A dinucleotide tag-based parallel reporter gene assay method
Ren, N.; Li, B.; Liu, Q.; Yang, L.; Liu, X.; Huang, Q.
Show abstract
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.
Matching journals
The top 11 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Research of the mechanism on miRNA193 in exosomes promotes cisplatin resistance in esophageal cancer cells 93%
- Amplified DNA Heterogeneity Assessment with Oxford Nanopore Sequencing Applied to Cell Free Expression Templates 93%
- Single-cell alternative polyadenylation analysis reveals mechanistic insights of COVID-19-associated neurological and psychiatric effects 93%
Similar papers in this journal
- Reprogramming an RNA-guided archaeal TnpB endonuclease for genome editing 92%
- Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs 90%
- A conditional protein diffusion model generates artificial programmable endonuclease sequences with enhanced activity 90%
Similar papers in this journal
Similar papers in this journal
- FOXP2 confers oncogenic effects in prostate cancer through activating MET signalling 93%
- Mapping of single-cell landscape of acral melanoma and analysis of molecular regulatory network of tumor microenvironment 93%
- Development of a versatile high-throughput mutagenesis assay with multiplexed short read NGS using DNA-barcoded supF shuttle vector library amplified in non-SOS E. coli 92%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.