/978-3-031-52193-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Throughout their life cycle, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Each mRNA is part of multiple successive mRNP complexes that participate in their biogenesis, cellular localization, translation and decay. The dynamic composition of mRNP complexes and their structural remodelling play crucial roles in the control of gene expression. Studying the endogenous composition of different mRNP complexes is a major challenge. In this chapter, we describe the variety of protein-centric immunoprecipitation methods available for the identification of mRNP complexes and the requirements for their experimental settings.
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Affiliation(s)
- Hassan Hayek
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Lauriane Gross
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Fatima Alghoul
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Franck Martin
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Christine Allmang
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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25
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Roscoe S, Guo Y, Vacratsis PO, Ananvoranich S. Proteomic profile of Toxoplasma gondii stress granules by high-resolution mass spectrometry. Can J Microbiol 2024; 70:32-39. [PMID: 37826860 DOI: 10.1139/cjm-2023-0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Ribonucleoprotein granules are bio-condensates that form a diverse group of dynamic membrane-less organelles implicated in several cellular functions, including stress response and cellular survival. In Toxoplasma gondii, a type of bio-condensates referred to as stress granules (SGs) are formed prior to the parasites' egress from the host cell and are implicated in the survival and invasion competency of extracellular tachyzoites. We used paraformaldehyde to fix and cross-link SG proteins to allow purification by centrifugation and analysis by mass spectrometry. We profiled protein components of SGs at 10 and 30 min post-egress when parasite's invasion ability is significantly diminished. Thirty-three proteins were identified from 10 min SGs, and additional 43 proteins were identified from 30 min SGs. Notably, common SG components such as proteins with intrinsically disordered domains were not identified. Gene ontology analysis of both 10 and 30 min SGs shows that overall molecular functions of SGs' proteins are ATP-binding, GTP-binding, and GTPase activity. Discernable differences between 10 and 30 min SGs are in the proportions of translation and microtubule-related proteins. Ten-minute SGs have a higher proportion of microtubule-related proteins and a lower proportion of ribosome-related proteins, while a reverse correlation was identified for those of 30 min. It remains to be investigated whether this reverse correlation contributes to the ability of extracellular tachyzoites to reinvade host cells.
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Affiliation(s)
- Scott Roscoe
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B3P4, Canada
| | - Yue Guo
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B3P4, Canada
| | - Panayiotis O Vacratsis
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B3P4, Canada
| | - Sirinart Ananvoranich
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B3P4, Canada
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26
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Becker NA, Peters JP, James Maher L. High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria. Methods Mol Biol 2024; 2819:103-123. [PMID: 39028504 DOI: 10.1007/978-1-0716-3930-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The occurrence of DNA looping is ubiquitous. This process plays a well-documented role in the regulation of prokaryotic gene expression, such as in regulation of the Escherichia coli lactose (lac) operon. Here we present two complementary methods for high-resolution in vivo detection of DNA/protein binding within the bacterial nucleoid by using either chromatin immunoprecipitation combined with phage λ exonuclease digestion (ChIP-exo) or chromatin endogenous cleavage (ChEC), coupled with ligation-mediated polymerase chain reaction (LM-PCR) and Southern blot analysis. As an example, we apply these in vivo protein-mapping methods to E. coli to show direct binding of architectural proteins in the Lac repressor-mediated DNA repression loop.
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Affiliation(s)
- Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Department of Chemistry and Biochemistry, University of Northern Iowa, Cedar Falls, IA, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.
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27
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McKenzie AT, Nnadi O, Slagell KD, Thorn EL, Farrell K, Crary JF. Fluid preservation in brain banking: a review. FREE NEUROPATHOLOGY 2024; 5:5-10. [PMID: 38690035 PMCID: PMC11058410 DOI: 10.17879/freeneuropathology-2024-5373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Fluid preservation is nearly universally used in brain banking to store fixed tissue specimens for future research applications. However, the effects of long-term immersion on neural circuitry and biomolecules are not well characterized. As a result, there is a need to synthesize studies investigating fluid preservation of brain tissue. We searched PubMed and other databases to identify studies measuring the effects of fluid preservation in nervous system tissue. We categorized studies based on the fluid preservative used: formaldehyde solutions, buffer solutions, alcohol solutions, storage after tissue clearing, and cryoprotectant solutions. We identified 91 studies containing 197 independent observations of the effects of long-term storage on cellular morphology. Most studies did not report any significant alterations due to long-term storage. When present, the most frequent alteration was decreased antigenicity, commonly attributed to progressive crosslinking by aldehydes that renders biomolecules increasingly inaccessible over time. To build a mechanistic understanding, we discuss biochemical aspects of long-term fluid preservation. A subset of lipids appears to be chemical altered or extracted over time due to incomplete retention in the crosslinked gel. Alternative storage fluids mitigate the problem of antigen masking but have not been extensively characterized and may have other downsides. We also compare fluid preservation to cryopreservation, paraffin embedding, and resin embedding. Overall, existing evidence suggests that fluid preservation provides maintenance of neural architecture for decades, including precise structural details. However, to avoid the well-established problem of overfixation caused by storage in high concentration formaldehyde solutions, fluid preservation procedures can use an initial fixation step followed by an alternative long-term storage fluid. Further research is warranted on optimizing protocols and characterizing the generalizability of the storage artifacts that have been identified.
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Affiliation(s)
| | - Oge Nnadi
- Brain Preservation Foundation, Ashburn, Virginia, USA
| | - Kat D. Slagell
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma L. Thorn
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kurt Farrell
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John F. Crary
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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28
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Li K, Li Y, Nakamura F. Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin. Sci Rep 2023; 13:21723. [PMID: 38066085 PMCID: PMC10709462 DOI: 10.1038/s41598-023-49100-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
The contact inhibition of proliferation (CIP) denotes the cell density-dependent inhibition of growth, and the loss of CIP represents a hallmark of cancer. However, the mechanism by which CIP regulates gene expression remains poorly understood. Chromatin is a highly complex structure consisting of DNA, histones, and trans-acting factors (TAFs). The binding of TAF proteins to specific chromosomal loci regulates gene expression. Therefore, profiling chromatin is crucial for gaining insight into the gene expression mechanism of CIP. In this study, using modified proteomics of TAFs bound to DNA, we identified a protein that shuttles between the nucleus and cytosol in a cell density-dependent manner. We identified TIPARP, PTGES3, CBFB, and SMAD4 as cell density-dependent nucleocytoplasmic shuttling proteins. In low-density cells, these proteins predominantly reside in the nucleus; however, upon reaching high density, they relocate to the cytosol. Given their established roles in gene regulation, our findings propose their involvement as CIP-dependent TAFs. We also identified and characterized potential open chromatin regions sensitive to changes in cell density. These findings provide insights into the modulation of chromatin structure by CIP.
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Affiliation(s)
- Kangjing Li
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China
| | - Yaxin Li
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China
| | - Fumihiko Nakamura
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China.
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29
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Sarkar S, Saikia A, Kundu S. Transparent and Superhydrophilic Flexible Protein Films with Antifogging and Self-Cleaning Attributes. ACS APPLIED MATERIALS & INTERFACES 2023; 15:56397-56412. [PMID: 38011283 DOI: 10.1021/acsami.3c11100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Cyanoglycoside-modified flexible protein films, exhibiting a high level of transparency of ≈46 to 83%, were successfully prepared from lysozyme and glycerol with varying amounts of amygdalin (20, 40, and 60%) using water as a solvent. The increasing percentage of amygdalin leads to a drastic improvement of the hydrophilicity of the surface with a decrease in the water contact angle to 5.6°, resulting in superhydrophilicity. The increasing percentage of amygdalin led to a significant improvement in the surface's hydrophilicity, resulting in a reduced water contact angle of 5.6° and achieving superhydrophilicity. This superhydrophilic characteristic is particularly relevant to the excellent antifogging and self-cleaning properties of the resulting protein films. In addition to enhanced flexibility, the films also exhibited considerably improved thermal stability with a 40% loading of amygdalin in the protein solution. The superior mechanical, optical, and thermal properties of amygdalin-modified films are due to the strong hydrogen bonding with the peptides of lysozyme, as evidenced by the disappearance of amide bands in the cured protein films. Therefore, these transparent protein films, with their antifogging and enhanced thermal stability properties, can be potentially used for different packaging and coating applications.
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Affiliation(s)
- Sanu Sarkar
- Soft Nano Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
| | - Aditi Saikia
- Soft Nano Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
| | - Sarathi Kundu
- Soft Nano Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
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30
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Gaetano AJ, King RS. A simplified and rapid in situ hybridization protocol for planarians. Biotechniques 2023; 75:231-239. [PMID: 37851365 DOI: 10.2144/btn-2023-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
Whole-mount in situ hybridization is a critical technique for analyzing gene expression in planarians. While robust in situ protocols have been developed, these protocols are laborious, making them challenging to incorporate in an academic setting, reducing throughput and increasing time to results. Here, the authors systematically tested modifications to all phases of the protocol with the goal of eliminating steps and reducing time without impacting quality. This modified protocol allows for whole-mount colorimetric in situ hybridization and multicolor fluorescence in situ hybridization to be completed in two days with a significant reduction in steps and hands-on processing time.
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31
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Rua AJ, Whitehead RD, Alexandrescu AT. NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol X 2023; 8:100093. [PMID: 37655311 PMCID: PMC10465944 DOI: 10.1016/j.yjsbx.2023.100093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
ZNF750 is a nuclear transcription factor that activates skin differentiation and has tumor suppressor roles in several cancers. Unusually, ZNF750 has only a single zinc-finger (ZNF) domain, Z*, with an amino acid sequence that differs markedly from the CCHH family consensus. Because of its sequence differences Z* is classified as degenerate, presumed to have lost the ability to bind the zinc ion required for folding. AlphaFold predicts an irregular structure for Z* with low confidence. Low confidence predictions are often inferred to be intrinsically disordered regions of proteins, which would be the case if Z* did not bind Zn2+. We use NMR and CD spectroscopy to show that a 25-51 segment of ZNF750 corresponding to the Z* domain folds into a well-defined antiparallel ββα tertiary structure with a pM dissociation constant for Zn2+ and a thermal stability >80 °C. Of three alternative Zn2+ ligand sets, Z* uses a CCHC rather than the expected CCHH ligating motif. The switch in the last ligand maintains the folding topology and hydrophobic core of the classical ZNF motif. CCHC ZNFs are typically associated with protein-protein interactions, raising the possibility that ZNF750 interacts with DNA through other proteins rather than directly. The structure of Z* provides context for understanding the function of the domain and its cancer-associated mutations. We expect other ZNFs currently classified as degenerate could be CCHC-type structures like Z*.
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Affiliation(s)
- Antonio J. Rua
- Department of Molecular and Cellular Biology, University of Connecticut, United States
| | - Richard D. Whitehead
- Department of Molecular and Cellular Biology, University of Connecticut, United States
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32
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Zhang Z, Fan H, Richardson W, Gao BZ, Ye T. Management of autofluorescence in formaldehyde-fixed myocardium: choosing the right treatment. Eur J Histochem 2023; 67:3812. [PMID: 37781779 PMCID: PMC10614721 DOI: 10.4081/ejh.2023.3812] [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: 06/21/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Abstract
Autofluorescence (AF) poses challenges for detecting proteins of interest in situ when employing immunofluorescence (IF) microscopy. This interference is particularly pronounced in strongly autofluorescent tissues such as myocardium, where tissue AF can be comparable to IF. Although various histochemical methods have been developed to achieve effective AF suppression in different types of tissue, their applications on myocardial samples have not been well validated. Due to inconsistency across different autofluorescent structures in sometypes of tissue, it is unclear if these methods can effectively suppress AF across all autofluorescent structures within the myocardium. Here, we quantitatively evaluated the performance of several commonly used quenching treatments on formaldehyde-fixed myocardial samples, including 0.3 M glycine, 0.3% Sudan Black B (SBB), 0.1% and 1% sodium borohydride (NaBH4), TrueVIEW® and TrueBlack®. We further assessed their quenching performance by employing the pre-treatment and post-treatment protocols, designed to cover two common IF staining scenarios where buffers contained detergents or not. The results suggest that SBB and TrueBlack® outperform other reagents in AF suppression on formaldehyde-fixed myocardial samples in both protocols. Furthermore, we inspected the quenching performance of SBB and TrueBlack® on major autofluorescent myocardial structures and evaluated their influence on IF imaging. The results suggest that SBB outperforms TrueBlack® in quenching major autofluorescent structures, while TrueBlack® excels in preserving IF labeling signal. Surprisingly, we found the treatment of NaBH4 increased AF signal and enhanced the AF contrast of major autofluorescent structures. This finding suggests that NaBH4 has the potential to act as an AF enhancer and may facilitate the interpretation of myocardial structures without the need for counterstaining.
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Affiliation(s)
- Zhao Zhang
- Department of Bioengineering, Clemson University, Clemson, SC.
| | - Hongming Fan
- Department of Bioengineering, Clemson University, Clemson, SC.
| | - William Richardson
- Department of Chemical Engineering, University of Arkansas, Fayetteville, AR.
| | - Bruce Z Gao
- Department of Bioengineering, Clemson University, Clemson, SC.
| | - Tong Ye
- Department of Bioengineering, Clemson University, Clemson, SC; Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC.
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33
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Poceviciute R, Bogatyrev SR, Romano AE, Dilmore AH, Mondragón-Palomino O, Takko H, Pradhan O, Ismagilov RF. Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa. NPJ Biofilms Microbiomes 2023; 9:64. [PMID: 37679412 PMCID: PMC10485000 DOI: 10.1038/s41522-023-00423-2] [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: 08/25/2022] [Accepted: 07/31/2023] [Indexed: 09/09/2023] Open
Abstract
Because the small intestine (SI) epithelium lacks a thick protective mucus layer, microbes that colonize the thin SI mucosa may exert a substantial effect on the host. For example, bacterial colonization of the human SI may contribute to environmental enteropathy dysfunction (EED) in malnourished children. Thus far, potential bacterial colonization of the mucosal surface of the SI has only been documented in disease states, suggesting mucosal colonization is rare, likely requiring multiple perturbations. Furthermore, conclusive proof of bacterial colonization of the SI mucosal surface is challenging, and the three-dimensional (3D) spatial structure of mucosal colonies remains unknown. Here, we tested whether we could induce dense bacterial association with jejunum mucosa by subjecting mice to a combination of malnutrition and oral co-gavage with a bacterial cocktail (E. coli and Bacteroides spp.) known to induce EED. To visualize these events, we optimized our previously developed whole-tissue 3D imaging tools with third-generation hybridization chain reaction (HCR v3.0) probes. Only in mice that were malnourished and gavaged with the bacterial cocktail did we detect dense bacterial clusters surrounding intestinal villi suggestive of colonization. Furthermore, in these mice we detected villus loss, which may represent one possible consequence that bacterial colonization of the SI mucosa has on the host. Our results suggest that dense bacterial colonization of jejunum mucosa is possible in the presence of multiple perturbations and that whole-tissue 3D imaging tools can enable the study of these rare events.
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Affiliation(s)
- Roberta Poceviciute
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Said R Bogatyrev
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Medically Associated Science and Technology Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anna E Romano
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Amanda H Dilmore
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Biomedical Sciences Program, University of California San Diego, San Diego, CA, USA
| | - Octavio Mondragón-Palomino
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Heli Takko
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ojas Pradhan
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rustem F Ismagilov
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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34
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Wang K, Kumar T, Wang J, Minussi DC, Sei E, Li J, Tran TM, Thennavan A, Hu M, Casasent AK, Xiao Z, Bai S, Yang L, King LM, Shah V, Kristel P, van der Borden CL, Marks JR, Zhao Y, Zurita AJ, Aparicio A, Chapin B, Ye J, Zhang J, Gibbons DL, Sawyer E, Thompson AM, Futreal A, Hwang ES, Wesseling J, Lips EH, Navin NE. Archival single-cell genomics reveals persistent subclones during DCIS progression. Cell 2023; 186:3968-3982.e15. [PMID: 37586362 DOI: 10.1016/j.cell.2023.07.024] [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: 01/08/2023] [Revised: 05/09/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.
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Affiliation(s)
- Kaile Wang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tapsi Kumar
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junke Wang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Darlan Conterno Minussi
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Emi Sei
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianzhuo Li
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tuan M Tran
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aatish Thennavan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Min Hu
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anna K Casasent
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhenna Xiao
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shanshan Bai
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Yang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Lorraine M King
- Department of Surgery, Duke University School of Medicine, Durham, NC 27707, USA
| | - Vandna Shah
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London WC2R 2LS, UK
| | - Petra Kristel
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Carolien L van der Borden
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Jeffrey R Marks
- Department of Surgery, Duke University School of Medicine, Durham, NC 27707, USA
| | - Yuehui Zhao
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amado J Zurita
- Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Aparicio
- Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Brian Chapin
- Department of Urology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Ye
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ellinor Sawyer
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London WC2R 2LS, UK
| | - Alastair M Thompson
- Department of Surgery, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, NC 27707, USA
| | - Jelle Wesseling
- Department of Pathology, the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam 1066 CX, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Esther H Lips
- Department of Pathology, the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam 1066 CX, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Nicholas E Navin
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Bioinformatics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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Gutierrez-Bayona NE, Scruggs SS, Yang HC, Chai M, Gross ML, Taylor JS. Post- and Pre-Radiolabeling Assays for anti Thymidine Cyclobutane Dimers as Intrinsic Photoprobes of Various Types of G-Quadruplexes, Reverse Hoogsteen Hairpins, and Other Non-B DNA Structures. Biochemistry 2023; 62:2269-2279. [PMID: 37459251 PMCID: PMC10474795 DOI: 10.1021/acs.biochem.3c00155] [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] [Indexed: 08/02/2023]
Abstract
G-quadruplexes are thought to play an important role in gene regulation and telomere maintenance, but developing probes for their presence and location is challenging due to their transitory and highly dynamic nature. The majority of probes for G-quadruplexes have relied on antibody or small-molecule binding agents, many of which can also alter the dynamics and relative populations of G-quadruplexes. Recently, it was discovered that ultraviolet B (UVB) irradiation of human telomeric DNA and various G-quadruplex forming sequences found in human promoters, as well as reverse Hoogsteen hairpins, produces a unique class of non-adjacent anti cyclobutane pyrimidine dimers (CPDs). Therefore, one can envision using a pulse of UVB light to irreversibly trap these non-B DNA structures via anti CPD formation without perturbing their dynamics, after which the anti CPDs can be identified and mapped. As a first step toward this goal, we report radioactive post- and pre-labeling assays for the detection of non-adjacent CPDs and illustrate their use in detecting trans,anti T=(T) CPD formation in a human telomeric DNA sequence. Both assays make use of snake venom phosphodiesterase (SVP) to degrade the trans,anti T=(T) CPD-containing DNA to the tetranucleotide pTT=(pTT) corresponding to CPD formation between the underlined T's of two separate dinucleotides while degrading the adjacent syn TT CPDs to the trinucleotide pGT=T. In the post-labeling assay, calf intestinal phosphodiesterase is used to dephosphorylate the tetranucleotides, which are then rephosphorylated with kinase and [32P]-ATP to produce radiolabeled mono- and diphosphorylated tetranucleotides. The tetranucleotides are confirmed to be non-adjacent CPDs by 254 nm photoreversion to the dinucleotide p*TT. In the pre-labeling assay, radiolabeled phosphates are introduced into non-adjacent CPD-forming sites by ligation prior to irradiation, thereby eliminating the dephosphorylation and rephosphorylation steps. The assays are also demonstrated to detect the stereoisomeric cis,anti T=(T) CPD.
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Affiliation(s)
| | - Savannah S Scruggs
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
| | - Hsin-Chieh Yang
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
| | - Mengqi Chai
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
| | - John-Stephen Taylor
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, United States
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36
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Sallis S, Bérubé-Simard FA, Grondin B, Leduc E, Azouz F, Bélanger C, Pilon N. The CHARGE syndrome-associated protein FAM172A controls AGO2 nuclear import. Life Sci Alliance 2023; 6:e202302133. [PMID: 37221016 PMCID: PMC10205598 DOI: 10.26508/lsa.202302133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
CHARGE syndrome is a neural crest-related disorder mainly caused by mutation of the chromatin remodeler-coding gene CHD7 Alternative causes include mutation of other chromatin and/or splicing factors. One of these additional players is the poorly characterized FAM172A, which we previously found in a complex with CHD7 and the small RNA-binding protein AGO2 at the chromatin-spliceosome interface. Focusing on the FAM172A-AGO2 interplay, we now report that FAM172A is a direct binding partner of AGO2 and, as such, one of the long sought-after regulators of AGO2 nuclear import. We show that this FAM172A function mainly relies on its classical bipartite nuclear localization signal and associated canonical importin-α/β pathway, being enhanced by CK2-induced phosphorylation and abrogated by a CHARGE syndrome-associated missense mutation. Overall, this study thus strengthens the notion that noncanonical nuclear functions of AGO2 and associated regulatory mechanisms might be clinically relevant.
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Affiliation(s)
- Sephora Sallis
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
| | - Félix-Antoine Bérubé-Simard
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
| | - Benoit Grondin
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
| | - Elizabeth Leduc
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
| | - Fatiha Azouz
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
| | - Catherine Bélanger
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
| | - Nicolas Pilon
- Molecular Genetics of Development Laboratory, Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois, Université du Québec à Montréal, Montreal, Canada
- Department of Pediatrics, Université de Montréal, Montreal, Canada
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37
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Rua AJ, Whitehead Iii RD, Alexandrescu AT. WITHDRAWN: NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol 2023:108003. [PMID: 37487847 DOI: 10.1016/j.jsb.2023.108003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
This article was initially published in the Journal of Structural Biology, instead of the Journal of Structural Biology: X, due to a publisher error. We regret the inconvenience. The link to the article published in Journal of Structural Biology: X is presented below: https://www.sciencedirect.com/science/article/pii/S2590152423000090. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/policies/article-withdrawal.
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Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut
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38
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MacKenzie TMG, Cisneros R, Maynard RD, Snyder MP. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome. Cells 2023; 12:1860. [PMID: 37508524 PMCID: PMC10377898 DOI: 10.3390/cells12141860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a 'reverse-ChIP' approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a 'reverse-ChIP' technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.
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Affiliation(s)
| | - Rocío Cisneros
- Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA
| | - Rajan D Maynard
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Genetics Department, Stanford University, Stanford, CA 94305, USA
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39
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Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, Jiang S. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology. Nat Commun 2023; 14:4013. [PMID: 37419873 PMCID: PMC10329015 DOI: 10.1038/s41467-023-39616-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.
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Affiliation(s)
- Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - John-Paul Oliveria
- Department of Translational Medicine, Genentech, Inc., South San Francisco, CA, USA
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bryan J Cannon
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Darci Phillips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Christian M Schürch
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Samuel M Naik
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael B Miller
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Xavier Rovira-Clavé
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA.
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40
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Han J, Wang S, Wu H, Zhao T, Guan X, Fang L. An upgraded method of high-throughput chromosome conformation capture (Hi-C 3.0) in cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1223591. [PMID: 37469786 PMCID: PMC10353440 DOI: 10.3389/fpls.2023.1223591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
High-throughput chromosome conformation capture (Hi-C) technology has been applied to explore the chromatin interactions and shed light on the biological functions of three-dimensional genomic features. However, it remains challenging to guarantee the high quality of Hi-C library in plants and hence the reliable capture of chromatin structures, especially loops, due to insufficient fragmentation and low efficiency of proximity ligations. To overcome these deficiencies, we optimized the parameters of the Hi-C protocol, principally the cross-linking agents and endonuclease fragmentation strategy. The double cross-linkers (FA+DSG) and double restriction enzymes (DpnII+DdeI) were utilized. Thus, a systematic in situ Hi-C protocol was designed using plant tissues embedded with comprehensive quality controls to monitor the library construction. This upgraded method, termed Hi-C 3.0, was applied to cotton leaves for trial. In comparison with the conventional Hi-C 2.0, Hi-C 3.0 can obtain more than 50% valid contacts at a given sequencing depth to improve the signal-to-noise ratio. Hi-C 3.0 can furthermore enhance the capturing of loops almost as twice as that of Hi-C 2.0. In addition, Hi-C 3.0 showed higher efficiency of compartment detection and identified compartmentalization more accurately. In general, Hi-C 3.0 contributes to the advancement of the Hi-C method in plants by promoting its capability on decoding the chromatin organization.
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Affiliation(s)
- Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Siyuan Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hongyu Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
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41
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Ren Z, Takacs CN, Brandão HB, Jacobs-Wagner C, Wang X. Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi. PLoS Genet 2023; 19:e1010857. [PMID: 37494383 PMCID: PMC10406323 DOI: 10.1371/journal.pgen.1010857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/07/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/Smc. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that Smc and the Smc-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.
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Affiliation(s)
- Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Constantin N. Takacs
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Hugo B. Brandão
- Illumina Inc., 5200 Illumina Way, San Diego, California, United States of America
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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Cherney RE, Mills CA, Herring LE, Braceros AK, Calabrese JM. A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB. Biol Open 2023; 12:bio059955. [PMID: 37283223 PMCID: PMC10259849 DOI: 10.1242/bio.059955] [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: 04/03/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
The Polycomb Repressive Complex 2 (PRC2) is a conserved enzyme that tri-methylates Lysine 27 on Histone 3 (H3K27me3) to promote gene silencing. PRC2 is remarkably responsive to the expression of certain long noncoding RNAs (lncRNAs). In the most notable example, PRC2 is recruited to the X-chromosome shortly after expression of the lncRNA Xist begins during X-chromosome inactivation. However, the mechanisms by which lncRNAs recruit PRC2 to chromatin are not yet clear. We report that a broadly used rabbit monoclonal antibody raised against human EZH2, a catalytic subunit of PRC2, cross-reacts with an RNA-binding protein called Scaffold Attachment Factor B (SAFB) in mouse embryonic stem cells (ESCs) under buffer conditions that are commonly used for chromatin immunoprecipitation (ChIP). Knockout of EZH2 in ESCs demonstrated that the antibody is specific for EZH2 by western blot (no cross-reactivity). Likewise, comparison to previously published datasets confirmed that the antibody recovers PRC2-bound sites by ChIP-Seq. However, RNA-IP from formaldehyde-crosslinked ESCs using ChIP wash conditions recovers distinct peaks of RNA association that co-localize with peaks of SAFB and whose enrichment disappears upon knockout of SAFB but not EZH2. IP and mass spectrometry-based proteomics in wild-type and EZH2 knockout ESCs confirm that the EZH2 antibody recovers SAFB in an EZH2-independent manner. Our data highlight the importance of orthogonal assays when studying interactions between chromatin-modifying enzymes and RNA.
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Affiliation(s)
- Rachel E. Cherney
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- RNA Discovery Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - Christine A. Mills
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Proteomics Core Facility, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - Laura E. Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Proteomics Core Facility, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - Aki K. Braceros
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- RNA Discovery Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Curriculum in Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - J. Mauro Calabrese
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- RNA Discovery Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
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43
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Veenstra BT, Veenstra TD. Proteomic applications in identifying protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:1-48. [PMID: 38220421 DOI: 10.1016/bs.apcsb.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
There are many things that can be used to characterize a protein. Size, isoelectric point, hydrophobicity, structure (primary to quaternary), and subcellular location are just a few parameters that are used. The most important feature of a protein, however, is its function. While there are many experiments that can indicate a protein's role, identifying the molecules it interacts with is probably the most definitive way of determining its function. Owing to technology limitations, protein interactions have historically been identified on a one molecule per experiment basis. The advent of high throughput multiplexed proteomic technologies in the 1990s, however, made identifying hundreds and thousands of proteins interactions within single experiments feasible. These proteomic technologies have dramatically increased the rate at which protein-protein interactions (PPIs) are discovered. While the improvement in mass spectrometry technology was an early driving force in the rapid pace of identifying PPIs, advances in sample preparation and chromatography have recently been propelling the field. In this chapter, we will discuss the importance of identifying PPIs and describe current state-of-the-art technologies that demonstrate what is currently possible in this important area of biological research.
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Affiliation(s)
- Benjamin T Veenstra
- Department of Math and Sciences, Cedarville University, Cedarville, OH, United States
| | - Timothy D Veenstra
- School of Pharmacy, Cedarville University, Cedarville, OH, United States.
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44
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Siris S, Gladstone CA, Guo Y, Patel R, Pinder CL, Shattock RJ, McKay PF, Langford PR, Bidmos FA. Increasing human monoclonal antibody cloning efficiency with a whole-cell modified immunoglobulin-capture assay (mICA). Front Immunol 2023; 14:1184510. [PMID: 37334357 PMCID: PMC10272928 DOI: 10.3389/fimmu.2023.1184510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
Expression cloning of fully human monoclonal antibodies (hmAbs) is seeing powerful utility in the field of vaccinology, especially for elucidating vaccine-induced B-cell responses and novel vaccine candidate antigen discovery. Precision of the hmAb cloning process relies on efficient isolation of hmAb-producing plasmablasts of interest. Previously, a novel immunoglobulin-capture assay (ICA) was developed, using single protein vaccine antigens, to enhance the pathogen-specific hmAb cloning output. Here, we report a novel modification of this single-antigen ICA using formalin-treated, fluorescently stained whole cell suspensions of the human bacterial invasive pathogens, Streptococcus pneumoniae and Neisseria meningitidis. Sequestration of IgG secreted by individual vaccine antigen-specific plasmablasts was achieved by the formation of an anti-CD45-streptavidin and biotin anti-IgG scaffold. Suspensions containing heterologous pneumococcal and meningococcal strains were then used to enrich for polysaccharide- and protein antigen-specific plasmablasts, respectively, during single cell sorting. Following application of the modified whole-cell ICA (mICA), ~61% (19/31) of anti-pneumococcal polysaccharide hmAbs were cloned compared to 14% (8/59) obtained using standard (non-mICA) methods - representing a ~4.4-fold increase in hmAb cloning precision. A more modest ~1.7-fold difference was obtained for anti-meningococcal vaccine hmAb cloning; ~88% of hmAbs cloned via mICA versus ~53% cloned via the standard method were specific for a meningococcal surface protein. VDJ sequencing revealed that cloned hmAbs reflected an anamnestic response to both pneumococcal and meningococcal vaccines; diversification within hmAb clones occurred by positive selection for replacement mutations. Thus, we have shown successful utilization of whole bacterial cells in the ICA protocol enabling isolation of hmAbs targeting multiple disparate epitopes, thereby increasing the power of approaches such as reverse vaccinology 2.0 (RV 2.0) for bacterial vaccine antigen discovery.
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Affiliation(s)
- Sara Siris
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Camilla A. Gladstone
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Yanping Guo
- Flow Cytometry Core Facility, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Radhika Patel
- Flow Cytometry Core Facility, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Christopher L. Pinder
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Robin J. Shattock
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul F. McKay
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul R. Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Fadil A. Bidmos
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
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45
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Kim A, Martinez-Valbuena I, Li J, Lang AE, Kovacs GG. Disease-Specific α-Synuclein Seeding in Lewy Body Disease and Multiple System Atrophy Are Preserved in Formaldehyde-Fixed Paraffin-Embedded Human Brain. Biomolecules 2023; 13:936. [PMID: 37371515 DOI: 10.3390/biom13060936] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Recent studies have been able to detect α-synuclein (αSyn) seeding in formaldehyde-fixed paraffin-embedded (FFPE) tissues from patients with synucleinopathies using seed amplification assays (SAAs), but with relatively low sensitivity due to limited protein extraction efficiency. With the aim of introducing an alternative option to frozen tissues, we developed a streamlined protein extraction protocol for evaluating disease-specific seeding in FFPE human brain. We evaluated the protein extraction efficiency of different tissue preparations, deparaffinizations, and protein extraction buffers using formaldehyde-fixed and FFPE tissue of a single Lewy body disease (LBD) subject. Alternatively, we incorporated heat-induced antigen retrieval and dissociation using a commercially available kit. Our novel protein extraction protocol has been optimized to work with 10 sections of 4.5-µm-thickness or 2-mm-diameter micro-punch of FFPE tissue that can be used to seed SAAs. We demonstrated that extracted proteins from FFPE still preserve seeding potential and further show disease-specific seeding in LBD and multiple system atrophy. To the best of our knowledge, our study is the first to recapitulate disease-specific αSyn seeding behaviour in FFPE human brain. Our findings open new perspectives in re-evaluating archived human brain tissue, extending the disease-specific seeding assays to larger cohorts to facilitate molecular subtyping of synucleinopathies.
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Affiliation(s)
- Ain Kim
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ivan Martinez-Valbuena
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
- Krembil Brain Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Jun Li
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
| | - Anthony E Lang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
- Krembil Brain Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON M5T 2S6, Canada
| | - Gabor G Kovacs
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Krembil Brain Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON M5T 2S6, Canada
- Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
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46
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Marine polysaccharide-based hydrogels for critical materials selective removal and recovery: A review. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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47
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Ghimici L, Ghiorghiță CA, Năfureanu MM. Abatement of some commercial fungicide content from model dispersions by a new thiourea-graft-polyethyleneimine derivative. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:67539-67551. [PMID: 37115448 DOI: 10.1007/s11356-023-27260-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/23/2023] [Indexed: 05/25/2023]
Abstract
A new derivative of polyethyleneimine (PEI) with 9% degree of substitution of its primary and secondary amino groups with thiourea moieties (TU9-PEI) has been synthesized and investigated as flocculant in model suspensions of commercial fungicide formulations Dithane M45, Melody Compact 49 WG, Cabrio®Top, and their mixtures. The structure of TU9-PEI, obtained by an aqueous one-pot strategy involving formaldehyde mediated coupling of PEI and TU, was confirmed by FTIR and 1H NMR spectroscopy as well as the streaming potential measurements. The settling time, polymer dose, and fungicide type and concentration were the parameters used for assessing the flocculation ability of the new polycation sample. The UV-Vis spectroscopy measurements revealed a good removal efficiency of TU9-PEI for all of the fungicides investigated, between 88 and 94%. Slightly higher removal percent was found for greater fungicide concentrations. The charge neutralization was indicated by zeta potential measurements (values close to zero recorded at the optimum polymer dose) as the main mechanism which contributed to the Dithane and Cabrio®Top particle removal and a combined effect of the TU9-PEI/fungicide particle electrostatic attractions and hydrogen bonds between both the amine and thiourea groups of the polycation chains and the hydroxyl ones on the copper oxychloride particles (negative values) in case of the Melody Compact 49 WG particle separation. Particle size and surface morphology analysis data gave supplementary evidences regarding the TU9-PEI ability to separate the fungicides investigated from simulated wastewater.
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Affiliation(s)
- Luminita Ghimici
- "Petru Poni" Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487, Iasi, Romania.
| | | | - Maria-Magdalena Năfureanu
- "Petru Poni" Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487, Iasi, Romania
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48
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Guo AD, Yan KN, Hu H, Zhai L, Hu TF, Su H, Chi Y, Zha J, Xu Y, Zhao D, Lu X, Xu YJ, Zhang J, Tan M, Chen XH. Spatiotemporal and global profiling of DNA-protein interactions enables discovery of low-affinity transcription factors. Nat Chem 2023:10.1038/s41557-023-01196-z. [PMID: 37106095 DOI: 10.1038/s41557-023-01196-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
Precise dissection of DNA-protein interactions is essential for elucidating the recognition basis, dynamics and gene regulation mechanism. However, global profiling of weak and dynamic DNA-protein interactions remains a long-standing challenge. Here, we establish the light-induced lysine (K) enabled crosslinking (LIKE-XL) strategy for spatiotemporal and global profiling of DNA-protein interactions. Harnessing unique abilities to capture weak and transient DNA-protein interactions, we demonstrate that LIKE-XL enables the discovery of low-affinity transcription-factor/DNA interactions via sequence-specific DNA baits, determining the binding sites for transcription factors that have been previously unknown. More importantly, we successfully decipher the dynamics of the transcription factor subproteome in response to drug treatment in a time-resolved manner, and find downstream target transcription factors from drug perturbations, providing insight into their dynamic transcriptional networks. The LIKE-XL strategy offers a complementary method to expand the DNA-protein profiling toolbox and map accurate DNA-protein interactomes that were previously inaccessible via non-covalent strategies, for better understanding of protein function in health and disease.
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Affiliation(s)
- An-Di Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke-Nian Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Teng-Fei Hu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yijia Chi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyin Zha
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dongxin Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Jiang Xu
- School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Jian Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China.
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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49
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Liu J, Duan Q, Shao Z, Chen K, Zhu Y, Li J, Tan W. Formaldehyde Cross-Linking-Assisted Phase Separation for Protein Aptamer Selection. Anal Chem 2023; 95:6700-6708. [PMID: 37052573 DOI: 10.1021/acs.analchem.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
With the merits of easy synthesis, strong modifiability, and high affinity, aptamers have been broadly applied for protein targeting in bioanalysis, diagnosis, and therapeutics. The selection of protein-targeted aptamers is currently largely dependent on solid-liquid separation by using different types of nano- or micro-beads. However, the use of beads inescapably introduces unwanted nonspecific binding and thus affects selection efficiency. In order to sidestep this obstacle, we herein report an integrated technique to facilitate the discovery and development of protein-targeting aptamers by incorporating formaldehyde cross-linking with phase separation (FCPS). The feasibility and universality of FCPS were confirmed by the successful selection of two aptamers that could target various antibodies. Unlike traditional approaches, the proposed technique avoids the use of beads and enables the rapid generation of aptamers after only one to three rounds of selection. The as-selected aptamers were further used to regulate and control antibody activity, showing potential applications in biomedicine.
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Affiliation(s)
- Jia Liu
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiao Duan
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhentao Shao
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Kaiming Chen
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yingdi Zhu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Juan Li
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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50
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Cherney RE, Mills CA, Herring LE, Braceros AK, Calabrese JM. A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535391. [PMID: 37066147 PMCID: PMC10103960 DOI: 10.1101/2023.04.03.535391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The Polycomb Repressive Complex 2 (PRC2) is a conserved enzyme that tri-methylates Lysine 27 on Histone 3 (H3K27me3) to promote gene silencing. PRC2 is remarkably responsive to the expression of certain long noncoding RNAs (lncRNAs). In the most notable example, PRC2 is recruited to the X-chromosome shortly after expression of the lncRNA Xist begins during X-chromosome inactivation. However, the mechanisms by which lncRNAs recruit PRC2 to chromatin are not yet clear. We report that a broadly used rabbit monoclonal antibody raised against human EZH2, a catalytic subunit of PRC2, cross-reacts with an RNA-binding protein called Scaffold Attachment Factor B (SAFB) in mouse embryonic stem cells (ESCs) under buffer conditions that are commonly used for chromatin immunoprecipitation (ChIP). Knockout of EZH2 in ESCs demonstrated that the antibody is specific for EZH2 by western blot (no cross-reactivity). Likewise, comparison to previously published datasets confirmed that the antibody recovers PRC2-bound sites by ChIP-Seq. However, RNA-IP from formaldehyde-crosslinked ESCs using ChIP wash conditions recovers distinct peaks of RNA association that co-localize with peaks of SAFB and whose enrichment disappears upon knockout of SAFB but not EZH2. IP and mass spectrometry-based proteomics in wild-type and EZH2 knockout ESCs confirm that the EZH2 antibody recovers SAFB in an EZH2-independent manner. Our data highlight the importance of orthogonal assays when studying interactions between chromatin-modifying enzymes and RNA.
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