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      Impaired energy expenditure following exposure to either DDT or DDE in mice may be mediated by DNA methylation changes in brown adipose

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          Abstract

          The insecticide dichlorodiphenyltrichloroethane (DDT) and its persistent metabolite, dichlorodiphenyldichloroethylene (DDE), have been associated with increased adiposity and obesity in multiple generations of rodents and humans. These lipophilic pollutants accumulate in adipose tissue and appear to decrease energy expenditure through the impairment of thermogenesis in brown adipose tissue (BAT). We hypothesized that impaired thermogenesis is due to persistent epigenetic modifications of BAT. To address this, we exposed C57BL/6 J mice to DDT or DDE from gestational day (GD) 11.5 to postnatal day (PND) 5, evaluated longitudinal body temperature, and performed reduced representation bisulfite sequencing and RNA sequencing of BAT from infant and adult offspring. Exposure to DDT or DDE reduced core body temperature in adult mice, and differential methylation at the pathway and gene level was persistent from infancy to adulthood. Furthermore, thermogenesis and biological pathways essential for thermogenic function, such as oxidative phosphorylation and mechanistic target of rapamycin kinase (mTOR) signaling, were enriched with differential methylation and RNA transcription in adult mice exposed to DDT or DDE. PAZ6 human brown preadipocytes were differentiated in the presence of DDT or DDE to understand the brown adipocyte-autonomous effect of these pollutants. In vitro exposure led to limited changes in RNA expression; however, mitochondrial membrane potential was decreased in vitro with 0.1 µM and 1 µM doses of DDT or DDE. These results demonstrate that concentrations of DDT and DDE relevant to human exposure have a significant effect on thermogenesis, the transcriptome, and DNA methylome of mouse BAT and the mitochondrial function of human brown adipocytes.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

              Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data. Together, they allow biologists to identify new genes and new splice variants of known ones, as well as compare gene and transcript expression under two or more conditions. This protocol describes in detail how to use TopHat and Cufflinks to perform such analyses. It also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-seq analysis results. Although the procedure assumes basic informatics skills, these tools assume little to no background with RNA-seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results. The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time.
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                Author and article information

                Contributors
                Journal
                Environ Epigenet
                Environ Epigenet
                eep
                Environmental Epigenetics
                Oxford University Press (UK )
                2058-5888
                2024
                23 August 2024
                23 August 2024
                : 10
                : 1
                : dvae011
                Affiliations
                departmentDepartment of Environmental Toxicology, University of California, Davis , Davis, CA 95616, United States
                departmentDepartment of Environmental Toxicology, University of California, Davis , Davis, CA 95616, United States
                departmentDepartment of Environmental Toxicology, University of California, Davis , Davis, CA 95616, United States
                departmentDepartment of Environmental Toxicology, University of California, Davis , Davis, CA 95616, United States
                Author notes
                *Corresponding author. Department of Environmental Toxicology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States. E-mail: mlamerrill@ 123456ucdavis.edu
                Author information
                https://orcid.org/0000-0002-5720-5862
                Article
                dvae011
                10.1093/eep/dvae011
                11472829
                39403345
                7bd4d2e8-1133-4b5a-bb60-1c29b7b76146
                © The Author(s) 2024. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 18 April 2024
                : 09 July 2024
                : 16 August 2024
                : 30 July 2024
                : 14 October 2024
                Page count
                Pages: 15
                Funding
                Funded by: National Institutes of Health R01;
                Award ID: ES024946
                Funded by: USDA National Institute of Food and Agriculture, DOI 10.13039/100005825;
                Award ID: CA-D-ETX-2233-H
                Funded by: National Institutes of Health T32;
                Award ID: ES007059
                Funded by: National Institutes of Health R01;
                Award ID: ES024946
                Funded by: USDA National Institute of Food and Agriculture, DOI 10.13039/100005825;
                Award ID: CA-D-ETX-2233-H
                Funded by: National Institutes of Health T32;
                Award ID: ES007059
                Categories
                Research Article
                AcademicSubjects/SCI02302

                dna methylation,brown adipose tissue,ddt,dde,thermogenesis,oxidative phosphorylation,transcription,mtor,steroidogenesis

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