Abstract
Bacteria and bacterial derived metabolites are known to influence the host epigenetic regulation patterns such as DNA methylation and histone modifications, thus altering the expression of critical genes in pathologic processes, for example in metabolic syndrome. Fermentation end products, especially butyrate and LPS (lipopolysaccharides), the latter being cell-wall components of gram-negative bacteria, have been suggested as bioactive metabolites influencing epigenetic modifications by directly influencing enzymes catalyzing epigenetic modifications, by altering the availability of substrates, or by interactions with receptors. Thus, identification and quantification of gut microbiota via molecular based methods are of importance to address different epigenetic patterns and gene expression. We discuss methods for microbiota, epigenetic methylation, and expression analysis of our own research which will have a role in future studies.
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Abbreviations
- AMV:
-
Avian myeloblastosis virus
- APS:
-
Ammonium persulfate solution
- BGS:
-
Bisulfite genomic sequencing
- cDNA:
-
Complementary DNA
- DGGE:
-
Denaturing gradient gel electrophoresis
- DNMT1:
-
DNA-methyltransferase 1
- EDTA:
-
Ethylenediaminetetraacetic acid
- FRAR3:
-
Free fatty acid receptor 3
- FRET:
-
Fluorescence resonance energy transfer
- HDACs:
-
Histone deacetylases
- LPS:
-
Lipopolysaccharide
- 5mC:
-
5-methylcytosine
- MeDIP:
-
Methylated DNA immunoprecipitation
- MMLV:
-
Moloney murine leukemia virus
- MSRE:
-
Methylation sensitive restriction enzyme
- NF-kB:
-
Nuclease factor kB
- PTM:
-
Posttranslational modification
- qPCR:
-
Quantitative real-time polymerase chain reaction
- RT:
-
Reverse transcription
- SCFAs:
-
Short chain fatty acids
- SEM:
-
Structural equation modelling
- TE buffer:
-
Tris-EDTA buffer
- TEMED:
-
N,N,N,N-tetramethylethylenediamine
- TLR:
-
Toll-like receptor
References
Aziz Q, Doré J, Emmanuel A, Guarner F, Quigley EM (2013) Gut microbiota and gastrointestinal health: current concepts and future directions. Neurogastroenterol Motil 25(1):4–15
Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sorensen SJ, Hansen LH, Jakobsen M (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 5(2), e9085
Vrieze A, Holleman F, Zoetendal EG, de Vos WM, Hoekstra JB, Nieuwdorp M (2010) The environment within: how gut microbiota may influence metabolism and body composition. Diabetologia 53(4):606–613
Creely SJ, McTernan PG, Kusminski CM, Fisher FM, Da Silva NF, Khanolkar M, Evans M, Harte AL, Kumar S (2007) Lipopolysaccharide activates an innate immune system response in human adipose tissue in obesity and type 2 diabetes. Am J Physiol Endocrinol Metab 292(3):E740–E747
Remely M, Aumueller E, Jahn D, Hippe B, Brath H, Haslberger AG (2014) Microbiota and epigenetic regulation of inflammatory mediators in type 2 diabetes and obesity. Benef Microbes 5(1):33–43
Remely M, Aumueller E, Merold C, Dworzak S, Hippe B, Zanner J, Pointner A, Brath H, Haslberger AG (2013) Effects of short chain fatty acid producing bacteria on epigenetic regulation of FFAR3 in type 2 diabetes and obesity. Gene 537(1):85–92
Canani RB, Costanzo MD, Leone L, Bedogni G, Brambilla P, Cianfarani S, Nobili V, Pietrobelli A, Agostoni C (2011) Epigenetic mechanisms elicited by nutrition in early life. Nutr Res Rev 24(2):198–205
Dahaliwal A (2013) DNA extraction and purification. Mater Methods 3(191)
Kotorashvili A, Ramnauth A, Liu C, Lin J, Ye K, Kim R, Hazan R, Rohan T, Fineberg S, Loudig O (2012) Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens. PLoS One 7(4), e34683
Wilfinger WW, Mackey K, Chomczynski P (1997) Effect of pH and ionic strength on the spectrophotometric assessment of nucleic acid purity. Biotechniques 22(3):474–476, 478-81
Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59(3):695–700
Neefs JM, Van de Peer Y, De Rijk P, Goris A, De Wachter R (1991) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 19(Suppl):1987–2015
Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73(1):127–141
Beutler E, Gelbart T, Kuhl W (1990) Interference of heparin with the polymerase chain reaction. Biotechniques 9(2):166
Willems M, Moshage H, Nevens F, Fevery J, Yap SH (1993) Plasma collected from heparinized blood is not suitable for HCV-RNA detection by conventional RT-PCR assay. J Virol Methods 42(1):127–130
(1993) Recommendations of the International Council for Standardization in Haematology for Ethylenediaminetetraacetic Acid Anticoagulation of Blood for Blood Cell Counting and Sizing. International Council for Standardization in Haematology: Expert Panel on Cytometry. Am J Clin Pathol 100(4):371–372
Raabe BM, Artwohl JE, Purcell JE, Lovaglio J, Fortman JD (2011) Effects of weekly blood collection in C57BL/6 mice. J Am Assoc Lab Anim Sci 50(5):680–685
Bustin SA (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25(2):169–193
Griffiths-Jones S (2006) miRBase: the microRNA sequence database. Methods Mol Biol 342:129–138
Bui TV, Mendell JT (2010) Myc: maestro of MicroRNAs. Genes Cancer 1(6):568–575
Langevin SM, Stone RA, Bunker CH, Grandis JR, Sobol RW, Taioli E (2010) MicroRNA-137 promoter methylation in oral rinses from patients with squamous cell carcinoma of the head and neck is associated with gender and body mass index. Carcinogenesis 31(5):864–870
Langevin SM, Stone RA, Bunker CH, Lyons-Weiler MA, LaFramboise WA, Kelly L, Seethala RR, Grandis JR, Sobol RW, Taioli E (2011) MicroRNA-137 promoter methylation is associated with poorer overall survival in patients with squamous cell carcinoma of the head and neck. Cancer 117(7):1454–1462
Egger G, Wielscher M, Pulverer W, Kriegner A, Weinhausel A (2012) DNA methylation testing and marker validation using PCR: diagnostic applications. Expert Rev Mol Diagn 12(1):75–92
Noehammer C, Pulverer W, Hassler MR, Hofner M, Wielscher M, Vierlinger K, Liloglou T, McCarthy D, Jensen TJ, Nygren A, Gohlke H, Trooskens G, Braspenning M, Van Criekinge W, Egger G, Weinhaeusel A (2014) Strategies for validation and testing of DNA methylation biomarkers. Epigenomics 6(6):603–622
Pulverer W, Hofner M, Preusser M, Dirnberger E, Hainfellner JA, Weinhaeusel A (2014) A simple quantitative diagnostic alternative for MGMT DNA-methylation testing on RCL2 fixed paraffin embedded tumors using restriction coupled qPCR. Clin Neuropathol 33(1):50–60
Morris T, Lowe R (2012) Report on the Infinium 450 k methylation array analysis workshop: April 20, 2012 UCL, London, UK. Epigenetics 7(8):961–962
Fortin JP, Fertig E, Hansen K (2014) shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R. F1000Res 3:175
Fortin JP, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD (2014) Functional normalization of 450 k methylation array data improves replication in large cancer studies. Genome Biol 15(11):503
Martens JH, Stunnenberg HG (2013) BLUEPRINT: mapping human blood cell epigenomes. Haematologica 98(10):1487–1489
Martens JH, Stunnenberg HG, Logie C (2011) The decade of the epigenomes? Genes Cancer 2(6):680–687
Ptitsyn AA, Weil MM, Thamm DH (2008) Systems biology approach to identification of biomarkers for metastatic progression in cancer. BMC Bioinformatics 9(Suppl 9):S8
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Remely, M., Karlic, H., Rebhan, I., Greunz, M., Haslberger, A.G. (2017). Microbiota and Epigenetic Regulation of Inflammatory Mediators. In: Stefanska, B., MacEwan, D. (eds) Epigenetics and Gene Expression in Cancer, Inflammatory and Immune Diseases. Methods in Pharmacology and Toxicology. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6743-8_8
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DOI: https://doi.org/10.1007/978-1-4939-6743-8_8
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