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Li L, Liu Z, Hu H, Cai R, Bi J, Wang Q, Zhou X, Luo H, Zhang C, Wan R. Dendrobium Nobile Alcohol Extract Extends the Lifespan of Caenorhabditis elegans via hsf-1 and daf-16. Molecules 2024; 29:908. [PMID: 38398658 PMCID: PMC10891841 DOI: 10.3390/molecules29040908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/01/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Dendrobium nobile is a traditional Chinese herb with anti-inflammatory, antioxidant, and neuroprotective properties. However, its antiaging effects are unclear. Herein, we studied the aging-related functions and the mechanism of action of the alcohol extract of Dendrobium nobile (DnAE) in the model organism Caenorhabditis elegans. The results indicated that 1 mg/mL DnAE slowed lipofuscin accumulation, decreased the levels of reactive oxygen species, elevated superoxide dismutase activity, enhanced oxidative and heat stress resistance, extended the lifespan of nematodes, protected their dopamine neurons from 6-hydroxydopamine-induced neurodegeneration, and reduced Aβ-induced neurotoxicity. DnAE upregulated the mRNA expression of the transcription factors DAF-16 and HSF-1, promoted the nuclear localization of DAF-16, and enhanced the fluorescence intensity of HSP-16.2. However, it had no effect on the lifespan of DAF-16 mutants. Thus, DnAE can significantly extend lifespan, enhance heat stress tolerance, and delay age-related diseases through a DAF-16-dependent pathway.
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Affiliation(s)
- Linfeng Li
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Key Laboratory of Luzhou City for Aging Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Zhen Liu
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Key Laboratory of Luzhou City for Aging Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Huiling Hu
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Key Laboratory of Luzhou City for Aging Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Renming Cai
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Key Laboratory of Luzhou City for Aging Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Jingdou Bi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Qin Wang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Dazhou Vocational College of Chinese Medicine, Dazhou 635000, China
| | - Xiaogang Zhou
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Huairong Luo
- Key Laboratory of Luzhou City for Aging Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Chun Zhang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Key Laboratory of Luzhou City for Aging Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Runlan Wan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Key Laboratory of Luzhou City for Aging Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
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2
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Chen Y, Arlt VM, Stürzenbaum SR. MosSCI-mediated exogenous gene expression is modulated by genomic positioning. Biotechnol J 2023; 18:e2300062. [PMID: 37177911 DOI: 10.1002/biot.202300062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/15/2023]
Abstract
Although the Mos1-mediated single-copy insertion (MosSCI) technique has been widely used to generate stable transgenic Caenorhabditis elegans strains, the link between stability of expression and integration site still needs to be explored. Here, experimental evidence is provided that transgenes are not able to match the level of transcription of their native counterpart, and that insertions at certain locations can result in an external stress-mediated increase in expression. Insertion site ttTi5605 on chromosome II was shown to be a superior location, at least when introducing reproduction related genes. Thus, this study provides a reference for the selection of an optimal site for MosSCI which provides acceptable expression performance whilst minimizing undesirable secondary effects.
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Affiliation(s)
- Yuzhi Chen
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Volker M Arlt
- Toxicology Department, GAB Consulting GmbH, Heidelberg, Germany
| | - Stephen R Stürzenbaum
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
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Esse R, Gushchanskaia ES, Lord A, Grishok A. DOT1L complex suppresses transcription from enhancer elements and ectopic RNAi in Caenorhabditis elegans. RNA (NEW YORK, N.Y.) 2019; 25:1259-1273. [PMID: 31300558 PMCID: PMC6800474 DOI: 10.1261/rna.070292.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/10/2019] [Indexed: 05/14/2023]
Abstract
Methylation of histone H3 on lysine 79 (H3K79) by DOT1L is associated with actively transcribed genes. Earlier, we described that DOT-1.1, the Caenorhabditis elegans homolog of mammalian DOT1L, cooperates with the chromatin-binding protein ZFP-1 (AF10 homolog) to negatively modulate transcription of highly and widely expressed target genes. Also, the reduction of ZFP-1 levels has consistently been associated with lower efficiency of RNA interference (RNAi) triggered by exogenous double-stranded RNA (dsRNA), but the reason for this is not clear. Here, we demonstrate that the DOT1L complex suppresses transcription originating from enhancer elements and antisense transcription, thus potentiating the expression of enhancer-regulated genes. We also show that worms lacking H3K79 methylation do not survive, and this lethality is suppressed by a loss of caspase-3 or Dicer complex components that initiate gene silencing response to exogenous dsRNA. Our results suggest that ectopic elevation of endogenous dsRNA directly or indirectly resulting from global misregulation of transcription in DOT1L complex mutants may engage the Dicer complex and, therefore, limit the efficiency of exogenous RNAi.
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Affiliation(s)
- Ruben Esse
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | | | - Avery Lord
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Alla Grishok
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
- Genome Science Institute, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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4
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Gushchanskaia ES, Esse R, Ma Q, Lau NC, Grishok A. Interplay between small RNA pathways shapes chromatin landscapes in C. elegans. Nucleic Acids Res 2019; 47:5603-5616. [PMID: 31216042 PMCID: PMC6582410 DOI: 10.1093/nar/gkz275] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
The nematode Caenorhabditis elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both 'silencing' siRNAs bound by Worm-specific Argonautes (WAGO) and 'activating' siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here, we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partially rescued null mutant strain (WM193), this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements and an increased number of small RNAs that match enhancers in both drh-3 and csr-1 mutants. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to sites with increased silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.
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Affiliation(s)
| | - Ruben Esse
- Boston University School of Medicine, Department of Biochemistry, Boston, MA 02118, USA
| | - Qicheng Ma
- Boston University School of Medicine, Department of Biochemistry, Boston, MA 02118, USA
| | - Nelson C Lau
- Boston University School of Medicine, Department of Biochemistry, Boston, MA 02118, USA
- Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alla Grishok
- Boston University School of Medicine, Department of Biochemistry, Boston, MA 02118, USA
- Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
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5
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Ho MCW, Quintero-Cadena P, Sternberg PW. Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq. Genome Res 2017; 27:2108-2119. [PMID: 29074739 PMCID: PMC5741056 DOI: 10.1101/gr.223735.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/18/2017] [Indexed: 12/23/2022]
Abstract
Deep sequencing of size-selected DNase I–treated chromatin (DNase-seq) allows high-resolution measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo active cis-regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1 arrest larvae to generate high-resolution maps of TF binding. Over half of embryonic DNase I hypersensitive sites (DHSs) were annotated as noncoding, with 24% in intergenic, 12% in promoters, and 28% in introns, with similar statistics observed in L1 arrest larvae. Noncoding DHSs are highly conserved and enriched in marks of enhancer activity and transcription. We validated noncoding DHSs against known enhancers from myo-2, myo-3, hlh-1, elt-2, and lin-26/lir-1 and recapitulated 15 of 17 known enhancers. We then mined DNase-seq data to identify putative active CRMs and TF footprints. Using DNase-seq data improved predictions of tissue-specific expression compared with motifs alone. In a pilot functional test, 10 of 15 DHSs from pha-4, icl-1, and ceh-13 drove reporter gene expression in transgenic C. elegans. Overall, we provide experimental annotation of 26,644 putative CRMs in the embryo containing 55,890 TF footprints, as well as 15,841 putative CRMs in the L1 arrest larvae containing 32,685 TF footprints.
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Affiliation(s)
- Margaret C W Ho
- Division of Biology and Bioengineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
| | - Porfirio Quintero-Cadena
- Division of Biology and Bioengineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
| | - Paul W Sternberg
- Division of Biology and Bioengineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
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Narasimhan K, Lambert SA, Yang AWH, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJM, Weirauch MT, Hughes TR. Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. eLife 2015; 4. [PMID: 25905672 PMCID: PMC4434323 DOI: 10.7554/elife.06967] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/22/2015] [Indexed: 12/13/2022] Open
Abstract
Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C. elegans TFs (∼40%). These data highlight the diversification of binding motifs for the nuclear hormone receptor and C2H2 zinc finger families and reveal unexpected diversity of motifs for T-box and DM families. Motif enrichment in promoters of functionally related genes is consistent with known biology and also identifies putative regulatory roles for unstudied TFs. DOI:http://dx.doi.org/10.7554/eLife.06967.001 Many scientists use ‘model’ species—such as the fruit fly or a nematode worm called Caenorhabditis elegans—in their research because these organisms have useful features that make it easier to carry out many experiments. For example, C. elegans has a smaller genome compared to many other animals, which is useful for studying the roles of individual genes or stretches of DNA. Transcription factors are a type of protein that can bind to specific stretches of DNA and help to switch certain genes on or off. These ‘motifs’ may be close to the gene or further away in the genome, and therefore, must stand out amongst the rest of the DNA, like lights on a landing strip. However, the motifs for only 10% of the estimated 763 transcription factors in C. elegans have been identified so far. In this study, Narasimhan, Lambert, Yang et al. used a technique called a ‘protein binding microarray’ to identify the motifs for many more of the C. elegans transcription factors. These findings were then used to predict motifs for other transcription factors. Together, these methods increased the proportion of C. elegans transcription factors with known DNA-binding motifs from 10% to around 40%. Now that more DNA motifs have been identified, it is possible to look for similarities and differences between them. For example, Narasimhan, Lambert, Yang et al. found that transcription factors with similar sequences can bind to very varied motifs. On the other hand, some transcription factors that are very different are able to recognize very similar motifs. The experiments also indicate that motifs found very close to genes—in sequences known as ‘promoters’—may be able to interact with many proteins to influence the activity of genes. Narasimhan, Lambert, Yang et al.'s findings increase the number of C. elegans transcription factors with a motif, bringing the knowledge of these proteins more in line with the better-studied transcription factors of humans and fruit flies. The next challenge is to identify DNA motifs for the remaining 60% of transcription factors. DOI:http://dx.doi.org/10.7554/eLife.06967.002
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Affiliation(s)
- Kamesh Narasimhan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Samuel A Lambert
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ally W H Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Jeremy Riddell
- Department of Molecular and Cellular Physiology, Systems Biology and Physiology Program, University of Cincinnati, Cincinnati, United States
| | - Sanie Mnaimneh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Hong Zheng
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Mihai Albu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Hamed S Najafabadi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - John S Reece-Hoyes
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States
| | - Juan I Fuxman Bass
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States
| | - Albertha J M Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
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Reinke V, Krause M, Okkema P. Transcriptional regulation of gene expression in C. elegans. ACTA ACUST UNITED AC 2013:1-34. [PMID: 23801596 DOI: 10.1895/wormbook.1.45.2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single-cell and minute-time-scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated proteins and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.
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Affiliation(s)
- Valerie Reinke
- Department of Genetics, Yale University, New Haven, CT 06520, USA.
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