Dinucleotide tag‐based parallel reporter gene assay method enables efficient identification of regulatory mutations

2021 ◽  
pp. 2100341
Author(s):  
Naixia Ren ◽  
Bo Li ◽  
Qingqing Liu ◽  
Lele Yang ◽  
Xiaodan Liu ◽  
...  
2001 ◽  
Vol 280 (1) ◽  
pp. 85-91 ◽  
Author(s):  
Kayo Sumida ◽  
Norihisa Ooe ◽  
Hirohisa Nagahori ◽  
Koichi Saito ◽  
Naohiko Isobe ◽  
...  

2021 ◽  
Author(s):  
Naixia Ren ◽  
Bo Li ◽  
Qingqing Liu ◽  
Lele Yang ◽  
Xiaodan Liu ◽  
...  

The causal SNPs leading to increased cancer predisposition mainly function as gene regulatory elements, the evaluation of which largely rely on the parallel reporter gene assay system. However, the common DNA barcode-based parallel reporter gene assay systems are troubled with tag bias, mainly due to the tag nucleotide composition. Here we describe a versatile dinucleotide-tag reporter system (DiR) that enables parallel analysis of regulatory elements with minimized bias based on the next-generation sequencing. The DiR system is also more robust than the classical luciferase assay method, especially in the investigation of moderate-level regulatory elements. We applied DiR-seq assay in the functional evaluation of the prostate cancer risk SNPs in prostate cancer cell lines and disclosed 2, and 6 regulatory SNPs in PC-3 and LNCaP cells. The DiR system has great potential to advance the functional study of risk SNPs that have associations with polygenic diseases.


2021 ◽  
Vol 33 (1) ◽  
Author(s):  
Alberto Celma ◽  
Geeta Mandava ◽  
Agneta Oskarsson ◽  
Juan Vicente Sancho ◽  
Lubertus Bijlsma ◽  
...  

Abstract Background Fresh water bodies represent less than 1% of overall amount of water on earth and ensuring their quality and sustainability is pivotal. Although several campaigns have been performed to monitor the occurrence of micropollutants by means of chemical analysis, this might not cover the whole set of chemicals present in the sample nor the potential toxic effects of mixtures of natural and anthropogenic chemicals. In this sense, by selecting relevant toxicity endpoints when performing in vitro bioanalysis, effect-based methodologies can be of help to perform a comprehensive assessment of water quality and reveal biological activities relevant to adverse health effects. However, no prior bioanalytical study was performed in wetland water samples from the Spanish Mediterranean coastline. Methods Eleven samples from relevant water bodies from the Spanish Mediterranean coastline were collected to monitor water quality on 8 toxicity endpoints. Aryl hydrocarbon receptor (AhR), androgenicity (AR+ and AR−), estrogenicity (ER+ and ER−), oxidative stress response (Nrf2) and vitamin D receptor (VDR+ and VDR−) reporter gene assays were evaluated. Results AhR was the reporter gene assay showing a more frequent response over the set of samples (activated by 9 out of 11 samples), with TCDD-eq in the range 7.7–22.2 pM. For AR, ER and VDR assays sporadic activations were observed. Moreover, no activity was observed on the Nrf2 reporter gene assay. Wastewater and street runaway streams from Valencia could be responsible for enhanced activities in one of the water inputs in the Natural Park ‘L’Albufera’. Conclusions Water quality of relevant wetlands from the Spanish Mediterranean coastline has been evaluated. The utilization of a panel of 5 different bioassays to cover for different toxicity endpoints has demonstrated to be a good tool to assess water quality.


2005 ◽  
Vol 15 (4) ◽  
pp. 271-280 ◽  
Author(s):  
Mihoko Kojima ◽  
Kenji Fukunaga * ◽  
Mari Sasaki ◽  
Masafumi Nakamura ◽  
Motohiro Tsuji ◽  
...  

2021 ◽  
Vol 100 ◽  
pp. 108112
Author(s):  
Chunyu Liu ◽  
Chuanfei Yu ◽  
Yalan Yang ◽  
Jing Huang ◽  
Xiaojuan Yu ◽  
...  

2021 ◽  
Vol 101 ◽  
pp. 108277
Author(s):  
Chunyu Liu ◽  
Chuanfei Yu ◽  
Yalan Yang ◽  
Yongfei Cui ◽  
Feng Zhang ◽  
...  

2014 ◽  
Vol 229 ◽  
pp. S181-S182
Author(s):  
Danilo Pitardi ◽  
Daniela Meloni ◽  
Fabio Olivo ◽  
Maria Cavarretta ◽  
Daniela Loprevite ◽  
...  

2015 ◽  
Vol 49 (10) ◽  
pp. 6319-6326 ◽  
Author(s):  
Masaru Ihara ◽  
Tomokazu Kitamura ◽  
Vimal Kumar ◽  
Chang-Beom Park ◽  
Mariko O. Ihara ◽  
...  

Foods ◽  
2016 ◽  
Vol 5 (1) ◽  
pp. 15 ◽  
Author(s):  
Yoshiaki Amakura ◽  
Tomoaki Tsutsumi ◽  
Morio Yoshimura ◽  
Masafumi Nakamura ◽  
Hiroshi Handa ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document