1
|
Larter CZ and Yeh MM: Animal models of
NASH: getting both pathology and metabolic context right. J
Gastroenterol Hepatol. 23:1635–1648. 2008. View Article : Google Scholar : PubMed/NCBI
|
2
|
Hotamisligil GS: Inflammation and
metabolic disorders. Nature. 444:860–867. 2006. View Article : Google Scholar
|
3
|
Curat CA, Miranville A, Sengenès C, Diehl
M, Tonus C, Busse R and Bouloumié A: From blood monocytes to
adipose tissue-resident macrophages: induction of diapedesis by
human mature adipocytes. Diabetes. 53:1285–1292. 2004. View Article : Google Scholar : PubMed/NCBI
|
4
|
Kamei N, Tobe K, Suzuki R, et al:
Overexpression of monocyte chemoattractant protein-1 in adipose
tissues causes macrophage recruitment and insulin resistance. J
Biol Chem. 281:26602–26614. 2006. View Article : Google Scholar
|
5
|
Musso G, Gambino R and Cassader M:
Obesity, diabetes, and gut microbiota: the hygiene hypothesis
expanded? Diabetes Care. 33:2277–2284. 2010. View Article : Google Scholar : PubMed/NCBI
|
6
|
Moreno-Indias I, Cardona F, Tinahones FJ
and Queipo-Ortuño MI: Impact of the gut microbiota on the
development of obesity and type 2 diabetes mellitus. Front
Microbiol. 5:1902014. View Article : Google Scholar : PubMed/NCBI
|
7
|
Cani PD and Delzenne NM: The role of the
gut microbiota in energy metabolism and metabolic disease. Curr
Pharm Des. 15:1546–1558. 2009. View Article : Google Scholar : PubMed/NCBI
|
8
|
Nesteruk M, Hennig EE, Mikula M, et al:
Mitochondrial-related proteomic changes during obesity and fasting
in mice are greater in the liver than skeletal muscles. Funct
Integr Genomics. 14:245–259. 2014. View Article : Google Scholar : PubMed/NCBI
|
9
|
Hennig EE, Mikula M, Goryca K, et al:
Extracellular matrix and cytochrome P450 gene expression can
distinguish steatohepatitis from steatosis in mice. J Cell Mol Med.
18:1762–1772. 2014. View Article : Google Scholar : PubMed/NCBI
|
10
|
Prinjha R and Tarakhovsky A: Chromatin
targeting drugs in cancer and immunity. Genes Dev. 27:1731–1738.
2013. View Article : Google Scholar : PubMed/NCBI
|
11
|
Bannister AJ and Kouzarides T: Regulation
of chromatin by histone modifications. Cell Res. 21:381–395. 2011.
View Article : Google Scholar : PubMed/NCBI
|
12
|
Kouzarides T: Chromatin modifications and
their function. Cell. 128:693–705. 2007. View Article : Google Scholar : PubMed/NCBI
|
13
|
Dahl JA and Collas P: MicroChIP: chromatin
immunoprecipitation for small cell numbers. Methods Mol Biol.
567:59–74. 2009. View Article : Google Scholar : PubMed/NCBI
|
14
|
Flanagin S, Nelson JD, Castner DG,
Denisenko O and Bomsztyk K: Microplate-based chromatin
immunoprecipitation method, Matrix ChIP: a platform to study
signaling of complex genomic events. Nucleic Acids Res. 36:e172008.
View Article : Google Scholar : PubMed/NCBI
|
15
|
Bomsztyk K, Flanagin S, Mar D, Mikula M,
Johnson A, Zager R and Denisenko O: Synchronous recruitment of
epigenetic modifiers to endotoxin synergistically activated Tnf-α
gene in acute kidney injury. PLoS ONE. 8:e703222013.PubMed/NCBI
|
16
|
Yu J, Feng Q, Ruan Y, Komers R, Kiviat N
and Bomsztyk K: Microplate-based platform for combined chromatin
and DNA methylation immunoprecipitation assays. BMC Mol Biol.
12:492011. View Article : Google Scholar : PubMed/NCBI
|
17
|
Vandesompele J, De Preter K, Pattyn F,
Poppe B, Van Roy N, De Paepe A and Speleman F: Accurate
normalization of real-time quantitative RT-PCR data by geometric
averaging of multiple internal control genes. Genome Biol.
3:RESEARCH00342002. View Article : Google Scholar : PubMed/NCBI
|
18
|
Tian Y, Wong VWS, Chan HLY and Cheng ASL:
Epigenetic regulation of hepatocellular carcinoma in non-alcoholic
fatty liver disease. Semin Cancer Biol. 23:471–482. 2013.
View Article : Google Scholar : PubMed/NCBI
|
19
|
Lawrence T: The nuclear factor NF-kappaB
pathway in inflammation. Cold Spring Harb Perspect Biol.
1:a0016512009. View Article : Google Scholar : PubMed/NCBI
|
20
|
Medzhitov R and Horng T: Transcriptional
control of the inflammatory response. Nat Rev Immunol. 9:692–703.
2009. View
Article : Google Scholar : PubMed/NCBI
|
21
|
Freaney JE, Kim R, Mandhana R and Horvath
CM: Extensive cooperation of immune master regulators IRF3 and
NF-κB in RNA Pol II recruitment and pause release in human innate
antiviral transcription. Cell Rep. 4:959–973. 2013.PubMed/NCBI
|
22
|
Martone R, Euskirchen G, Bertone P, et al:
Distribution of NF-kappaB-binding sites across human chromosome 22.
Proc Natl Acad Sci USA. 100:12247–12252. 2003. View Article : Google Scholar : PubMed/NCBI
|
23
|
Shanmugam MK and Sethi G: Role of
epigenetics in inflammation-associated diseases. Subcell Biochem.
61:627–657. 2013. View Article : Google Scholar : PubMed/NCBI
|
24
|
Naik A, Košir R and Rozman D: Genomic
aspects of NAFLD pathogenesis. Genomics. 102:84–95. 2013.
View Article : Google Scholar
|
25
|
Kim Y and Park T: DNA microarrays to
define and search for genes associated with obesity. Biotechnol J.
5:99–112. 2010. View Article : Google Scholar : PubMed/NCBI
|
26
|
Xu C, Wang G, Hao Y, Zhi J, Zhang L and
Chang C: Correlation analysis between gene expression profile of
rat liver tissues and high-fat emulsion-induced nonalcoholic fatty
liver. Dig Dis Sci. 56:2299–2308. 2011. View Article : Google Scholar : PubMed/NCBI
|
27
|
Nishida T, Tsuneyama K, Fujimoto M, et al:
Spontaneous onset of nonalcoholic steatohepatitis and
hepatocellular carcinoma in a mouse model of metabolic syndrome.
Lab Invest. 93:230–241. 2013. View Article : Google Scholar : PubMed/NCBI
|
28
|
Stanton MC, Chen SC, Jackson JV, et al:
Inflammatory Signals shift from adipose to liver during high fat
feeding and influence the development of steatohepatitis in mice. J
Inflamm (Lond). 8:82011. View Article : Google Scholar : PubMed/NCBI
|
29
|
Semaan N, Frenzel L, Alsaleh G, et al:
miR-346 controls release of TNF-α protein and stability of its mRNA
in rheumatoid arthritis via tristetraprolin stabilization. PLoS
ONE. 6:e198272011.PubMed/NCBI
|
30
|
Deleault KM, Skinner SJ and Brooks SA:
Tristetraprolin regulates TNF TNF-alpha mRNA stability via a
proteasome dependent mechanism involving the combined action of the
ERK and p38 pathways. Mol Immunol. 45:13–24. 2008. View Article : Google Scholar : PubMed/NCBI
|
31
|
Li Z, Chao TC, Chang KY, et al: The long
noncoding RNA THRIL regulates TNFα expression through its
interaction with hnRNPL. Proc Natl Acad Sci USA. 111:1002–1007.
2014.PubMed/NCBI
|
32
|
Naito M, Bomsztyk K and Zager RA:
Endotoxin mediates recruitment of RNA polymerase II to target genes
in acute renal failure. J Am Soc Nephrol. 19:1321–1330. 2008.
View Article : Google Scholar : PubMed/NCBI
|
33
|
Struhl K: Histone acetylation and
transcriptional regulatory mechanisms. Genes Dev. 12:599–606. 1998.
View Article : Google Scholar : PubMed/NCBI
|
34
|
Shebzukhov YV, Horn K, Brazhnik KI,
Drutskaya MS, Kuchmiy AA, Kuprash DV and Nedospasov SA: Dynamic
changes in chromatin conformation at the TNF transcription start
site in T helper lymphocyte subsets. Eur J Immunol. 44:251–264.
2014. View Article : Google Scholar : PubMed/NCBI
|
35
|
Miao F, Gonzalo IG, Lanting L and
Natarajan R: In vivo chromatin remodeling events leading to
inflammatory gene transcription under diabetic conditions. J Biol
Chem. 279:18091–18097. 2004. View Article : Google Scholar : PubMed/NCBI
|
36
|
Sullivan KE, Reddy ABM, Dietzmann K,
Suriano AR, Kocieda VP, Stewart M and Bhatia M: Epigenetic
regulation of tumor necrosis factor alpha. Mol Cell Biol.
27:5147–5160. 2007. View Article : Google Scholar : PubMed/NCBI
|
37
|
Garrett S, Dietzmann-Maurer K, Song L and
Sullivan KE: Polarization of primary human monocytes by IFN-gamma
induces chromatin changes and recruits RNA Pol II to the TNF-alpha
promoter. J Immunol. 180:5257–5266. 2008. View Article : Google Scholar : PubMed/NCBI
|
38
|
Falvo JV, Tsytsykova AV and Goldfeld AE:
Transcriptional control of the TNF gene. Current Directions in
Autoimmunity. 11. Kollias G and Sfikakis PP: Karger; Basel: pp.
27–60. 2010, View Article : Google Scholar : PubMed/NCBI
|
39
|
Nicodeme E, Jeffrey KL, Schaefer U, et al:
Suppression of inflammation by a synthetic histone mimic. Nature.
468:1119–1123. 2010. View Article : Google Scholar : PubMed/NCBI
|
40
|
Wang F, Liu H, Blanton WP, Belkina A,
Lebrasseur NK and Denis GV: Brd2 disruption in mice causes severe
obesity without Type 2 diabetes. Biochem J. 425:71–83. 2010.
View Article : Google Scholar : PubMed/NCBI
|
41
|
Wang F, Deeney JT and Denis GV: Brd2 gene
disruption causes ‘metabolically healthy’ obesity: epigenetic and
chromatin-based mechanisms that uncouple obesity from type 2
diabetes. Vitam Horm. 91:49–75. 2013.
|
42
|
Belkina AC and Denis GV: BET domain
co-regulators in obesity, inflammation and cancer. Nat Rev Cancer.
12:465–477. 2012. View Article : Google Scholar : PubMed/NCBI
|
43
|
Zhang Y and Reinberg D: Transcription
regulation by histone methylation: interplay between different
covalent modifications of the core histone tails. Genes Dev.
15:2343–2360. 2001. View Article : Google Scholar : PubMed/NCBI
|
44
|
Shilatifard A: Chromatin modifications by
methylation and ubiquitination: implications in the regulation of
gene expression. Annu Rev Biochem. 75:243–269. 2006. View Article : Google Scholar : PubMed/NCBI
|
45
|
Zhang H, Gao L, Anandhakumar J and Gross
DS: Uncoupling transcription from covalent histone modification.
PLoS Genet. 10:e10042022014. View Article : Google Scholar : PubMed/NCBI
|