Analysis of Chromatin–Nuclear Receptor Interactions by Laser-Chromatin Immunoprecipitation

Author(s):  
Rosaria Benedetti ◽  
Mariarosaria Conte ◽  
Vincenzo Carafa ◽  
Bartolomeo Della Ventura ◽  
Carlo Altucci ◽  
...  
2009 ◽  
Vol 5 (12) ◽  
pp. e1000594 ◽  
Author(s):  
Sean Ekins ◽  
Sandhya Kortagere ◽  
Manisha Iyer ◽  
Erica J. Reschly ◽  
Markus A. Lill ◽  
...  

2009 ◽  
Vol 96 (3) ◽  
pp. 44a
Author(s):  
Patrick J. Macdonald ◽  
Jolene Johnson ◽  
Yan Chen ◽  
Bin Wu ◽  
Joachim Mueller

2010 ◽  
Vol 24 (12) ◽  
pp. 2281-2291 ◽  
Author(s):  
Victoria R. Kelly ◽  
Bin Xu ◽  
Rork Kuick ◽  
Ronald J. Koenig ◽  
Gary D. Hammer

Abstract Dax1 (Nr0b1) is an atypical orphan nuclear receptor that has recently been shown to play a role in mouse embryonic stem (mES) cell pluripotency. Here we describe a mechanism by which Dax1 maintains pluripotency. In steroidogenic cells, Dax1 protein interacts with the NR5A nuclear receptor steroidogenic factor 1 (Nr5a1) to inhibit transcription of target genes. In mES cells, liver receptor homolog 1 (LRH-1, Nr5a2), the other NR5A family member, is expressed, and LRH-1 has been shown to interact with Dax1. We demonstrate by coimmunoprecipitation that Dax1 is, indeed, able to form a complex with LRH-1 in mES cells. Because Dax1 was historically characterized as an inhibitor of steroidogenic factor 1-mediated transcriptional activation, we hypothesized that Dax1 would inhibit LRH-1 action in mES cells. Therefore, we examined the effect of Dax1 on the LRH-1-mediated activation of the critical ES cell factor Oct4 (Pou5f1). Chromatin immunoprecipitation localized Dax1 to the Oct4 promoter at the LRH-1 binding site, and luciferase assays together with Dax1 overexpression and knockdown experiments revealed that, rather than repress, Dax1 accentuated LRH-1-mediated activation of the Oct4 gene. Similar to our previously published studies that defined the RNA coactivator steroid receptor RNA activator as the critical mediator of Dax1 coactivation function, Dax1 augmentation of LRH-1-mediated Oct4 activation is dependent upon steroid receptor RNA activator. Finally, utilizing published chromatin immunoprecipitation data of whole-genome binding sites of LRH-1 and Dax1, we show that LRH-1 and Dax1 commonly colocalize at 288 genes (43% of LRH-1 target genes), many of which are involved in mES cell pluripotency. Thus, our results indicate that Dax1 plays an important role in the maintenance of pluripotency in mES cells through interaction with LRH-1 and transcriptional activation of Oct4 and other genes.


2019 ◽  
Vol 62 (4) ◽  
pp. 169-177
Author(s):  
Ann Louise Hunter ◽  
Natasha Narang ◽  
Matthew Baxter ◽  
David W Ray ◽  
Toryn M Poolman

Chromatin immunoprecipitation (ChIP) is a valuable tool for the endocrine researcher, providing a means to measure the recruitment of hormone-activated nuclear receptors, for example. However, the technique can be challenging to perform and has multiple experimental steps, risking introduction of error at each. The data produced can be challenging to interpret; several different methods are commonly used for normalising data and thus comparing between conditions. Absolute, sensitive quantification of protein-bound DNA is important for correct interpretation of the data. In addition, such quantification can help the investigator in troubleshooting experiments. Here, we outline a ChIP strategy combining droplet digital PCR for accurate quantification with an internal spike-in control for normalisation. This combination strengthens the reliability of ChIP data and allows the operator to optimise their protocol with greater confidence.


2021 ◽  
Vol 17 (12) ◽  
pp. e1010140
Author(s):  
Aracely A. Romero ◽  
Sarah A. Cobb ◽  
Julie N. R. Collins ◽  
Steven A. Kliewer ◽  
David J. Mangelsdorf ◽  
...  

Schistosomes infect over 200 million of the world’s poorest people, but unfortunately treatment relies on a single drug. Nuclear hormone receptors are ligand-activated transcription factors that regulate diverse processes in metazoans, yet few have been functionally characterized in schistosomes. During a systematic analysis of nuclear receptor function, we found that an FTZ-F1-like receptor was essential for parasite survival. Using a combination of transcriptional profiling and chromatin immunoprecipitation (ChIP), we discovered that the micro-exon gene meg-8.3 is a transcriptional target of SmFTZ-F1. We found that both Smftz-f1 and meg-8.3 are required for esophageal gland maintenance as well as integrity of the worm’s head. Together, these studies define a new role for micro-exon gene function in the parasite and suggest that factors associated with the esophageal gland could represent viable therapeutic targets.


2001 ◽  
Vol 26 (6) ◽  
pp. 384-390 ◽  
Author(s):  
Sepideh Khorasanizadeh ◽  
Fraydoon Rastinejad

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