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Dong F, Sun X, Su J, Li Q, He Y, Li W, Wang B, Wang B, Xu G, Wu X. Hypoxia-inducible PRMT2 addiction in glioblastomas. Cell Signal 2024; 117:111094. [PMID: 38341123 DOI: 10.1016/j.cellsig.2024.111094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Hypoxia-inducible transcription factors (HIFs) are key transcription factors for cellular response to low oxygen levels. However, the specific mediators responsible for activating downstream transcription are not well characterized. We previously identified Protein Arginine methyltransferase 2 (PRMT2), a highly expressed methyltransferase in glioblastoma multiforme, as a transcription co-activator. And we established a connection between PRMT2-mediated histone H3R8 asymmetric methylation (H3R8me2a) and transcription activation. Here we find that PRMT2 is activated by HIF1α under hypoxic conditions. And we demonstrate that PRMT2 and its H3R8me2a activity are required for the transcription activation of a significant subset of hypoxia-induced genes. Consequently, the inactivation of PRMT2 suppresses hypoxia-induced glioblastoma cell migration, attenuates tumor progression, and enhances chemotherapeutic sensitivity in mouse xenograft models. In addition, our analysis of clinical glioma specimens reveals a correlation between PRMT2 protein levels, HIF1α abundance, and an unfavorable prognosis. Our study establishes HIF1α-induced PRMT2 as a critical modulator in the activation of hypoxia-related transcriptional programs, ultimately driving malignant progression.
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Affiliation(s)
- Feng Dong
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, School of Biomedical Engineering & Technology, Tianjin Medical University, Tianjin 300070, China; Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Xiaoyu Sun
- Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Jiacheng Su
- Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Qian Li
- Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - You He
- Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Wei Li
- Department of Pathology, Tianjin First Central Hospital, Tianjin 300192, China
| | - Baofeng Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Bo Wang
- Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative diseases, Tianjin Neurosurgical Institute, No. 6 Jizhao Road, Tianjin 300350, China
| | - Guogang Xu
- Health Management Institute, The Second Medical Center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing 100853, China.
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, School of Biomedical Engineering & Technology, Tianjin Medical University, Tianjin 300070, China; Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China; Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China.
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Bairamukov VY, Kovalev RA, Ankudinov AV, Pantina RA, Fedorova ND, Bukatin AS, Grigoriev SV, Varfolomeeva EY. Alterations in the chromatin packaging, driven by transcriptional activity, revealed by AFM. Biochim Biophys Acta Gen Subj 2024; 1868:130568. [PMID: 38242181 DOI: 10.1016/j.bbagen.2024.130568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND The gene expression differs in the nuclei of normal and malignant mammalian cells, and transcription is a critical initial step, which defines the difference. The mechanical properties of transcriptionally active chromatin are still poorly understood. Recently we have probed transcriptionally active chromatin of the nuclei subjected to mechanical stress, by Atomic Force Microscopy (AFM) [1]. Nonetheless, a systematic study of the phenomenon is needed. METHODS Nuclei were deformed and studied by AFM. Non-deformed nuclei were studied by fluorescence confocal microscopy. Their transcriptional activity was studied by RNA electrophoresis. RESULTS The malignant nuclei under the study were stable to deformation and assembled of 100-300 nm beads-like units, while normal cell nuclei were prone to deformation. The difference in stability to deformation of the nuclei correlated with DNA supercoiling, and transcription-depended units were responsive to supercoils breakage. The inhibitors of the topoisomerases I and II disrupted supercoiling and made the malignant nucleus prone to deformation. Cell nuclei treatment with histone deacetylase inhibitors (HDACIs) preserved the mechanical stability of deformed malignant nuclei and, at the same time, made it possible to observe chromatin decondensation up to 20-60 nm units. The AFM results were supplemented with confocal microscopy and RNA electrophoresis data. CONCLUSIONS Self-assembly of transcriptionally active chromatin and its decondensation, driven by DNA supercoiling-dependent rigidity, was visualized by AFM in the mechanically deformed nuclei. GENERAL SIGNIFICANCE We demonstrated that supercoiled DNA defines the transcription mechanics, and hypothesized the nuclear mechanics in vivo should depend on the chromatin architecture.
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Affiliation(s)
- V Yu Bairamukov
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia.
| | - R A Kovalev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - A V Ankudinov
- The Ioffe Physical-Technical Institute of the Russian Academy of Sciences, 26, Politekhnicheskaya, 194021 Saint Petersburg, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - N D Fedorova
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - A S Bukatin
- Alferov Saint Petersburg National Research Academic University of the Russian Academy of Sciences, 8/3, Khlopina St., 194021 Saint Petersburg, Russia
| | - S V Grigoriev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
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Koestler SA, Ball ML, Muresan L, Dinakaran V, White R. Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters. Epigenetics Chromatin 2024; 17:8. [PMID: 38528624 DOI: 10.1186/s13072-024-00535-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/14/2024] [Indexed: 03/27/2024] Open
Abstract
Chromatin state is thought to impart regulatory function to the underlying DNA sequence. This can be established through histone modifications and chromatin organisation, but exactly how these factors relate to one another to regulate gene expression is unclear. In this study, we have used super-resolution microscopy to image the Y loops of Drosophila melanogaster primary spermatocytes, which are enormous transcriptionally active chromatin fibres, each representing single transcription units that are individually resolvable in the nuclear interior. We previously found that the Y loops consist of regular clusters of nucleosomes, with an estimated median of 54 nucleosomes per cluster with wide variation.In this study, we report that the histone modifications H3K4me3, H3K27me3, and H3K36me3 are also clustered along the Y loops, with H3K4me3 more associated with diffuse chromatin compared to H3K27me3. These histone modifications form domains that can be stretches of Y loop chromatin micrometres long, or can be in short alternating domains. The different histone modifications are associated with different sizes of chromatin clusters and unique morphologies. Strikingly, a single chromatin cluster almost always only contains only one type of the histone modifications that were labelled, suggesting exclusivity, and therefore regulation at the level of individual chromatin clusters. The active mark H3K36me3 is more associated with actively elongating RNA polymerase II than H3K27me3, with polymerase often appearing on what are assumed to be looping regions on the periphery of chromatin clusters.These results provide a foundation for understanding the relationship between chromatin state, chromatin organisation, and transcription regulation - with potential implications for pause-release dynamics, splicing complex organisation and chromatin dynamics during polymerase progression along a gene.
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Affiliation(s)
- Stefan A Koestler
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK
| | - Madeleine L Ball
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK
| | - Leila Muresan
- Cambridge Advanced Imaging Centre, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK
| | - Vineet Dinakaran
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge, CB2 3DY, UK.
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Liu SX, Ramakrishnan A, Shen L, Gewirtz JC, Georgieff MK, Tran PV. Chromatin accessibility and H3K9me3 landscapes reveal long-term epigenetic effects of fetal-neonatal iron deficiency in rat hippocampus. BMC Genomics 2024; 25:301. [PMID: 38515015 PMCID: PMC10956188 DOI: 10.1186/s12864-024-10230-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Iron deficiency (ID) during the fetal-neonatal period results in long-term neurodevelopmental impairments associated with pervasive hippocampal gene dysregulation. Prenatal choline supplementation partially normalizes these effects, suggesting an interaction between iron and choline in hippocampal transcriptome regulation. To understand the regulatory mechanisms, we investigated epigenetic marks of genes with altered chromatin accessibility (ATAC-seq) or poised to be repressed (H3K9me3 ChIP-seq) in iron-repleted adult rats having experienced fetal-neonatal ID exposure with or without prenatal choline supplementation. RESULTS Fetal-neonatal ID was induced by limiting maternal iron intake from gestational day (G) 2 through postnatal day (P) 7. Half of the pregnant dams were given supplemental choline (5.0 g/kg) from G11-18. This resulted in 4 groups at P65 (Iron-sufficient [IS], Formerly Iron-deficient [FID], IS with choline [ISch], and FID with choline [FIDch]). Hippocampi were collected from P65 iron-repleted male offspring and analyzed for chromatin accessibility and H3K9me3 enrichment. 22% and 24% of differentially transcribed genes in FID- and FIDch-groups, respectively, exhibited significant differences in chromatin accessibility, whereas 1.7% and 13% exhibited significant differences in H3K9me3 enrichment. These changes mapped onto gene networks regulating synaptic plasticity, neuroinflammation, and reward circuits. Motif analysis of differentially modified genomic sites revealed significantly stronger choline effects than early-life ID and identified multiple epigenetically modified transcription factor binding sites. CONCLUSIONS This study reveals genome-wide, stable epigenetic changes and epigenetically modifiable gene networks associated with specific chromatin marks in the hippocampus, and lays a foundation to further elucidate iron-dependent epigenetic mechanisms that underlie the long-term effects of fetal-neonatal ID, choline, and their interactions.
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Affiliation(s)
- Shirelle X Liu
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Psychology, University of Minnesota, Minneapolis, MN, 55455, USA
| | | | - Li Shen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jonathan C Gewirtz
- Department of Psychology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael K Georgieff
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Phu V Tran
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA.
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Atanasoff-Kardjalieff AK, Berger H, Steinert K, Janevska S, Ponts N, Humpf HU, Kalinina S, Studt-Reinhold L. Incorporation of the histone variant H2A.Z counteracts gene silencing mediated by H3K27 trimethylation in Fusarium fujikuroi. Epigenetics Chromatin 2024; 17:7. [PMID: 38509556 PMCID: PMC10953111 DOI: 10.1186/s13072-024-00532-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Fusarium fujikuroi is a pathogen of rice causing diverse disease symptoms such as 'bakanae' or stunting, most likely due to the production of various natural products (NPs) during infection. Fusaria have the genetic potential to synthesize a plethora of these compounds with often diverse bioactivity. The capability to synthesize NPs exceeds the number of those being produced by far, implying a gene regulatory network decisive to induce production. One such regulatory layer is the chromatin structure and chromatin-based modifications associated with it. One prominent example is the exchange of histones against histone variants such as the H2A variant H2A.Z. Though H2A.Z already is well studied in several model organisms, its regulatory functions are not well understood. Here, we used F. fujikuroi as a model to explore the role of the prominent histone variant FfH2A.Z in gene expression within euchromatin and facultative heterochromatin. RESULTS Through the combination of diverse '-omics' methods, we show the global distribution of FfH2A.Z and analyze putative crosstalks between the histone variant and two prominent histone marks, i.e., H3K4me3 and H3K27me3, important for active gene transcription and silencing, respectively. We demonstrate that, if FfH2A.Z is positioned at the + 1-nucleosome, it poises chromatin for gene transcription, also within facultative heterochromatin. Lastly, functional characterization of FfH2A.Z overexpression and depletion mutants revealed that FfH2A.Z is important for wild type-like fungal development and secondary metabolism. CONCLUSION In this study, we show that the histone variant FfH2A.Z is a mark of positive gene transcription and acts independently of the chromatin state most likely through the stabilization of the + 1-nucleosome. Furthermore, we demonstrate that FfH2A.Z depletion does not influence the establishment of both H3K27me3 and H3K4me3, thus indicating no crosstalk between FfH2A.Z and both histone marks. These results highlight the manifold functions of the histone variant FfH2A.Z in the phytopathogen F. fujikuroi, which are distinct regarding gene transcription and crosstalk with the two prominent histone marks H3K27me3 and H3K4me3, as proposed for other model organisms.
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Affiliation(s)
- Anna K Atanasoff-Kardjalieff
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz Strasse 24, Tulln an der Donau, 3430, Austria
| | - Harald Berger
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz Strasse 24, Tulln an der Donau, 3430, Austria
| | - Katharina Steinert
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Slavica Janevska
- (Epi-)Genetic Regulation of Fungal Virulence, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, 07745, Jena, Germany
| | - Nadia Ponts
- INRAE, UR1264 Mycology and Food Safety (MycSA), Villenave d'Ornon, 33882, France
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Svetlana Kalinina
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz Strasse 24, Tulln an der Donau, 3430, Austria.
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6
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Samuels TJ, Gui J, Gebert D, Karam Teixeira F. Two distinct waves of transcriptome and translatome changes drive Drosophila germline stem cell differentiation. EMBO J 2024:10.1038/s44318-024-00070-z. [PMID: 38480936 DOI: 10.1038/s44318-024-00070-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/18/2024] Open
Abstract
The tight control of fate transitions during stem cell differentiation is essential for proper tissue development and maintenance. However, the challenges in studying sparsely distributed adult stem cells in a systematic manner have hindered efforts to identify how the multilayered regulation of gene expression programs orchestrates stem cell differentiation in vivo. Here, we synchronised Drosophila female germline stem cell (GSC) differentiation in vivo to perform in-depth transcriptome and translatome analyses at high temporal resolution. This characterisation revealed widespread and dynamic changes in mRNA level, promoter usage, exon inclusion, and translation efficiency. Transient expression of the master regulator, Bam, drives a first wave of expression changes, primarily modifying the cell cycle program. Surprisingly, as Bam levels recede, differentiating cells return to a remarkably stem cell-like transcription and translation program, with a few crucial changes feeding into a second phase driving terminal differentiation to form the oocyte. Altogether, these findings reveal that rather than a unidirectional accumulation of changes, the in vivo differentiation of stem cells relies on distinctly regulated and developmentally sequential waves.
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Affiliation(s)
- Tamsin J Samuels
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK
| | - Jinghua Gui
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK
| | - Daniel Gebert
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK
| | - Felipe Karam Teixeira
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK.
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7
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Philips SJ, Danda A, Ansari AZ. Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review. Methods 2024; 225:20-27. [PMID: 38471600 DOI: 10.1016/j.ymeth.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Aberrant gene expression underlies numerous human ailments. Hence, developing small molecules to target and remedy dysfunctional gene regulation has been a long-standing goal at the interface of chemistry and medicine. A major challenge for designing small molecule therapeutics aimed at targeting desired genomic loci is the minimization of widescale disruption of genomic functions. To address this challenge, we rationally design polyamide-based multi-functional molecules, i.e., Synthetic Genome Readers/Regulators (SynGRs), which, by design, target distinct sequences in the genome. Herein, we briefly review how SynGRs access chromatin-bound and chromatin-free genomic sites, then highlight the methods for the study of chromatin processes using SynGRs on positioned nucleosomes in vitro or disease-causing repressive genomic loci in vivo.
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Affiliation(s)
- Steven J Philips
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adithi Danda
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aseem Z Ansari
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Raphael HE, Hassan GF, Osorio OA, Cohen LS, Payne MD, Katz-Kiriakos E, Tata I, Hicks J, Byers DE, Zhang B, Alexander-Brett J. Activator protein transcription factors coordinate human IL-33 expression from noncanonical promoters in chronic airway disease. JCI Insight 2024; 9:e174786. [PMID: 38456508 DOI: 10.1172/jci.insight.174786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/22/2024] [Indexed: 03/09/2024] Open
Abstract
IL-33 is a cytokine central to type 2 immune pathology in chronic airway disease. This cytokine is abundantly expressed in the respiratory epithelium and increased in disease, but how expression is regulated is undefined. Here we show that increased IL33 expression occurs from multiple noncanonical promoters in human chronic obstructive pulmonary disease (COPD), and it facilitates production of alternatively spliced isoforms in airway cells. We found that phorbol 12-myristate 13-acetate (PMA) can activate IL33 promoters through protein kinase C in primary airway cells and lines. Transcription factor (TF) binding arrays combined with RNA interference identified activator protein (AP) TFs as regulators of baseline and induced IL33 promoter activity. ATAC-Seq and ChIP-PCR identified chromatin accessibility and differential TF binding as additional control points for transcription from noncanonical promoters. In support of a role for these TFs in COPD pathogenesis, we found that AP-2 (TFAP2A, TFAP2C) and AP-1 (FOS and JUN) family members are upregulated in human COPD specimens. This study implicates integrative and pioneer TFs in regulating IL33 promoters and alternative splicing in human airway basal cells. Our work reveals a potentially novel approach for targeting IL-33 in development of therapeutics for COPD.
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Affiliation(s)
- Heather E Raphael
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Ghandi F Hassan
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Omar A Osorio
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Lucy S Cohen
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Morgan D Payne
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Ella Katz-Kiriakos
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Ishana Tata
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Jamie Hicks
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Derek E Byers
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Bo Zhang
- Department of Developmental Biology, and
| | - Jen Alexander-Brett
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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Wang CS, Fang GZ, Li XP, Huang GY, Xie L, Ying GG. Combined effects of binary mixtures of 17β-estradiol and testosterone in western mosquitofish (Gambusia affinis) after full life-cycle exposure. Comp Biochem Physiol C Toxicol Pharmacol 2024; 280:109887. [PMID: 38460577 DOI: 10.1016/j.cbpc.2024.109887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/04/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Estrogens and androgens are typical steroid hormones and often occur together in contaminated aquatic environments, but their mixed effects in aquatic organisms have been less well reported. In this study, the endocrine disrupting effects of binary mixtures of 17β-estradiol (E2) and testosterone (T) in western mosquitofish (Gambusia affinis) were assessed by analyzing the sex ratio, secondary sex characteristics, gonadal histology, and transcriptional expression of target genes related to the hypothalamic-pituitary-gonadal (HPG) axis in G. affinis (from embryos) continuously exposed to E2 (50 ng/L), T (T1: 50 ng/L; T2: 200 ng/L), and mixtures of both (E2 + T1: 50 + 50 ng/L; E2 + T2: 50 + 200 ng/L) for 119 d. The results showed that exposure to E2 + T1 and E2 + T2 reduced the length ratio of ray 4/6 ratio in male G. affinis, suggesting feminized phenomenon in male G. affinis. Furthermore, 16.7-38.5 % of female G. affinis showed masculinized anal fins and hemal spines when exposed to T alone and in combination with E2. Importantly, the transcriptional levels of certain target genes related to the HPG axis were significantly altered in G. affinis following exposure to E2 and T alone and in combinations. Moreover, exposure to E2 and T in combinations can lead to combined effects (such as synergistic and antagonistic effects) on the transcriptional levels of some genes. These results collectively suggest that exposure to environmentally relevant concentrations of E2 and T alone and in mixtures can impact the endocrine system of G. affinis, and may pose potential risks in aquatic systems.
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Affiliation(s)
- Chen-Si Wang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Gui-Zhen Fang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Xiao-Pei Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guo-Yong Huang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
| | - Lingtian Xie
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
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10
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Kala M, Babok S, Mikhailava N, Piirsoo M, Piirsoo A. The POU-HD TFs impede the replication efficiency of several human papillomavirus genomes. Virol J 2024; 21:54. [PMID: 38444021 PMCID: PMC10916165 DOI: 10.1186/s12985-024-02334-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
Human papillomavirus (HPV) is a double-stranded DNA virus that infects cutaneous and mucosal epithelial cells. HPV replication initiates at the origin (ori), located within a noncoding region near the major early promoter. Only two viral proteins, E1 and E2, are essential for replication, with the host cell contributing other necessary factors. However, the role of host cell proteins in regulating HPV replication remains poorly understood. While several binding sites for cellular transcription factors (TFs), such as POU-HD proteins, have been mapped in the regulatory region, their functional importance is unclear. Some POU-HD TFs have been shown to influence replication in a system where E1 and E2 are provided exogenously. In this study, we investigated the impact of several POU-HD TFs on the replication of the HPV5, HPV11, and HPV18 genomes in U2OS cells and human primary keratinocytes. We demonstrated that OCT1, OCT6, BRN5A, and SKN1A are expressed in HPV host cells and that their overexpression inhibits HPV genome replication, whereas knocking down OCT1 had a positive effect. Using the replication-deficient HPV18-E1- genome, we demonstrated that OCT1-mediated inhibition of HPV replication involves modulation of HPV early promoters controlling E1 and E2 expression. Moreover, using Oct6 mutants deficient either in DNA binding or transcriptional regulation, we showed that the inhibition of HPV18 replication is solely dependent on Oct6's DNA binding activity. Our study highlights the complex regulatory roles of POU-HD factors in the HPV replication.
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Affiliation(s)
- Martin Kala
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Sofiya Babok
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Nika Mikhailava
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Marko Piirsoo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Alla Piirsoo
- Institute of Technology, University of Tartu, Tartu, Estonia.
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11
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Haruna S, Okuda K, Shibata A, Isono M, Tateno K, Sato H, Oike T, Uchihara Y, Kato Y, Shibata A. Characterization of the signal transduction cascade for inflammatory gene expression in fibroblasts with ATM-ATR deficiencies after Ionizing radiation. Radiother Oncol 2024; 194:110198. [PMID: 38438016 DOI: 10.1016/j.radonc.2024.110198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND AND PURPOSE Ionizing radiation (IR) induces DNA double-strand breaks (DSBs), leading to micronuclei formation, which has emerged as a key mediator of inflammatory responses after IR. This study aimed to investigate the signaling cascade in inflammatory gene expression using fibroblasts harboring DNA damage response deficiency after exposure to IR. MATERIALS AND METHODS Micronuclei formation was examined in human dermal fibroblasts derived from patients with deficiencies in ATM, ATR, MRE11, XLF, Artemis, or BRCA2 after IR. RNA-sequencing analysis was performed to assess gene expression, pathway mapping, and the balance of transcriptional activity using the transcription factor-based downstream gene expression mapping (TDEM) method developed in this study. RESULTS Deficiencies in ATM, ATR, or MRE11 led to increased micronuclei formation after IR compared to normal cells. RNA-seq analysis revealed significant upregulation of inflammatory expression in cells deficient in ATM, ATR, or MRE11 following IR. Pathway mapping analysis identified the upregulation of RIG-I, MDA-5, IRF7, IL6, and interferon stimulated gene expression after IR. These changes were pronounced in cells deficient in ATM, ATR, or MRE11. TDEM analysis suggested the differential activation of STAT1/3-pathway between ATM and ATR deficiency. CONCLUSION Enhanced micronuclei formation upon ATM, ATR, or MRE11 deficiency activated the cGAS/STING, RIG-I-MDA-5-IRF7-IL6 pathway, resulting in its downstream interferon stimulated gene expression following exposure to IR. Our study provides comprehensive information regarding the status of inflammation-related gene expression under DSB repair deficiency after IR. The generated dataset may be useful in developing functional biomarkers to accurately identify patients sensitive to radiotherapy.
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Affiliation(s)
- Shunji Haruna
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Ken Okuda
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Akiko Shibata
- Gunma University Heavy Ion Medical Center, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Mayu Isono
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Kohei Tateno
- Department of General Surgical Science, Graduate School of Medicine, Gunma University, 3-39-22, Showa-machi, Maebashi 371-8511, Japan
| | - Hiro Sato
- Gunma University Heavy Ion Medical Center, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan; Department of Radiation Oncology, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Takahiro Oike
- Gunma University Heavy Ion Medical Center, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan; Department of Radiation Oncology, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Yuki Uchihara
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Yu Kato
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
| | - Atsushi Shibata
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
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12
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Cuevas-Bermúdez A, Martínez-Fernández V, Garrido-Godino AI, Jordán-Pla A, Peñate X, Martín-Expósito M, Gutiérrez G, Govind CK, Chávez S, Pelechano V, Navarro F. The association of the RSC remodeler complex with chromatin is influenced by the prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae. Biochim Biophys Acta Gene Regul Mech 2024; 1867:194995. [PMID: 37967810 DOI: 10.1016/j.bbagrm.2023.194995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023]
Abstract
The tripartite interaction between the chromatin remodeler complex RSC, RNA polymerase subunit Rpb5 and prefoldin-like Bud27 is necessary for proper RNA pol II elongation. Indeed lack of Bud27 alters this association and affects transcription elongation. This work investigates the consequences of lack of Bud27 on the chromatin association of RSC and RNA pol II, and on nucleosome positioning. Our results demonstrate that RSC binds chromatin in gene bodies and lack of Bud27 alters this association, mainly around polyA sites. This alteration impacts chromatin organization and leads to the accumulation of RNA pol II molecules around polyA sites, likely due to pausing or arrest. Our data suggest that RSC is necessary to maintain chromatin organization around those sites, and any alteration of this organization results in the widespread use of alternative polyA sites. Finally, we also find a similar molecular phenotype that occurs upon TOR inhibition with rapamycin, which suggests that alternative polyadenylation observed upon TOR inhibition is likely Bud27-dependent.
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Affiliation(s)
- Abel Cuevas-Bermúdez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Verónica Martínez-Fernández
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Ana I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Antonio Jordán-Pla
- Instituto Biotecmed, Facultad de Biológicas, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | - Xenia Peñate
- Departamento de Genética, Universidad de Sevilla, Seville, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Manuel Martín-Expósito
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | | | - Chhabi K Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla, Seville, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain; Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain.
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Bandau S, Alvarez V, Jiang H, Graff S, Sundaramoorthy R, Gierlinski M, Toman M, Owen-Hughes T, Sidoli S, Lamond A, Alabert C. RNA polymerase II promotes the organization of chromatin following DNA replication. EMBO Rep 2024; 25:1387-1414. [PMID: 38347224 PMCID: PMC10933433 DOI: 10.1038/s44319-024-00085-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
Understanding how chromatin organisation is duplicated on the two daughter strands is a central question in epigenetics. In mammals, following the passage of the replisome, nucleosomes lose their defined positioning and transcription contributes to their re-organisation. However, whether transcription plays a greater role in the organization of chromatin following DNA replication remains unclear. Here we analysed protein re-association with newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription. However, RNAPII acts to promote the re-association of hundreds of proteins with newly replicated chromatin via pathways that are not observed in steady-state chromatin. These include ATP-dependent remodellers, transcription factors and histone methyltransferases. We also identify a set of DNA repair factors that may handle transcription-replication conflicts during normal transcription in human non-transformed cells. Our study reveals that transcription plays a greater role in the organization of chromatin post-replication than previously anticipated.
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Affiliation(s)
- Susanne Bandau
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Vanesa Alvarez
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Sarah Graff
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | | | - Marek Gierlinski
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Matt Toman
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Simone Sidoli
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Constance Alabert
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK.
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14
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Hardin-Jones MA, Dahill AE, Heimbaugh L, Baylis A, Cummings C, Chapman KL. Correspondence between consonant inventories obtained using modified naturalistic listening in real time (NLRT) and parent report. J Commun Disord 2024; 108:106417. [PMID: 38422565 PMCID: PMC10939712 DOI: 10.1016/j.jcomdis.2024.106417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 02/08/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The current study examined the correspondence between consonant inventories obtained using the modified NLRT approach and parent report. DESIGN Prospective comparative study. SETTING Multisite institutional. PARTICIPANTS Participants included 70 children with repaired CP + L (mean age = 16 months) who were participating in the multicenter study. PROCEDURES Parents of participants were asked to record approximately two hours of their child's vocalizations/words at home using a Language ENvironmental Analysis (LENATM) recorder. Four ten-minute audio-recorded samples of vocalizations were extracted from the original recording for each participant and analyzed for size of consonant inventory. Parent reported consonant inventory was compared to coder identified consonant inventory. Coders identified an in-inventory consonant using two different criteria: 2+ tokens of each consonant were required in the first analysis and 10+ tokens of each consonant were required in the second analysis. RESULTS Coder identified consonant inventory was larger (mean = 7.90) than that reported by parents (mean = 6.06) when a minimum of two tokens per consonant was required for inclusion of a consonant in inventory, while the inventory transcribed by coders was smaller (mean = 4.46) than that reported by parents when inclusion criteria required a minimum of ten tokens per consonant. CONCLUSIONS Although the mean number of consonants in inventory between coders and parents was slightly closer using the 10+ versus 2+ criterion for consonant inclusion, the difference was not significant enough to recommend one protocol over the other.
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Affiliation(s)
- Mary A Hardin-Jones
- Division of Communication Disorders, University of Wyoming, Laramie, WY, United States.
| | - Ann E Dahill
- Division of Communication Disorders, University of Wyoming, Laramie, WY, United States
| | - Libby Heimbaugh
- Division of Communication Disorders, University of Wyoming, Laramie, WY, United States
| | - Adriane Baylis
- Department of Plastic and Reconstructive Surgery, The Ohio State University College of Medicine, Nationwide Childrens Hospital, Columbus, OH, United States
| | - Caitlin Cummings
- Department of Speech-Language Pathology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Kathy L Chapman
- Department of Communication Sciences and Disorders, University of Utah, Salt Lake City, UT, United States
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15
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Ha SY, Kim JY, Choi JH. Transcriptional regulation of genetic variants in the SLC40A1 promoter. Korean J Physiol Pharmacol 2024; 28:113-120. [PMID: 38414394 PMCID: PMC10902591 DOI: 10.4196/kjpp.2024.28.2.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/02/2023] [Indexed: 02/29/2024]
Abstract
Solute carrier 40A1 (SLC40A1) encodes ferroportin, which is the only known transmembrane protein that exports elemental iron from mammalian cells and is essential for iron homeostasis. Mutations in SLC40A1 are associated with iron-overload disorders. In addition to ferroportin diseases, SLC40A1 expression is downregulated in various cancer types. Despite the clinical significance of the SLC40A1 transporter, only a few studies have investigated genetic variants in SLC40A1. The present study was performed to identify genetic variations in the SLC40A1 promoter and functionally characterize each variant using in vitro assays. We investigated four haplotypes and five variants in the SLC40A1 promoter. We observed that haplotype 3 (H3) had significantly lower promoter activity than H1, whereas the activity of H4 was significantly higher than that of H1. Luciferase activity of H2 was comparable to that of H1. In addition, four variants of SLC40A1, c.-1355G>C, c.-662C>T, c.-98G>C, and c.-8C>G, showed significantly increased luciferase activity compared to the wild type (WT), whereas c.-750G>A showed significantly decreased luciferase activity compared to the WT. Three transcription factors, cAMP response element-binding protein-1 (CREB-1), chicken ovalbumin upstream promoter transcription factor 1, and hepatic leukemia factor (HLF), were predicted to bind to the promoter regions of SLC40A1 near c.-662C>T, c.-98G>C, and c.-8C>G, respectively. Among these, CREB-1 and HLF bound more strongly to the variant sequences than to the WT and functioned as activators of SLC40A1 transcription. Collectively, our findings indicate that the two SLC40A1 promoter haplotypes affect SLC40A1 transcription, which is regulated by CREB-1 and HLF.
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Affiliation(s)
- Seung Yeon Ha
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Jin-Young Kim
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Ji Ha Choi
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
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16
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Guo S, Wang E, Wang B, Xue Y, Kuang Y, Liu H. Comprehensive Multiomics Analyses Establish the Optimal Prognostic Model for Resectable Gastric Cancer : Prognosis Prediction for Resectable GC. Ann Surg Oncol 2024; 31:2078-2089. [PMID: 37996637 DOI: 10.1245/s10434-023-14249-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/14/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Prognostic models based on multiomics data may provide better predictive capability than those established at the single-omics level. Here we aimed to establish a prognostic model for resectable gastric cancer (GC) with multiomics information involving mutational, copy number, transcriptional, methylation, and clinicopathological alterations. PATIENTS AND METHODS The mutational, copy number, transcriptional, methylation data of 268, 265, 226, and 252 patients with stages I-III GC were downloaded from the TCGA database, respectively. Alterations from all omics were characterized, and prognostic models were established at the individual omics level and optimized at the multiomics level. All models were validated with a cohort of 99 patients with stages I-III GC. RESULTS TTN, TP53, and MUC16 were among the genes with the highest mutational frequency, while UBR5, ZFHX4, PREX2, and ARID1A exhibited the most prominent copy number variations (CNVs). Upregulated COL10A1, CST1, and HOXC10 and downregulated GAST represented the biggest transcriptional alterations. Aberrant methylation of some well-known genes was revealed, including CLDN18, NDRG4, and SDC2. Many alterations were found to predict the patient prognosis by univariate analysis, while four mutant genes, two CNVs, five transcriptionally altered genes, and seven aberrantly methylated genes were identified as independent risk factors in multivariate analysis. Prognostic models at the single-omics level were established with these alterations, and optimized combination of selected alterations with clinicopathological factors was used to establish a final multiomics model. All single-omics models and the final multiomics model were validated by an independent cohort. The optimal area under the curve (AUC) was 0.73, 0.71, 0.71, and 0.85 for mutational, CNV, transcriptional, and methylation models, respectively. The final multiomics model significantly increased the AUC to 0.92 (P < 0.05). CONCLUSIONS Multiomics model exhibited significantly better capability in predicting the prognosis of resectable GC than single-omics models.
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Affiliation(s)
- Shaohua Guo
- Department of General Surgery, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Erpeng Wang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Baishi Wang
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Yonggan Xue
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Yanshen Kuang
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Hongyi Liu
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China.
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17
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Alpuche-Lazcano SP, Scarborough RJ, Gatignol A. MicroRNAs and long non-coding RNAs during transcriptional regulation and latency of HIV and HTLV. Retrovirology 2024; 21:5. [PMID: 38424561 PMCID: PMC10905857 DOI: 10.1186/s12977-024-00637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus (HIV) and human T cell leukemia virus (HTLV) have replicative and latent stages of infection. The status of the viruses is dependent on the cells that harbour them and on different events that change the transcriptional and post-transcriptional events. Non-coding (nc)RNAs are key factors in the regulation of retrovirus replication cycles. Notably, micro (mi)RNAs and long non-coding (lnc)RNAs are important regulators that can induce switches between active transcription-replication and latency of retroviruses and have important impacts on their pathogenesis. Here, we review the functions of miRNAs and lncRNAs in the context of HIV and HTLV. We describe how specific miRNAs and lncRNAs are involved in the regulation of the viruses' transcription, post-transcriptional regulation and latency. We further discuss treatment strategies using ncRNAs for HIV and HTLV long remission, reactivation or possible cure.
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Affiliation(s)
- Sergio P Alpuche-Lazcano
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
- National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - Robert J Scarborough
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Anne Gatignol
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Medicine, Division of Infectious Diseases, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
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18
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Guo S, Guo Y, Chen Y, Cui S, Zhang C, Chen D. The role of CEMIP in cancers and its transcriptional and post-transcriptional regulation. PeerJ 2024; 12:e16930. [PMID: 38390387 PMCID: PMC10883155 DOI: 10.7717/peerj.16930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
CEMIP is a protein known for inducing cell migration and binding to hyaluronic acid. Functioning as a hyaluronidase, CEMIP primarily facilitates the breakdown of the extracellular matrix component, hyaluronic acid, thereby regulating various signaling pathways. Recent evidence has highlighted the significant role of CEMIP in different cancers, associating it with diverse pathological states. While identified as a biomarker for several diseases, CEMIP's mechanism in cancer seems distinct. Accumulating data suggests that CEMIP expression is triggered by chemical modifications to itself and other influencing factors. Transcriptionally, chemical alterations to the CEMIP promoter and involvement of transcription factors such as AP-1, HIF, and NF-κB regulate CEMIP levels. Similarly, specific miRNAs have been found to post-transcriptionally regulate CEMIP. This review provides a comprehensive summary of CEMIP's role in various cancers and explores how both transcriptional and post-transcriptional mechanisms control its expression.
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Affiliation(s)
- Song Guo
- Shandong University of Technology, School of Life Sciences and Medicine, Zibo, Shandong, China
| | - Yunfei Guo
- Shandong University of Technology, School of Life Sciences and Medicine, Zibo, Shandong, China
| | - Yuanyuan Chen
- Shandong University of Technology, School of Life Sciences and Medicine, Zibo, Shandong, China
| | - Shuaishuai Cui
- Shandong University of Technology, School of Life Sciences and Medicine, Zibo, Shandong, China
| | - Chunmei Zhang
- Shandong University of Technology, School of Life Sciences and Medicine, Zibo, Shandong, China
| | - Dahu Chen
- Shandong University of Technology, School of Life Sciences and Medicine, Zibo, Shandong, China
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19
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Redó-Riveiro A, Al-Mousawi J, Linneberg-Agerholm M, Proks M, Perera M, Salehin N, Brickman JM. Transcription factor co-expression mediates lineage priming for embryonic and extra-embryonic differentiation. Stem Cell Reports 2024; 19:174-186. [PMID: 38215757 PMCID: PMC10874857 DOI: 10.1016/j.stemcr.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/14/2024] Open
Abstract
In early mammalian development, cleavage stage blastomeres and inner cell mass (ICM) cells co-express embryonic and extra-embryonic transcriptional determinants. Using a protein-based double reporter we identify an embryonic stem cell (ESC) population that co-expresses the extra-embryonic factor GATA6 alongside the embryonic factor SOX2. Based on single cell transcriptomics, we find this population resembles the unsegregated ICM, exhibiting enhanced differentiation potential for endoderm while maintaining epiblast competence. To relate transcription factor binding in these cells to future fate, we describe a complete enhancer set in both ESCs and naive extra-embryonic endoderm stem cells and assess SOX2 and GATA6 binding at these elements in the ICM-like ESC sub-population. Both factors support cooperative recognition in these lineages, with GATA6 bound alongside SOX2 on a fraction of pluripotency enhancers and SOX2 alongside GATA6 more extensively on endoderm enhancers, suggesting that cooperative binding between these antagonistic factors both supports self-renewal and prepares progenitor cells for later differentiation.
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Affiliation(s)
- Alba Redó-Riveiro
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Jasmina Al-Mousawi
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Madeleine Linneberg-Agerholm
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Martin Proks
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Marta Perera
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Nazmus Salehin
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Joshua M Brickman
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
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20
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Devos X, Fiche JB, Bardou M, Messina O, Houbron C, Gurgo J, Schaeffer M, Götz M, Walter T, Mueller F, Nollmann M. pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging. Genome Biol 2024; 25:47. [PMID: 38351149 PMCID: PMC10863255 DOI: 10.1186/s13059-024-03178-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these limitations, new imaging-based methods have emerged, giving rise to the field of spatial genomics. Here, we present pyHiM, a user-friendly python toolbox specifically designed for the analysis of multiplexed DNA-FISH data and the reconstruction of chromatin traces in individual cells. pyHiM employs a modular architecture, allowing independent execution of analysis steps and customization according to sample specificity and computing resources. pyHiM aims to facilitate the democratization and standardization of spatial genomics analysis.
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Affiliation(s)
- Xavier Devos
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Marion Bardou
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Olivier Messina
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Christophe Houbron
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Julian Gurgo
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Marie Schaeffer
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Markus Götz
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France
| | - Thomas Walter
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, 75006, Paris, France
- Institut Curie, 75248, Paris, Cedex, France
- INSERM, U900, 75248, Paris, Cedex, France
| | - Florian Mueller
- Imaging and Modeling Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U1054, 34090, Montpellier, France.
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21
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Huang Y, Huo Y, Huang L, Zhang L, Zheng Y, Zhang N, Yang M. Super-enhancers: Implications in gastric cancer. Mutat Res Rev Mutat Res 2024; 793:108489. [PMID: 38355091 DOI: 10.1016/j.mrrev.2024.108489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Gastric cancer (GC) is the fifth most prevalent malignancy and the third leading cause of cancer-related mortality globally. Despite intensive efforts to enhance the efficiencies of various therapeutics (chemotherapy, surgical interventions, molecular-targeted therapies, immunotherapies), the prognosis for patients with GC remains poor. This might be predominantly due to the limited understanding of the complicated etiology of GC. Importantly, epigenetic modifications and alterations are crucial during GC development. Super-enhancers (SEs) are a large cluster of adjacent enhancers that greatly activate transcription. SEs sustain cell-specific identity by enhancing the transcription of specific oncogenes. In this review, we systematically summarize how SEs are involved in GC development, including the SE landscape in GC, the SE target genes in GC, and the interventions related to SE functions for treating GC.
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Affiliation(s)
- Yizhou Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Yanfei Huo
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Linying Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Long Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Yanxiu Zheng
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China.
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China.
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22
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Recktenwald M, Hutt E, Davis L, MacAulay J, Daringer NM, Galie PA, Staehle MM, Vega SL. Engineering transcriptional regulation for cell-based therapies. SLAS Technol 2024:100121. [PMID: 38340892 DOI: 10.1016/j.slast.2024.100121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
A major aim in the field of synthetic biology is developing tools capable of responding to user-defined inputs by activating therapeutically relevant cellular functions. Gene transcription and regulation in response to external stimuli are some of the most powerful and versatile of these cellular functions being explored. Motivated by the success of chimeric antigen receptor (CAR) T-cell therapies, transmembrane receptor-based platforms have been embraced for their ability to sense extracellular ligands and to subsequently activate intracellular signal transduction. The integration of transmembrane receptors with transcriptional activation platforms has not yet achieved its full potential. Transient expression of plasmid DNA is often used to explore gene regulation platforms in vitro. However, applications capable of targeting therapeutically relevant endogenous or stably integrated genes are more clinically relevant. Gene regulation may allow for engineered cells to traffic into tissues of interest and secrete functional proteins into the extracellular space or to differentiate into functional cells. Transmembrane receptors that regulate transcription have the potential to revolutionize cell therapies in a myriad of applications, including cancer treatment and regenerative medicine. In this review, we will examine current engineering approaches to control transcription in mammalian cells with an emphasis on systems that can be selectively activated in response to extracellular signals. We will also speculate on the potential therapeutic applications of these technologies and examine promising approaches to expand their capabilities and tighten the control of gene regulation in cellular therapies.
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Affiliation(s)
- Matthias Recktenwald
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Evan Hutt
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Leah Davis
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - James MacAulay
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Nichole M Daringer
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Peter A Galie
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Mary M Staehle
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Sebastián L Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; Department of Orthopaedic Surgery, Cooper Medical School of Rowan University, Camden, NJ 08103, USA.
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23
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Sepulveda GP, Gushchanskaia ES, Mora-Martin A, Esse R, Nikorich I, Ceballos A, Kwan J, Blum BC, Dholiya P, Emili A, Perissi V, Cardamone MD, Grishok A. DOT1L stimulates MYC/Mondo transcription factor activity by promoting its degradation cycle on chromatin. bioRxiv 2024:2024.02.06.579191. [PMID: 38370658 PMCID: PMC10871221 DOI: 10.1101/2024.02.06.579191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The proto-oncogene c-MYC is a key representative of the MYC transcription factor network regulating growth and metabolism. MML-1 (Myc- and Mondo-like) is its homolog in C. elegans. The functional and molecular cooperation between c-MYC and H3 lysine 79 methyltransferase DOT1L was demonstrated in several human cancer types, and we have earlier discovered the connection between C. elegans MML-1 and DOT-1.1. Here, we demonstrate the critical role of DOT1L/DOT-1.1 in regulating c-MYC/MML-1 target genes genome-wide by ensuring the removal of "spent" transcription factors from chromatin by the nuclear proteasome. Moreover, we uncover a previously unrecognized proteolytic activity of DOT1L, which may facilitate c-MYC turnover. This new mechanism of c-MYC regulation by DOT1L may lead to the development of new approaches for cancer treatment.
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Affiliation(s)
- Gian P. Sepulveda
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ekaterina S. Gushchanskaia
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Tessera Therapeutics, Somerville, MA, 02143, USA
| | - Alexandra Mora-Martin
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Ruben Esse
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Cell and Gene Therapy Catapult, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Iana Nikorich
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ainhoa Ceballos
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Present address: Research Unit, Diagnostica Longwood S.L. 50011 Zaragoza, Spain
| | - Julian Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Benjamin C. Blum
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Prakruti Dholiya
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Andrew Emili
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
- Division of Computational Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: OHSU Knight Cancer Institute, School of Medicine, Portland, OR, 97239, USA
| | - Valentina Perissi
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Maria D. Cardamone
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Korro Bio Inc., Cambridge, MA, 02139, USA
| | - Alla Grishok
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Genome Science Institute, Boston University, Boston, MA, 02118, USA
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24
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Fetian T, Grover A, Arndt KM. Histone H2B ubiquitylation: Connections to transcription and effects on chromatin structure. Biochim Biophys Acta Gene Regul Mech 2024; 1867:195018. [PMID: 38331024 DOI: 10.1016/j.bbagrm.2024.195018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Nucleosomes are major determinants of eukaryotic genome organization and regulation. Many studies, incorporating a diversity of experimental approaches, have been focused on identifying and discerning the contributions of histone post-translational modifications to DNA-centered processes. Among these, monoubiquitylation of H2B (H2Bub) on K120 in humans or K123 in budding yeast is a critical histone modification that has been implicated in a wide array of DNA transactions. H2B is co-transcriptionally ubiquitylated and deubiquitylated via the concerted action of an extensive network of proteins. In addition to altering the chemical and physical properties of the nucleosome, H2Bub is important for the proper control of gene expression and for the deposition of other histone modifications. In this review, we discuss the molecular mechanisms underlying the ubiquitylation cycle of H2B and how it connects to the regulation of transcription and chromatin structure.
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Affiliation(s)
- Tasniem Fetian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Aakash Grover
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America.
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25
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Ortiz Charneco G, Kelleher P, Buivydas A, de Waal PP, van Rijswijck IM, van Peij NN, Mahony J, Van Sinderen D. Transcriptional control of two distinct lactococcal plasmid-encoded conjugation systems. Curr Res Microb Sci 2024; 6:100224. [PMID: 38371911 PMCID: PMC10873654 DOI: 10.1016/j.crmicr.2024.100224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
Lactococcal conjugative plasmids are poorly characterized compared to those harbored by numerous other Gram-positive bacteria, despite their significance in dairy fermentations and starter culture development. Furthermore, the transcriptional landscape of these lactococcal conjugation systems and their regulation have not been studied in any detail. Lactococcal plasmids pNP40 and pUC11B possess two genetically distinct and prevalent conjugation systems. Here, we describe the detailed transcriptional analysis of the pNP40 and pUC11B conjugation-associated gene clusters, revealing three and five promoters, respectively, for which the corresponding transcriptional start sites were identified. Regulation of several of these promoters, and therefore conjugation, is shown to involve the individual or concerted activities of the corresponding relaxase and transcriptional repressor(s) encoded by each conjugative plasmid. This work highlights how the conjugative potential of these systems may be unlocked, with significant implications for the starter culture and food fermentation industry.
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Affiliation(s)
- Guillermo Ortiz Charneco
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Andrius Buivydas
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Paul P. de Waal
- dsm-firmenich; Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Irma M.H. van Rijswijck
- dsm-firmenich; Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Noël N.M.E. van Peij
- dsm-firmenich; Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Douwe Van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
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26
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Zheng Y, Xu W, Guo H, Yu S, Xue L, Chen M, Zhang J, Xu Z, Wu Q, Wang J, Ding Y. The potential of lactose to inhibit cereulide biosynthesis of emetic Bacillus cereus in milk. Int J Food Microbiol 2024; 411:110517. [PMID: 38096676 DOI: 10.1016/j.ijfoodmicro.2023.110517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 10/07/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
This study aims to investigate the potential role of lactose on cereulide biosynthesis by emetic Bacillus cereus in dairy matrices. The cereulide yields in whole milk and lactose-free milk were investigated using the emetic reference strain F4810/72. To eliminate the influence of complex food substrates, the LB medium model was further used to characterize the effect of lactose on cereulide produced by F4810/72 and five other emetic B. cereus strains. Results showed that the lactose-free milk displayed a 13-fold higher amount of cereulide than whole milk, but the cereulide level could be reduced by 91 % when the lactose content was restored. The significant inhibition of lactose on cereulide yields of all tested B. cereus strains was observed in LB medium, showing a dose-dependent manner with inhibition rates ranging of 89-98 %. The growth curves and lactose utilization patterns of all strains demonstrated that B. cereus cannot utilize lactose as a carbon source and lactose might act as a signal molecule to regulate cereulide production. Moreover, lactose strongly repressed the expression of cereulide synthetase genes (ces), possibly by inhibiting the key regulator Spo0A at the transcriptional level. Our findings highlight the potential of lactose as an effective strategy to control cereulide production in food.
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Affiliation(s)
- Yin Zheng
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Wenxing Xu
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China; National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Hui Guo
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Shubo Yu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Liang Xue
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Moutong Chen
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jumei Zhang
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zhenlin Xu
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Qingping Wu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China.
| | - Yu Ding
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China.
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27
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Udupa A, Kotha SR, Staller MV. Commonly asked questions about transcriptional activation domains. Curr Opin Struct Biol 2024; 84:102732. [PMID: 38056064 DOI: 10.1016/j.sbi.2023.102732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Eukaryotic transcription factors activate gene expression with their DNA-binding domains and activation domains. DNA-binding domains bind the genome by recognizing structurally related DNA sequences; they are structured, conserved, and predictable from protein sequences. Activation domains recruit chromatin modifiers, coactivator complexes, or basal transcriptional machinery via structurally diverse protein-protein interactions. Activation domains and DNA-binding domains have been called independent, modular units, but there are many departures from modularity, including interactions between these regions and overlap in function. Compared to DNA-binding domains, activation domains are poorly understood because they are poorly conserved, intrinsically disordered, and difficult to predict from protein sequences. This review, organized around commonly asked questions, describes recent progress that the field has made in understanding the sequence features that control activation domains and predicting them from sequence.
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Affiliation(s)
- Aditya Udupa
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA
| | - Sanjana R Kotha
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA; Center for Computational Biology, University of California, Berkeley, 94720, USA
| | - Max V Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA; Center for Computational Biology, University of California, Berkeley, 94720, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA.
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28
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Asa TA, Kumar P, Seo YJ. Dual amplification-based ultrasensitive and highly selective colorimetric detection of miRNA. Talanta 2024; 268:125269. [PMID: 37839321 DOI: 10.1016/j.talanta.2023.125269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/01/2023] [Accepted: 10/01/2023] [Indexed: 10/17/2023]
Abstract
In this study, we combined a Pradeep Kumar (PK)-probe with a ligation-transcription-ramified RCA (LTR) dual-amplification system for the isothermal colorimetric detection of miRNA 25-3P, where the PK-probe transformed from its pink color to colorless in the presence of the amplification byproduct pyrophosphate (PPi), thereby allowing the simple naked-eye qualitative detection of the miRNA. Through this double-amplification strategy, the limit of detection reached as low as 91.4 aM-quite extraordinary sensitivity for a colorimetric miRNA detection system based on absorbance readings. Our detection system also operated with high specificity, the result of using two different target-selective ligation steps (linear DNA ligation and circular DNA ligation) mediated by SplintR ligase, and so could discriminate single-mismatched from perfectly matched target sequences. We suspect that this ultrasensitive and selective PK-probe/LTR dual-amplification system should be a great colorimetric diagnostic for the detection of any miRNA with high efficiency.
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Affiliation(s)
- Tasnima Alam Asa
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
| | - Pradeep Kumar
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
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29
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Wang Y, Xu L, Zhang Y, Fu H, Gao L, Guan Y, Gu W, Sun J, Chen X, Yang F, Lai E, Wang J, Jin Y, Kou Z, Qiu X, Mao J, Hu L. Dent disease 1-linked novel CLCN5 mutations result in aberrant location and reduced ion currents. Int J Biol Macromol 2024; 257:128564. [PMID: 38061527 DOI: 10.1016/j.ijbiomac.2023.128564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/12/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
Dent disease is a rare renal tubular disease with X-linked recessive inheritance characterized by low molecular weight proteinuria (LMWP), hypercalciuria, and nephrocalcinosis. Mutations disrupting the 2Cl-/1H+ exchange activity of chloride voltage-gated channel 5 (CLCN5) have been causally linked to the most common form, Dent disease 1 (DD1), although the pathophysiological mechanisms remain unclear. Here, we conducted the whole exome capture sequencing and bioinformatics analysis within our DD1 cohort to identify two novel causal mutations in CLCN5 (c.749 G > A, p. G250D, c.829 A > C, p. T277P). Molecular dynamics simulations of ClC-5 homology model suggested that these mutations potentially may induce structural changes, destabilizing ClC-5. Overexpression of variants in vitro revealed aberrant subcellular localization in the endoplasmic reticulum (ER), significant accumulation of insoluble aggregates, and disrupted ion transport function in voltage clamp recordings. Moreover, human kidney-2 (HK-2) cells overexpressing either G250D or T277P displayed higher cell-substrate adhesion, migration capability but reduced endocytic function, as well as substantially altered transcriptomic profiles with G250D resulting in stronger deleterious effects. These cumulative findings supported pathogenic role of these ClC-5 mutations in DD1 and suggested a cellular mechanism for disrupted renal function in Dent disease patients, as well as a potential target for diagnostic biomarker or therapeutic strategy development.
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Affiliation(s)
- Yan Wang
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Lizhen Xu
- Department of Biophysics, and Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ying Zhang
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Haidong Fu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Langping Gao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yuelin Guan
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Weizhong Gu
- Department of Pathology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jingmiao Sun
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310020, China
| | - Fan Yang
- Department of Biophysics, and Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - EnYin Lai
- Department of Physiology School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingjing Wang
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yanyan Jin
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Ziqi Kou
- Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou 510631, China
| | - Xingyu Qiu
- Department of Physiology School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianhua Mao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
| | - Lidan Hu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
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30
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Cooper SL, Lucius AL, Schneider DA. Quantifying the impact of initial RNA primer length on nucleotide addition by RNA polymerase I. Biophys Chem 2024; 305:107151. [PMID: 38088007 DOI: 10.1016/j.bpc.2023.107151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Transient state kinetic studies of eukaryotic DNA-dependent RNA polymerases (Pols) in vitro provide quantitative characterization of enzyme activity at the level of individual nucleotide addition events. Previous work revealed heterogeneity in the rate constants governing nucleotide addition by yeast RNA polymerase I (Pol I) for each position on a template DNA. In contrast, the rate constants that described nucleotide addition by yeast RNA polymerase II (Pol II) were more homogeneous. This observation led to the question, what drives the variability of rate constants governing RNA synthesis by Pol I? Are the kinetics of nucleotide addition dictated by the position of the nascent RNA within the polymerase or by the identity of the next encoded nucleotide? In this study, we examine the impact of nucleotide position (i.e. nascent RNA primer length) on the rate constants governing nine sequential nucleotide addition events catalyzed by Pol I. The results reveal a conserved trend in the observed rate constants at each position for all primer lengths used, and highlight that the 9-nucleotide, or 9-mer, RNA primer provides the fastest observed rate constants. These findings suggest that the observed heterogeneity of rate constants for RNA synthesis by Pol I in vitro is driven primarily by the template sequence.
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Affiliation(s)
- Stephanie L Cooper
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Arimbasseri AG, Shukla A, Pradhan AK, Bhargava P. Increased histone acetylation is the signature of repressed state on the genes transcribed by RNA polymerase III. Gene 2024; 893:147958. [PMID: 37923095 DOI: 10.1016/j.gene.2023.147958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Several covalent modifications are found associated with the transcriptionally active chromatin regions constituted by the genes transcribed by RNA polymerase (pol) II. Pol III-transcribed genes code for the small, stable RNA species, which participate in many cellular processes, essential for survival. Pol III transcription is repressed under most of the stress conditions by its negative regulator Maf1. We found that most of the histone acetylations increase with starvation-induced repression on several genes transcribed by the yeast pol III. On one of these genes, SNR6 (coding for the U6snRNA), a strongly positioned nucleosome in the gene upstream region plays regulatory role under repression. On this nucleosome, the changes in H3K9 and H3K14 acetylations show different dynamics. During repression, acetylation levels on H3K9 show steady increase whereas H3K14 acetylation increases with a peak at 40 min after which levels reduce. Both the levels settle by 2 hr to a level higher than the active state, which revert to normal levels with nutrient repletion. The increase in H3 acetylations is seen in the mutants reported to show reduced SNR6 transcription but not in the maf1Δ cells. This increase on a regulatory nucleosome may be part of the signaling mechanisms, which prepare cells for the stress-related quick repression as well as reactivation. The contrasting association of the histone acetylations with pol II and pol III transcription may be an important consideration to make in research studies focused on drug developments targeting histone modifications.
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Affiliation(s)
| | - Ashutosh Shukla
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ashis Kumar Pradhan
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Purnima Bhargava
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India.
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32
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Sato J, Satoh Y, Yamamoto T, Watanabe T, Matsubara S, Satake H, Kimura AP. PTBP2 binds to a testis-specific long noncoding RNA, Tesra, and activates transcription of the Prss42/Tessp-2 gene. Gene 2024; 893:147907. [PMID: 37858745 DOI: 10.1016/j.gene.2023.147907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Long noncoding RNAs (lncRNAs) have recently been proved to be functional in the testis. Tesra, a testis-specific lncRNA, was suggested to activate the transcription of Prss42/Tessp-2, a gene that is involved in meiotic progression, in mouse spermatocytes. To reveal the molecular mechanism underlying the activation, we searched for Tesra-binding proteins by a Ribotrap assay followed by LC-MS/MS analysis and identified polypyrimidine tract binding protein 2 (PTBP2) as a candidate. Analysis of public RNA-seq data and our qRT-PCR results indicated that Ptbp2 mRNA showed an expression pattern similar to the expression patterns of Tesra and Prss42/Tessp-2 during testis development. Moreover, PTBP2 was found to be associated with Tesra in testicular germ cells by RNA immunoprecipitation. To evaluate the effect of PTBP2 on the Prss42/Tessp-2 promoter, we established an in vitro reporter gene assay system in which Tesra expression could be induced by the Tet-on system and thereby Prss42/Tessp-2 promoter activity could be increased. In this system, the Prss42/Tessp-2 promoter activity was significantly decreased by the knockdown of PTBP2. These results suggest that PTBP2 contributes to Prss42/Tessp-2 transcriptional activation by Tesra in spermatocytes. The finding provides a precious example of a molecular mechanism of testis lncRNA functioning in spermatogenesis.
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Affiliation(s)
- Josei Sato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yui Satoh
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Takehiro Watanabe
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Atsushi P Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan.
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Wang Y, Zhang W, Hong C, Zhai L, Wang X, Zhou L, Song A, Jiang J, Wang L, Chen F, Chen S. Chrysanthemum (Chrysanthemum morifolium) CmHRE2-like negatively regulates the resistance of chrysanthemum to the aphid (Macrosiphoniella sanborni). BMC Plant Biol 2024; 24:76. [PMID: 38281936 PMCID: PMC10823704 DOI: 10.1186/s12870-024-04758-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND The growth and ornamental value of chrysanthemums are frequently hindered by aphid attacks. The ethylene-responsive factor (ERF) gene family is pivotal in responding to biotic stress, including insect stress. However, to date, little is known regarding the involvement of ERF transcription factors (TFs) in the response of chrysanthemum to aphids. RESULTS In the present study, CmHRE2-like from chrysanthemum (Chrysanthemum morifolium), a transcription activator that localizes mainly to the nucleus, was cloned. Expression is induced by aphid infestation. Overexpression of CmHRE2-like in chrysanthemum mediated its susceptibility to aphids, whereas CmHRE2-like-SRDX dominant repressor transgenic plants enhanced the resistance of chrysanthemum to aphids, suggesting that CmHRE2-like contributes to the susceptibility of chrysanthemum to aphids. The flavonoids in CmHRE2-like-overexpression plants were decreased by 29% and 28% in two different lines, whereas they were increased by 42% and 29% in CmHRE2-like-SRDX dominant repressor transgenic plants. The expression of Chrysanthemum-chalcone-synthase gene(CmCHS), chalcone isomerase gene (CmCHI), and flavonoid 3'-hydroxylase gene(CmF3'H) was downregulated in CmHRE2-like overexpression plants and upregulated in CmHRE2-like-SRDX dominant repressor transgenic plants, suggesting that CmHRE2-like regulates the resistance of chrysanthemum to aphids partially through the regulation of flavonoid biosynthesis. CONCLUSION CmHRE2-like was a key gene regulating the vulnerability of chrysanthemum to aphids. This study offers fresh perspectives on the molecular mechanisms of chrysanthemum-aphid interactions and may bear practical significance for developing new strategies to manage aphid infestation in chrysanthemums.
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Affiliation(s)
- You Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanwan Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chaojun Hong
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lisheng Zhai
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinhui Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lijie Zhou
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aiping Song
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiafu Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Likai Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sumei Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China.
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Beijing, P. R. China.
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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An H, Wang X, Li J, Sun H, Zhu S, Ge J, Han L, Shen B, Wang Q. KAS-seq profiling captures transcription dynamics during oocyte maturation. J Ovarian Res 2024; 17:23. [PMID: 38267939 PMCID: PMC10807090 DOI: 10.1186/s13048-023-01342-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/31/2023] [Indexed: 01/26/2024] Open
Abstract
In fully grown oocytes, the genome is considered to be globally transcriptionally silenced. However, this conclusion is primarily derived from the results obtained through immunofluorescence staining or inferred from the highly condensed state of chromosomes, lacking more direct evidence. Here, by using a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, we investigated the landscape of single-strand DNA (ssDNA) throughout the genome and provided a readout of the activity and dynamics of transcription during oocyte meiotic maturation. In non-surrounded nucleolus (NSN) oocytes, we observed a robust KAS-seq signal, indicating the high transcriptional activity. In surrounded nucleolus (SN) oocytes, the presence of ssDNA still persists although the KAS-seq signal was relatively weak, suggesting the presence of transcription. Accompanying with the meiotic resumption, the transcriptional activity gradually decreased, and global repression was detected in matured oocytes. Moreover, we preformed the integrative genomics analysis to dissect the transcriptional dynamics during mouse oocyte maturation. In sum, the present study delineates the detailed transcriptional activity during mammalian oocyte maturation.
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Affiliation(s)
- Huiqing An
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Xiuwan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Jiashuo Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Hongzheng Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Shuai Zhu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Juan Ge
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Longsen Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Qiang Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China.
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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35
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Luo M, Bao L, Xue Y, Zhu M, Kumar A, Xing C, Wang JE, Wang Y, Luo W. ZMYND8 protects breast cancer stem cells against oxidative stress and ferroptosis through activation of NRF2. J Clin Invest 2024; 134:e171166. [PMID: 38488001 PMCID: PMC10940091 DOI: 10.1172/jci171166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 01/17/2024] [Indexed: 03/18/2024] Open
Abstract
Breast cancer stem cells (BCSCs) mitigate oxidative stress to maintain their viability and plasticity. However, the regulatory mechanism of oxidative stress in BCSCs remains unclear. We recently found that the histone reader ZMYND8 was upregulated in BCSCs. Here, we showed that ZMYND8 reduced ROS and iron to inhibit ferroptosis in aldehyde dehydrogenase-high (ALDHhi) BCSCs, leading to BCSC expansion and tumor initiation in mice. The underlying mechanism involved a two-fold posttranslational regulation of nuclear factor erythroid 2-related factor 2 (NRF2). ZMYND8 increased stability of NRF2 protein through KEAP1 silencing. On the other hand, ZMYND8 interacted with and recruited NRF2 to the promoters of antioxidant genes to enhance gene transcription in mammospheres. NRF2 phenocopied ZMYND8 to enhance BCSC stemness and tumor initiation by inhibiting ROS and ferroptosis. Loss of NRF2 counteracted ZMYND8's effects on antioxidant genes and ROS in mammospheres. Interestingly, ZMYND8 expression was directly controlled by NRF2 in mammospheres. Collectively, these findings uncover a positive feedback loop that amplifies the antioxidant defense mechanism sustaining BCSC survival and stemness.
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Affiliation(s)
| | | | | | | | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development
- Lyda Hill Department of Bioinformatics
| | | | - Yingfei Wang
- Department of Pathology
- Department of Neurology
- Peter O’Donnell Jr. Brain Institute
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, and
| | - Weibo Luo
- Department of Pathology
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
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36
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Montibus B, Ragheb R, Diamanti E, Dunn SJ, Reynolds N, Hendrich B. The Nucleosome Remodelling and Deacetylation complex coordinates the transcriptional response to lineage commitment in pluripotent cells. Biol Open 2024; 13:bio060101. [PMID: 38149716 PMCID: PMC10836651 DOI: 10.1242/bio.060101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/18/2023] [Indexed: 12/28/2023] Open
Abstract
As cells exit the pluripotent state and begin to commit to a specific lineage they must activate genes appropriate for that lineage while silencing genes associated with pluripotency and preventing activation of lineage-inappropriate genes. The Nucleosome Remodelling and Deacetylation (NuRD) complex is essential for pluripotent cells to successfully undergo lineage commitment. NuRD controls nucleosome density at regulatory sequences to facilitate transcriptional responses, and also has been shown to prevent unscheduled transcription (transcriptional noise) in undifferentiated pluripotent cells. How these activities combine to ensure cells engage a gene expression program suitable for successful lineage commitment has not been determined. Here, we show that NuRD is not required to silence all genes. Rather, it restricts expression of genes primed for activation upon exit from the pluripotent state, but maintains them in a transcriptionally permissive state in self-renewing conditions, which facilitates their subsequent activation upon exit from naïve pluripotency. We further show that NuRD coordinates gene expression changes, which acts to maintain a barrier between different stable states. Thus NuRD-mediated chromatin remodelling serves multiple functions, including reducing transcriptional noise, priming genes for activation and coordinating the transcriptional response to facilitate lineage commitment.
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Affiliation(s)
- Bertille Montibus
- Wellcome – MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Ramy Ragheb
- Wellcome – MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Evangelia Diamanti
- Wellcome – MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
| | - Sara-Jane Dunn
- Microsoft Research, 21 Station Road, Cambridge CB1 2FB, UK
| | - Nicola Reynolds
- Wellcome – MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Brian Hendrich
- Wellcome – MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, UK
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37
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Seaton G, Smith H, Brancale A, Westwell AD, Clarkson R. Multifaceted roles for BCL3 in cancer: a proto-oncogene comes of age. Mol Cancer 2024; 23:7. [PMID: 38195591 PMCID: PMC10775530 DOI: 10.1186/s12943-023-01922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
In the early 1990's a group of unrelated genes were identified from the sites of recurring translocations in B-cell lymphomas. Despite sharing the nomenclature 'Bcl', and an association with blood-borne cancer, these genes have unrelated functions. Of these genes, BCL2 is best known as a key cancer target involved in the regulation of caspases and other cell viability mechanisms. BCL3 on the other hand was originally identified as a non-canonical regulator of NF-kB transcription factor pathways - a signaling mechanism associated with important cell outcomes including many of the hallmarks of cancer. Most of the early investigations into BCL3 function have since focused on its role in NF-kB mediated cell proliferation, inflammation/immunity and cancer. However, recent evidence is coming to light that this protein directly interacts with and modulates a number of other signaling pathways including DNA damage repair, WNT/β-catenin, AKT, TGFβ/SMAD3 and STAT3 - all of which have key roles in cancer development, metastatic progression and treatment of solid tumours. Here we review the direct evidence demonstrating BCL3's central role in a transcriptional network of signaling pathways that modulate cancer biology and treatment response in a range of solid tumour types and propose common mechanisms of action of BCL3 which may be exploited in the future to target its oncogenic effects for patient benefit.
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Affiliation(s)
- Gillian Seaton
- European Cancer Stem Cell Research Institute, Cardiff University School of Biosciences, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Hannah Smith
- European Cancer Stem Cell Research Institute, Cardiff University School of Biosciences, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Andrea Brancale
- UCT Prague, Technická 5, 166 28, 6 - Dejvice, IČO: 60461337, Prague, Czech Republic
| | - Andrew D Westwell
- Cardiff University School of Pharmacy and Pharmaceutical Sciences, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Richard Clarkson
- European Cancer Stem Cell Research Institute, Cardiff University School of Biosciences, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
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O'Brien MJ, Ansari A. Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle. Biochim Biophys Acta Proteins Proteom 2024; 1872:140968. [PMID: 37863410 PMCID: PMC10872477 DOI: 10.1016/j.bbapap.2023.140968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Although TFIIB is widely regarded as an initiation factor, recent reports have implicated it in multiple aspects of eukaryotic transcription. To investigate the broader role of TFIIB in transcription, we performed quantitative proteomic analysis of yeast TFIIB. We purified two different populations of TFIIB; one from soluble cell lysate, which is not engaged in transcription, and the other from the chromatin fraction which yields the transcriptionally active form of the protein. TFIIB purified from the chromatin exhibits several interactions that explain its non-canonical roles in transcription. RNAPII, TFIIF and TFIIH were the only components of the preinitiation complex with a significant presence in chromatin TFIIB. A notable feature was enrichment of all subunits of CF1 and Rat1 3' end processing-termination complexes in chromatin-TFIIB preparation. Subunits of the CPF termination complex were also detected in both chromatin and soluble derived TFIIB preparations. These results may explain the presence of TFIIB at the 3' end of genes during transcription as well as its role in promoter-termination interaction.
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Affiliation(s)
- Michael J O'Brien
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, United States of America
| | - Athar Ansari
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, United States of America.
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Fiche JB, Schaeffer M, Houbron C, Elkhoury Youhanna C, Messina O, Barho F, Nollmann M. Hi-M: A Multiplex Oligopaint FISH Method to Capture Chromatin Conformations In Situ and Accompanying Open-Source Acquisition Software. Methods Mol Biol 2024; 2784:227-257. [PMID: 38502490 DOI: 10.1007/978-1-0716-3766-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The simultaneous observation of three-dimensional (3D) chromatin structure and transcription in single cells is critical to understand how DNA is organized inside cells and how this organization influences or is affected by other processes, such as transcription. We have recently introduced an innovative technology known as Hi-M, which enables the sequential tagging, 3D visualization, and precise localization of multiple genomic DNA regions alongside RNA expression within individual cells. In this chapter, we present a comprehensive guide outlining the creation of probes, as well as sample preparation and labeling. Finally, we provide a step-by-step guide to conduct a complete Hi-M acquisition using our open-source software package, Qudi-HiM, which controls the robotic microscope handling the entire acquisition procedure.
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Affiliation(s)
- Jean-Bernard Fiche
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | - Marie Schaeffer
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | - Christophe Houbron
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | | | - Olivier Messina
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | - Franziska Barho
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France.
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40
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Jurėnas D. Metabolic Labeling: Snapshot of the Effect of Toxins on the Key Cellular Processes. Methods Mol Biol 2024; 2715:539-545. [PMID: 37930550 DOI: 10.1007/978-1-0716-3445-5_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Competing bacteria secrete vast variety of toxic effectors via secretion systems. Phospholipase, peptidoglycan-hydrolase, or pore forming toxins often manifest in the bursting of the prey cell. Other toxins reach cytoplasm of the prey where they affect cell division machinery, metabolism, nucleic acid integrity, or protein synthesis. Inhibition of cell division or DNA integrity, which summons SOS response, will often lead to bacterial cell filamentation readily observable under the microscope. However, other toxic activities will not manifest in interpretable phenotypic changes that would readily suggest their mechanism of toxicity. Activity measurements of the three fundamental cellular processes-replication, transcription and translation can pave the way for further understanding of the toxin's activity. Method commonly known as metabolic labeling makes use of radioactive precursors for DNA, RNA and protein synthesis. This method provides highly sensitive snapshot of the activity of key cellular processes.
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Affiliation(s)
- Dukas Jurėnas
- Laboratoire de Génétique et Physiologie Bactérienne, Département de Biologie Moléculaire, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium.
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41
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Masuda LHP, Sabino AU, Reinitz J, Ramos AF, Machado-Lima A, Andrioli LP. Global repression by tailless during segmentation. Dev Biol 2024; 505:11-23. [PMID: 37879494 PMCID: PMC10949167 DOI: 10.1016/j.ydbio.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
The orphan nuclear receptor Tailless (Tll) exhibits conserved roles in brain formation and maintenance that are shared, for example, with vertebrate orthologous forms (Tlx). However, the early expression of tll in two gap domains in the segmentation cascade of Drosophila is unusual even for most other insects. Here we investigate tll regulation on pair-rule stripes. With ectopic misexpression of tll we detected unexpected repression of almost all pair-rule stripes of hairy (h), even-skipped (eve), runt (run), and fushi-tarazu (ftz). Examining Tll embryonic ChIP-chip data with regions mapped as Cis-Regulatory Modules (CRMs) of pair-rule stripes we verified Tll interactions to these regions. With the ChIP-chip data we also verified Tll interactions to the CRMs of gap domains and in the misexpression assay, Tll-mediated repression on Kruppel (Kr), kni (kni) and giant (gt) according to their differential sensitivity to Tll. These results with gap genes confirmed previous data from the literature and argue against indirect repression roles of Tll in the striped pattern. Moreover, the prediction of Tll binding sites in the CRMs of eve stripes and the mathematical modeling of their removal using an experimentally validated theoretical framework shows effects on eve stripes compatible with the absence of a repressor binding to the CRMs. In addition, modeling increased tll levels in the embryo results in the differential repression of eve stripes, agreeing well with the results of the misexpression assay. In genetic assays we investigated eve 5, that is strongly repressed by the ectopic domain and representative of more central stripes not previously implied to be under direct regulation of tll. While this stripe is little affected in tll-, its posterior border is expanded in gt- but detected with even greater expansion in gt-;tll-. We end up by discussing tll with key roles in combinatorial repression mechanisms to contain the expression of medial patterns of the segmentation cascade in the extremities of the embryo.
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Affiliation(s)
| | - Alan Utsuni Sabino
- Departamento de Radiologia e Oncologia, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - John Reinitz
- Departments of Statistics, Ecology and Evolution, Molecular Genetics & Cell Biology, Institute of Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | | | - Ariane Machado-Lima
- Escola de Artes, Ciências e Humanidades da Universidade de São Paulo, São Paulo, Brazil
| | - Luiz Paulo Andrioli
- Escola de Artes, Ciências e Humanidades da Universidade de São Paulo, São Paulo, Brazil.
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42
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Ko DK, Brandizzi F. Multi-omics Resources for Understanding Gene Regulation in Response to ER Stress in Plants. Methods Mol Biol 2024; 2772:261-272. [PMID: 38411820 DOI: 10.1007/978-1-0716-3710-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Proteotoxic stress of the endoplasmic reticulum (ER) is a potentially lethal condition that ensues when the biosynthetic capacity of the ER is overwhelmed. A sophisticated and largely conserved signaling, known as the unfolded protein response (UPR), is designed to monitor and alleviate ER stress. In plants, the emerging picture of gene regulation by the UPR now appears to be more complex than ever before, requiring multi-omics-enabled network-level approaches to be untangled. In the past decade, with an increasing access and decreasing costs of next-generation sequencing (NGS) and high-throughput protein-DNA interaction (PDI) screening technologies, multitudes of global molecular measurements, known as omics, have been generated and analyzed by the research community to investigate the complex gene regulation of plant UPR. In this chapter, we present a comprehensive catalog of omics resources at different molecular levels (transcriptomes, protein-DNA interactomes, and networks) along with the introduction of key concepts in experimental and computational tools in data generation and analyses. This chapter will serve as a starting point for both experimentalists and bioinformaticians to explore diverse omics datasets for their biological questions in the plant UPR, with likely applications also in other species for conserved mechanisms.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
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Marzoog BA. Transcription Factors in Brain Regeneration: A Potential Novel Therapeutic Target. Curr Drug Targets 2024; 25:46-61. [PMID: 38444255 DOI: 10.2174/0113894501279977231210170231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 03/07/2024]
Abstract
Transcription factors play a crucial role in providing identity to each cell population. To maintain cell identity, it is essential to balance the expression of activator and inhibitor transcription factors. Cell plasticity and reprogramming offer great potential for future therapeutic applications, as they can regenerate damaged tissue. Specific niche factors can modify gene expression and differentiate or transdifferentiate the target cell to the required fate. Ongoing research is being carried out on the possibilities of transcription factors in regenerating neurons, with neural stem cells (NSCs) being considered the preferred cells for generating new neurons due to their epigenomic and transcriptome memory. NEUROD1/ASCL1, BRN2, MYTL1, and other transcription factors can induce direct reprogramming of somatic cells, such as fibroblasts, into neurons. However, the molecular biology of transcription factors in reprogramming and differentiation still needs to be fully understood.
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Affiliation(s)
- Basheer Abdullah Marzoog
- World-Class Research Center, Digital Biodesign and Personalized Healthcare», I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
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Kumar C, Remus D. Looping out of control: R-loops in transcription-replication conflict. Chromosoma 2024; 133:37-56. [PMID: 37419963 PMCID: PMC10771546 DOI: 10.1007/s00412-023-00804-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Transcription-replication conflict is a major cause of replication stress that arises when replication forks collide with the transcription machinery. Replication fork stalling at sites of transcription compromises chromosome replication fidelity and can induce DNA damage with potentially deleterious consequences for genome stability and organismal health. The block to DNA replication by the transcription machinery is complex and can involve stalled or elongating RNA polymerases, promoter-bound transcription factor complexes, or DNA topology constraints. In addition, studies over the past two decades have identified co-transcriptional R-loops as a major source for impairment of DNA replication forks at active genes. However, how R-loops impede DNA replication at the molecular level is incompletely understood. Current evidence suggests that RNA:DNA hybrids, DNA secondary structures, stalled RNA polymerases, and condensed chromatin states associated with R-loops contribute to the of fork progression. Moreover, since both R-loops and replication forks are intrinsically asymmetric structures, the outcome of R-loop-replisome collisions is influenced by collision orientation. Collectively, the data suggest that the impact of R-loops on DNA replication is highly dependent on their specific structural composition. Here, we will summarize our current understanding of the molecular basis for R-loop-induced replication fork progression defects.
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Affiliation(s)
- Charanya Kumar
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA.
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45
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Hani S, Mercier C, David P, Desnos T, Escudier JM, Bertrand E, Nussaume L. smFISH for Plants. Methods Mol Biol 2024; 2784:87-100. [PMID: 38502480 DOI: 10.1007/978-1-0716-3766-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Single-molecule fluorescence in situ hybridization (smFISH) is a powerful method for the visualization and quantification of individual RNA molecules within intact cells. With its ability to probe gene expression at the single cell and single-molecule level, the technique offers valuable insights into cellular processes and cell-to-cell heterogeneity. Although widely used in the animal field, its use in plants has been limited. Here, we present an experimental smFISH workflow that allows researchers to overcome hybridization and imaging challenges in plants, including sample preparation, probe hybridization, and signal detection. Overall, this protocol holds great promise for unraveling the intricacies of gene expression regulation and RNA dynamics at the single-molecule level in whole plants.
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Affiliation(s)
- Sahar Hani
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Caroline Mercier
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France
- Biochimie et Physiologie Moléculaire des Plantes, Univesité de Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Pascale David
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France
| | - Thierry Desnos
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France
| | - Jean-Marc Escudier
- Laboratoire Synthèse et Physico-Chimie de Molécules d'intérêt Biologique, Université Paul Sabatier, CNRS, Toulouse, France
| | - Edouard Bertrand
- Institut de Génétique Humaine, CNRS, UMR9002, Montpellier, France
| | - Laurent Nussaume
- Aix Marseille Univ, CEA, CNRS, BIAM, UMR7265, Saint-Paul lez Durance, France.
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46
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Toosinia S, Davoodian N, Arabi M, Kadivar A. Ameliorating Effect of Sodium Selenite on Developmental and Molecular Response of Bovine Cumulus-Oocyte Complexes Matured in Vitro Under Heat Stress Condition. Biol Trace Elem Res 2024; 202:161-174. [PMID: 37127784 DOI: 10.1007/s12011-023-03678-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Selenium (Se), an essential trace element, plays an important role in the antioxidative defense mechanism, and it has been proven to improve fertility and reproductive efficiency in dairy cattle. The present study evaluated the potential protective action of Se supplement of in vitro maturation (IVM) media on the maturation and subsequent development of bovine cumulus-oocyte complexes (COCs) exposed to heat stress (HS). The treatment with Se improved the viability of cumulus cells (CCs) and oocytes (P < 0.05). The proportion of oocytes reached metaphase II (MII) and those arrested at metaphase I (MI) was greater and lower in treatment than control respectively (P < 0.05). Supplementation with Se increased the percentage of cleaved embryos, total blastocysts, and blastocyst/cleavage ratio (P < 0.05). Moreover, the upregulation of CCND1, SEPP1, GPX-4, SOD, CAT, and downregulation of GRP78, CHOP, and BAX in both Se-treated CCs and oocytes were recorded. The upregulation of NRF2 was detected in Se-treated CCs other than in oocytes, which showed upregulation of IGF2R and SOX-2 as the markers of quality as well. Se supplement in IVM media improved the viability, maturation, and the level of transcripts related to antioxidant defense and quality of heat-treated oocytes, which coincided with greater subsequent development outcomes. Se ameliorated the viability of CCs along with upregulation of antioxidative candidate gene expression and downregulation of apoptosis-related ones to support their protective role on restoring the quality of oocytes against compromising effects of HS.
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Affiliation(s)
- Shervin Toosinia
- Department of Animal Sciences, Faculty of Basic Science, Shahrekord University, Shahrekord, Iran
| | - Najmeh Davoodian
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran.
| | - Mehran Arabi
- Department of Animal Sciences, Faculty of Basic Science, Shahrekord University, Shahrekord, Iran
| | - Ali Kadivar
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
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47
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Fox J, Cummins B, Moseley RC, Gameiro M, Haase SB. A yeast cell cycle pulse generator model shows consistency with multiple oscillatory and checkpoint mutant datasets. Math Biosci 2024; 367:109102. [PMID: 37939998 PMCID: PMC10842220 DOI: 10.1016/j.mbs.2023.109102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/13/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Modeling biological systems holds great promise for speeding up the rate of discovery in systems biology by predicting experimental outcomes and suggesting targeted interventions. However, this process is dogged by an identifiability issue, in which network models and their parameters are not sufficiently constrained by coarse and noisy data to ensure unique solutions. In this work, we evaluated the capability of a simplified yeast cell-cycle network model to reproduce multiple observed transcriptomic behaviors under genomic mutations. We matched time-series data from both cycling and checkpoint arrested cells to model predictions using an asynchronous multi-level Boolean approach. We showed that this single network model, despite its simplicity, is capable of exhibiting dynamical behavior similar to the datasets in most cases, and we demonstrated the drop in severity of the identifiability issue that results from matching multiple datasets.
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Affiliation(s)
- Julian Fox
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Breschine Cummins
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA.
| | | | - Marcio Gameiro
- Department of Mathematics, Rutgers University, New Brunswick, NJ, USA
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48
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Redwood-Sawyerr C, Aw R, Di Blasi R, Moya-Ramírez I, Kontoravdi C, Ceroni F, Polizzi K. High-Throughput Spectroscopic Analysis of mRNA Capping Level. Methods Mol Biol 2024; 2774:269-278. [PMID: 38441771 DOI: 10.1007/978-1-0716-3718-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Eukaryotic mRNAs are characterized by terminal 5' cap structures and 3' polyadenylation sites, which are essential for posttranscriptional processing, translation initiation, and stability. Here, we describe a novel biosensor method designed to detect the presence of both cap structures and polyadenylation sites on mRNA molecules. This novel biosensor is sensitive to mRNA degradation and can quantitatively determine capping levels of mRNA molecules within a mixture of capped and uncapped mRNA molecules. The biosensor displays a constant dynamic range between 254 nt and 6507 nt with reproducible sensitivity to increases in capping level of at least 20% and a limit of detection of 2.4 pmol of mRNA. Overall, the biosensor can provide key information about mRNA quality before mammalian cell transfection.
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Affiliation(s)
- Chileab Redwood-Sawyerr
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Rochelle Aw
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Roberto Di Blasi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Ignacio Moya-Ramírez
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Departamento de Ingeniería Química, Universidad de Granada, Granada, Spain
| | - Cleo Kontoravdi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Francesca Ceroni
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Karen Polizzi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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49
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Kislitsin VY, Chulkin AM, Dotsenko AS, Sinelnikov IG, Sinitsyn AP, Rozhkova AM. The role of intracellular β-glucosidase in cellulolytic response induction in filamentous fungus Penicillium verruculosum. Res Microbiol 2023:104178. [PMID: 38160731 DOI: 10.1016/j.resmic.2023.104178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
In this study, CRISPR/Cas9 genome editing was used to knockout the bgl2 gene encoding intracellular β-glucosidase filamentous fungus Penicillium verruculosum. This resulted in a dramatic reduction of secretion of cellulolytic enzymes. The study of P. verruculosum Δbgl2 found that the transcription of the cbh1 gene, which encodes cellobiohydrolase 1, was impaired when induced by cellobiose and cellotriose. However, the transcription of the cbh1 gene remains at level of the host strain when induced by gentiobiose. This implies that gentiobiose is the true inducer of the cellulolytic response in P. verruculosum, in contrast to Neurospora crassa where cellobiose acts as an inducer.
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Affiliation(s)
- Valeriy Yu Kislitsin
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Andrey M Chulkin
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Anna S Dotsenko
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Igor G Sinelnikov
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Arkady P Sinitsyn
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Aleksandra M Rozhkova
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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50
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Chen MN, Fang ZX, Wu Z, Bai JW, Li RH, Wen XF, Zhang GJ, Liu J. Notch3 restricts metastasis of breast cancers through regulation of the JAK/STAT5A signaling pathway. BMC Cancer 2023; 23:1257. [PMID: 38124049 PMCID: PMC10734157 DOI: 10.1186/s12885-023-11746-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE To explore the potential role of signal transducer and activator of transcription 5A (STAT5A) in the metastasis of breast cancer, and its mechanism of regulation underlying. METHODS AND RESULTS TCGA datasets were used to evaluate the expression of STAT5A in normal and different cancerous tissues through TIMER2.0, indicating that STAT5A level was decreased in breast cancer tissues compared with normal ones. Gene Set Enrichment Analysis predicted that STAT5A was associated with the activation of immune cells and cell cycle process. We further demonstrated that the infiltration of immune cells was positively associated with STAT5A level. Influorescence staining revealed the expression and distribution of F-actin was regulated by STAT5A, while colony formation assay, wound healing and transwell assays predicted the inhibitory role of STAT5A in the colony formation, migratory and invasive abilities in breast cancer cells. In addition, overexpression of the Notch3 intracellular domain (N3ICD), the active form of Notch3, resulted in the increased expression of STAT5A. Conversely, silencing of Notch3 expression by siNotch3 decreased STAT5A expression, supporting that STAT5A expression is positively associated with Notch3 in human breast cancer cell lines and breast cancer tissues. Mechanistically, chromatin immunoprecipitation showed that Notch3 was directly bound to the STAT5A promoter and induced the expression of STAT5A. Moreover, overexpressing STAT5A partially reversed the enhanced mobility of breast cancer cells following Notch3 silencing. Low expression of Notch3 and STAT5A predicted poorer prognosis of patients with breast cancer. CONCLUSION The present study demonstrates that Notch3 inhibits metastasis in breast cancer through inducing transcriptionally STAT5A, which was associated with tumor-infiltrating immune cells, providing a novel strategy to treat breast cancer.
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Affiliation(s)
- Min-Na Chen
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Ze-Xuan Fang
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Zheng Wu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jing-Wen Bai
- Department of Medical Oncology/Xiamen Key Laboratory for Endocrine-Related Cancer Precision Medicine, Xiamen University Medical School, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Rong-Hui Li
- Department of Medical Oncology/Xiamen Key Laboratory for Endocrine-Related Cancer Precision Medicine, Xiamen University Medical School, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Xiao-Fen Wen
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Guo-Jun Zhang
- Xiamen Key Laboratory for Endocrine-Related Cancer Precision Medicine/Department of Breast and Thyroid Surgery, Xiamen University Medical School, Xiang'an Hospital of Xiamen University, Xiamen, China.
| | - Jing Liu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, China.
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