Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress

Cypess AM, Lehman S, Williams G, Tal I, Rodman D, Goldfine AB, et al. Identification and importance of brown adipose tissue in adult humans. N Engl J Med. 2009;360(15):1509–17.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cypess AM, Kahn CR. Brown fat as a therapy for obesity and diabetes. Curr Opin Endocrinol Diabetes Obes. 2010;17(2):143–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Labbé SM, Caron A, Bakan I, Laplante M, Carpentier AC, Lecomte R, et al. In vivo measurement of energy substrate contribution to cold-induced brown adipose tissue thermogenesis. FASEB J Off Publ Fed Am Soc Exp Biol. 2015;29(5):2046–58.

Google Scholar 

van MarkenLichtenbelt WD, Vanhommerig JW, Smulders NM, Drossaerts JMAFL, Kemerink GJ, Bouvy ND, et al. Cold-activated brown adipose tissue in healthy men. N Engl J Med. 2009;360(15):1500–8.

Article  Google Scholar 

Saito M, Okamatsu-Ogura Y, Matsushita M, Watanabe K, Yoneshiro T, Nio-Kobayashi J, et al. High incidence of metabolically active brown adipose tissue in healthy adult humans: effects of cold exposure and adiposity. Diabetes. 2009;58(7):1526–31.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chondronikola M, Volpi E, Børsheim E, Porter C, Annamalai P, Enerbäck S, et al. Brown adipose tissue improves whole-body glucose homeostasis and insulin sensitivity in humans. Diabetes. 2014;63(12):4089–99.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Blondin DP, Labbé SM, Noll C, Kunach M, Phoenix S, Guérin B, et al. Selective impairment of glucose but not fatty acid or oxidative metabolism in brown adipose tissue of subjects with type 2 diabetes. Diabetes. 2015;64(7):2388–97.

Article  CAS  PubMed  Google Scholar 

Nic-Can GI, Rodas-Junco BA, Carrillo-Cocom LM, Zepeda-Pedreguera A, Peñaloza-Cuevas R, Aguilar-Ayala FJ, et al. Epigenetic regulation of adipogenic differentiation by histone lysine demethylation. Int J Mol Sci. 2019;20(16):3918.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xiao H, Kang S. The role of DNA methylation in thermogenic adipose biology. Epigenetics. 2019;14(9):837–43.

Article  PubMed  PubMed Central  Google Scholar 

Yi D, Nguyen HP, Sul HS. Epigenetic dynamics of the thermogenic gene program of adipocytes. Biochem J. 2020;477(6):1137–48.

Article  CAS  PubMed  Google Scholar 

Roh HC, Tsai LTY, Shao M, Tenen D, Shen Y, Kumari M, Lyubetskaya A, Jacobs C, Dawes B, Gupta RK, Rosen ED. Warming Induces Significant Reprogramming of Beige, but Not Brown, Adipocyte Cellular Identity. Cell Metab. 2018;27(5):1121-1137.e5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Leinonen R, Sugawara H, Shumway M, On behalf of the International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic Acids Res. 2011;39(Database):D19-21.

Article  CAS  PubMed  Google Scholar 

Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010.

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.

Article  CAS  PubMed  Google Scholar 

Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.

Article  PubMed  PubMed Central  Google Scholar 

Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, et al. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci USA. 2014;111(51):E5593-5601.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Blake JA, Baldarelli R, Kadin JA, Richardson JE, Smith CL, Bult CJ, et al. Mouse Genome Database (MGD): knowledgebase for mouse-human comparative biology. Nucleic Acids Res. 2021;49(D1):D981–7.

Article  CAS  PubMed  Google Scholar 

Smith CL, Eppig JT. The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med. 2009;1(3):390–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ochsner SA, Pillich RT, McKenna NJ. Consensus transcriptional regulatory networks of coronavirus-infected human cells. Sci Data. 2020;7(1):314.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zapata RC, Chaudry BS, Valencia ML, Zhang D, Ochsner SA, McKenna NJ, et al. Conserved immunomodulatory transcriptional networks underlie antipsychotic-induced weight gain. Transl Psychiatry. 2021;11(1):405.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bissig-Choisat B, Alves-Bezerra M, Zorman B, Ochsner SA, Barzi M, Legras X, et al. A human liver chimeric mouse model for non-alcoholic fatty liver disease. JHEP Rep. 2021;3(3): 100281.

Article  PubMed  PubMed Central  Google Scholar 

Chen KY, De Angulo A, Guo X, More A, Ochsner SA, Lopez E, et al. Adipocyte-specific ablation of PU.1 promotes energy expenditure and ameliorates metabolic syndrome in aging mice. Front Aging. 2022;2: 803482.

Article  PubMed  PubMed Central  Google Scholar 

Ochsner SA, Abraham D, Martin K, Ding W, McOwiti A, Kankanamge W, et al. The signaling pathways project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways. Sci Data. 2019;6(1):252.

Article  PubMed  PubMed Central  Google Scholar 

Oki S, Ohta T, Shioi G, Hatanaka H, Ogasawara O, Okuda Y, et al. ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. EMBO Rep. 2018;19(12): e46255.

Article  PubMed  PubMed Central  Google Scholar 

Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol. 1995;57(1):289–300.

Article  Google Scholar 

Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27(11):1571–2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012;13(10):R87.

Article  PubMed  PubMed Central  Google Scholar 

Liao Y, Wang J, Jaehnig EJ, Shi Z, Zhang B. WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs. Nucleic Acids Res. 2019;47(W1):W199-205.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Walter W, Sánchez-Cabo F, Ricote M. GOplot: an R package for visually combining expression data with functional analysis. Bioinformatics. 2015;31(17):2912–4.

Article  CAS  PubMed  Google Scholar 

Holt MV, Wang T, Young NL. Expeditious extraction of histones from limited cells or tissue samples and quantitative top-down proteomic analysis. Curr Protoc. 2021. https://doi.org/10.1002/cpz1.26.

Article  PubMed  PubMed Central  Google Scholar 

Taylor BC, Young NL. Histone H4 proteoforms and post-translational modifications in the Mus musculus brain with quantitative comparison of ages and brain regions. Anal Bioanal Chem. 2023;415(9):1627–39.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Holt MV, Wang T, Young NL. High-throughput quantitative top-down proteomics: histone H4. J Am Soc Mass Spectrom. 2019;30(12):2548–60.

Article  CAS  PubMed  Google Scholar 

DiMaggio PA, Young NL, Baliban RC, Garcia BA, Floudas CA. A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry. Mol Cell Proteomics. 2009;8(11):2527–43.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jiang T, Hoover ME, Holt MV, Freitas MA, Marshall AG, Young NL. Middle-down characterization of the cell cycle dependence of histone H4 posttranslational modifications and proteoforms. Proteomics. 2018;18(11):1700442.

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