Sequential Chromatin Immunoprecipitation from Animal Tissues

Chaya, D; Zaret, Kenneth S.

doi:10.1016/s0076-6879(03)76024-8

Cited by 37 publications

(15 citation statements)

References 3 publications

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“…For example, metamorphosis related differential coregulator recruitment to specific genes has been studied by the ChIP analysis of tadpole tissues; zebrafish development has been examined using ChIP on embryonic tissues; ChIP has also been used on the mouse liver chromatin to analyze specific enhancer complexes (Parrazis et al, 2001;Chaya and Zaret, 2003;Havis et al, 2003;Havis et al, 2006). The present report further extends the usefulness of tissue-directed ChIP to study chromatin events during aging.…”

Section: Discussionmentioning

confidence: 65%

Xenobiotic- and vitamin D-responsive induction of the steroid/bile acid-sulfotransferase Sult2A1 in young and old mice: The role of a gene enhancer in the liver chromatin

Seo

Chung

Kim

et al. 2007

Gene

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The xenobiotic-activated nuclear receptors PXR (pregnane X receptor) and CAR (constitutive androstane receptor) and the vitamin D 3 -activated nuclear receptor VDR regulate steroid and xenobiotic metabolism by inducing the phase I cytochrome P450 monooxygenases, phase II conjugating transferases, and the phase III transporters, which mediate the efflux of water-soluble lipid metabolites from cells. Metabolic stress due to the deviant expression of steroid-and xenobioticmetabolizing enzymes is known to have severe health consequences including accelerated aging, and increased expression of these enzymes is associated with extended longevity (Gachon et al, 2006;McElwee et al, 2004). Information on the similarities and dissimilarities in drug metabolism between the young and old, as may be uncovered by studying aging regulation of the genes relevant to steroid and xenobiotic metabolism, is likely to have clinical significance. In this report, we examined the VDR-and PXR-mediated gene induction of the phase II sulfotransferase Sult2A1 in the livers of 4-month and 20-month old mice. Sult2A1 converts bile acids, steroids and a number of drugs to the corresponding sulfated metabolites, which are readily eliminated from the body due to increased water solubility. In RT-PCR assay, aging did not change the induction of Sult2A1 mRNAs by the hormonally active vitamin D 3 and the catatoxic synthetic steroid PCN (pregnenolone-16α-carbonitrile). Chromatin immunoprecipitation (ChIP) from liver nuclei showed that aging had no effect on the activity of an IR0 enhancer in the Sult2A1 chromatin to recruit VDR, RXR-α (retinoid X receptor) and PXR in mice injected with D 3 or PCN. Thus, mice in late life are as competent as those in early life in responding to the hormonal and xenobiotic signaling for Sult2A1 induction. This is the first report describing the role of aging in the functional response of an enhancer in the liver chromatin to the nuclear receptor-dependent signaling.

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Section: Discussionmentioning

confidence: 65%

Xenobiotic- and vitamin D-responsive induction of the steroid/bile acid-sulfotransferase Sult2A1 in young and old mice: The role of a gene enhancer in the liver chromatin

Seo

Chung

Kim

et al. 2007

Gene

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show abstract

“…The method for in vivo ChIP analysis of liver has been modified from protocols for cells (3,6,8). In brief, mouse livers were sliced to small pieces and then incubated with 1% formaldehyde to cross-link proteins to genomic DNA in cells.…”

Section: Methodsmentioning

confidence: 99%

Nuclear factor-κB regulates the expression of multiple genes encoding liver transport proteins

Balasubramaniyan

Ananthanarayanan

Suchy

2016

American Journal of Physiology-Gastrointestinal and Liver Physi

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“…Chromatin immunoprecipitation (ChIP) analysis assays were conducted by a combination of previously described protocols (5,6,16) and manufacturer's instructions using EZ ChIP/MagnaChIP G kit from Upstate Biotechnology/Millipore (Millipore, MA). Briefly, cells from 3ϫ 100-mm culture dishes were harvested after fixation with 1% formaldehyde.…”

Section: Methodsmentioning

confidence: 99%

Direct methylation of FXR by Set7/9, a lysine methyltransferase, regulates the expression of FXR target genes

Balasubramaniyan

Ananthanarayanan

Suchy

2012

American Journal of Physiology-Gastrointestinal and Liver Physi

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The farnesoid X receptor (FXR) is a ligand (bile acid)-dependent nuclear receptor that regulates target genes involved in every aspect of bile acid homeostasis. Upon binding of ligand, FXR recruits an array of coactivators and associated proteins, some of which have intrinsic enzymatic activity that modify histones or even components of the transcriptional complex. In this study, we show chromatin occupancy by the Set7/9 methyltransferase at the FXR response element (FXRE) and direct methylation of FXR in vivo and in vitro at lysine 206. siRNA depletion of Set7/9 in the Huh-7 liver cell line decreased endogenous mRNAs of the FXR target genes, the short heterodimer partner (SHP) and bile salt export pump (BSEP). Mutation of the methylation site at K206 of FXR to an arginine prevented methylation by Set7/9. A pan-methyllysine antibody recognized the wild-type FXR but not the K206R mutant form. An electromobility shift assay showed that methylation by Set7/9 enhanced binding of FXR/retinoic X receptor-α to the FXRE. Interaction between hinge domain of FXR (containing K206) and Set7/9 was confirmed by coimmunoprecipitation, GST pull down, and mammalian two-hybrid experiments. Set7/9 overexpression in Huh-7 cells significantly enhanced transactivation of the SHP and BSEP promoters in a ligand-dependent fashion by wild-type FXR but not the K206R mutant FXR. A Set7/9 mutant deficient in methyltransferase activity was also not effective in increasing transactivation of the BSEP promoter. These studies demonstrate that posttranslational methylation of FXR by Set7/9 contributes to the transcriptional activation of FXR-target genes.

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Sequential Chromatin Immunoprecipitation from Animal Tissues

Cited by 37 publications

References 3 publications

Xenobiotic- and vitamin D-responsive induction of the steroid/bile acid-sulfotransferase Sult2A1 in young and old mice: The role of a gene enhancer in the liver chromatin

Xenobiotic- and vitamin D-responsive induction of the steroid/bile acid-sulfotransferase Sult2A1 in young and old mice: The role of a gene enhancer in the liver chromatin

Nuclear factor-κB regulates the expression of multiple genes encoding liver transport proteins

Direct methylation of FXR by Set7/9, a lysine methyltransferase, regulates the expression of FXR target genes

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