Chromatin Immunoprecipitation Assay

Das, P.; Ramachandran, K.; vanWert, Jane M.; Singal, Rakesh

doi:10.2144/04376rv01

Cited by 173 publications

(135 citation statements)

References 41 publications

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“…ChIP has been used to identify protein-DNA interactions regulating DNA replication and chromosome stability and transcription (31)(32)(33). Both ChIP and mIP provide a spatial map of DNA binding that may change depending, for example, on the cell cycle, intra-or extracellular signals, or response to stress.…”

Section: Resultsmentioning

confidence: 99%

Roles for the Human ATP-dependent Lon Protease in Mitochondrial DNA Maintenance

Lü

Yadav

Shah

et al. 2007

Journal of Biological Chemistry

129

121

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Human mitochondrial Lon is an ATP-powered proteolytic machine that specifically binds to single-stranded G-rich DNA and RNA in vitro. However, it is unknown whether Lon binds mitochondrial DNA (mtDNA) in living cells or functions in mtDNA integrity. Here, we demonstrate that Lon interacts with the mitochondrial genome in cultured cells using mtDNA immunoprecipitation (mIP). Lon associates with sites distributed primarily within one-half of the genome and preferentially with the control region for mtDNA replication and transcription. Bioinformatic analysis of mIP data revealed a G-rich consensus sequence. Consistent with these findings, in vitro experiments showed that the affinity of Lon for single-stranded DNA oligonucleotides correlates with conformity to this consensus. To examine the role of Lon in mtDNA maintenance, cells carrying an inducible short hairpin RNA for Lon depletion were used. In control and Lon-depleted cells, mtDNA copy number was essentially the same in the presence or absence of oxidative stress. However when oxidatively stressed, control cells exhibited an increased frequency of mtDNA lesions, whereas Lon-depleted cells showed little if any mtDNA damage. This suggests that oxidative mtDNA damage is permitted when Lon is present and prevented when Lon is substantially depleted. Upon oxidative stress, mIP showed reduced Lon binding to mtDNA; however binding to the control region was unaffected. It is unlikely that oxidative modification of Lon blocks its ability to bind DNA in vivo as results show that oxidized purified Lon retains sequence-specific DNA binding. Taken together, these results demonstrate that mtDNA binding is a physiological function of Lon and that cellular levels of Lon influence sensitivity to mtDNA damage. These findings suggest roles for Lon in linking protein and mtDNA quality control.

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Section: Resultsmentioning

confidence: 99%

Roles for the Human ATP-dependent Lon Protease in Mitochondrial DNA Maintenance

Lü

Yadav

Shah

et al. 2007

Journal of Biological Chemistry

129

121

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“…Chromatin Immunoprecipitation Analysis of Cultured Cell Lines and Mouse Liver-Chromatin immunoprecipitation (ChIP) assays were done by a combination of previously described protocols and manufacturer's instructions using the EZ ChIP/MagnaChIP G kit from Upstate Biotechnology/Millipore (Millipore, MA) (15,17). Briefly, cells from 4 ϫ 100-mm culture dishes were harvested after fixation with 1% formaldehyde.…”

Section: Methodsmentioning

confidence: 99%

SUMOylation of the Farnesoid X Receptor (FXR) Regulates the Expression of FXR Target Genes

Balasubramaniyan

Luo

Sun

et al. 2013

Journal of Biological Chemistry

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Background: Small ubiquitin-like modifiers (SUMO) are covalently conjugated to other proteins including nuclear receptors leading to modification of various cellular processes. Results: Ligand-dependent SUMOylation of farnesoid X receptor (FXR) negatively regulates the expression of its target genes. Conclusion: SUMO modification attenuates the capacity of FXR to function as a transcriptional activator. Significance: Defining post-translation modification of FXR by SUMO is important to understanding how this nuclear receptor functions in health and disease.

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“…34 For immunoprecipitation, 5 g of each antibody or negative control rabbit IgG was used. SYBR-Green semiquantitative PCR was performed as described.…”

Section: Chipmentioning

confidence: 99%

Lenalidomide treatment promotes CD154 expression on CLL cells and enhances production of antibodies by normal B cells through a PI3-kinase–dependent pathway

Lapalombella

Andritsos

Liu

et al. 2010

Blood

109

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Chronic lymphocytic leukemia (CLL) involves a profound humoral immune defect and tumor-specific humoral tolerance that directly contribute to disease morbidity and mortality. CD154 gene therapy can reverse this immune defect, but attempts to do this pharmacologically have been unsuccessful. The immunemodulatory agent lenalidomide shows clinical activity in CLL, but its mechanism is poorly understood. Here, we demonstrate that lenalidomide induces expression of functional CD154 antigen on CLL IntroductionChronic lymphocytic leukemia (CLL) is the most common adult leukemia, and is characterized by an elevated frequency of infections, secondary malignancy, and autoimmune complications compared with the general population. Current treatment options for CLL are palliative and further exacerbate the immune deficiency seen in this disease. Nonetheless, CLL represents an "immunoresponsive" disease as evidenced by extended disease remission and potential cure with reduced intensity allogeneic stem cell transplantation (reviewed in Gribben 1 ). This suggests that strategies that restore immune function have potential to effectively eliminate CLL.The immune defect in CLL is characterized by both humoral and cellular immune defects. Although detailed studies of normal B cells in CLL patients have not been performed due to the difficulty in isolating these cells, hypogammaglobulinemia is often present at diagnosis and becomes worse with disease progression. A profound cellular immune defect 2-4 is present in CLL with significant alterations in genes involved in differentiation, cytoskeleton formation, vesicle trafficking, and cell death. 4 Coculture of CLL cells with normal T cells produces the same T-cell defects observed in CLL patients, 4 suggesting a direct role of the leukemia cells in contributing to the T cell-dependent cellular immune deficiency. The clinical manifestation of the humoral and cellular immune defects in CLL patients includes hypogammaglobulinemia, 5,6 poor response to both polysaccharide-based 7-9 and proteinbased 10 vaccines, and a high predisposition to infections 11,12 that represents a leading cause of death.To date, attempts to reverse the immune defects in CLL have been limited. Most promising has been adenovirus-delivered CD154 gene therapy that in small numbers of patients reversed cellular and humoral tumor tolerance. CD154 is the surface ligand of CD40 and is expressed on activated T cells, natural killer cells, and dendritic cells, but not normal B cells. Activation of T cells promotes increased surface expression of CD154, thereby promoting both activation and antigen presentation in normal and transformed B cells. Congenital mutations in the CD154 gene promote profound cellular and humoral immune deficiency. Although mutations of the CD154 gene have not been described in CLL, these patients have diminished CD154 expression on T cells after CD3 ligation. 13 Transduction of murine or human CD154 into primary CLL cells ex vivo with adenovirus gene therapy vectors, followed by systemic reintr...

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Chromatin Immunoprecipitation Assay

Cited by 173 publications

References 41 publications

Roles for the Human ATP-dependent Lon Protease in Mitochondrial DNA Maintenance

Roles for the Human ATP-dependent Lon Protease in Mitochondrial DNA Maintenance

SUMOylation of the Farnesoid X Receptor (FXR) Regulates the Expression of FXR Target Genes

Lenalidomide treatment promotes CD154 expression on CLL cells and enhances production of antibodies by normal B cells through a PI3-kinase–dependent pathway

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