STARR-seq reporter activity of plasmid libraries delivered to mouse liver by hydrodynamic injection: In vivo MPRA assay for enhancer activity
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ABSTRACT:
ORGANISM(S): Mus musculus synthetic construct
PROVIDER: GSE267205 | GEO | 2024/06/17
REPOSITORIES: GEO
Similar Datasets
Project description:STARR-seq reporter activity of plasmid libraries delivered to mouse liver by hydrodynamic injection: In vivo MPRA assay for enhancer activity
| PRJNA1110236 | ENA
Project description:BackgroundMassively parallel reporter assays (MPRAs) enable high-throughput functional evaluation of various DNA regulatory elements and their mutant variants. The assays are based on construction of highly diverse plasmid libraries containing two variable fragments, a region of interest (a sequence under study; ROI) and a barcode (BC) used to uniquely tag each ROI, which are separated by a constant spacer sequence. The sequences of BC-ROI combinations present in the libraries may be either known a priori or not. In the latter case, it is necessary to identify these combinations before performing functional experiments. Typically, this is done by PCR amplification of the BC-ROI regions with flanking primers, followed by next-generation sequencing (NGS) of the products. However, chimeric DNA molecules formed on templates with identical spacer fragment during the amplification process may substantially hamper the identification of genuine BC-ROI combinations, and as a result lower the performance of the assays.ResultsTo identify settings that minimize formation of chimeric products we tested a number of PCR amplification parameters, such as conventional and emulsion types of PCR, one- or two-round amplification strategies, amount of DNA template, number of PCR cycles, and the duration of the extension step. Using specific MPRA libraries as templates, we found that the two-round amplification of the BC-ROI regions with a very low initial template amount, an elongated extension step, and a specific number of PCR cycles result in as low as 0.30 and 0.32% of chimeric products for emulsion and conventional PCR approaches, respectively.ConclusionsWe have identified PCR parameters that ensure synthesis of specific (non-chimeric) products from highly diverse MPRA plasmid libraries. In addition, we found that there is a negligible difference in performance of emulsion and conventional PCR approaches performed with the identified settings.
| S-EPMC6620194 | biostudies-literature
Project description:We designed 4 oligonucleotide libraries containing either a retained intron, a cassette exon, tandem 5' or tandem 3' splice sites, cloned them into dedicated reporter constructs, transfected and integrated these constructs in the genome of K562 cells, and performed targeted RNA sequencing to determine RNA splicing ratios and a FACSseq approach to determine protein isoform ratios.
2019-06-03 | GSE132064 | GEO
Project description:Massively parallel reporter assays (MPRA) are widely used to discover functional enhancers but have largely been limited to transfected cell models. Here, we combine hydrodynamic injection with a modified STARR-seq-based MPRA to determine condition-specific enhancer activity in mouse liver at scale, and we examine how different promoters affect STARR-seq reporter activity. Strong liver enhancer activity was observed with STARR-seq libraries containing an Albumin minimal promoter but not when using a Super Core promoter or an origin of replication (ORI) promoter. This work is part of a larger study where we prepare a global STARR-seq library, comprised of ~50,000 genomic sequences released by DNase-I digestion of mouse liver nuclei, and where we identify condition-specific enhancers with strong correlations between liver enhancer activity and the chromatin state of the corresponding endogenous genomic regions.
2024-06-17 | GSE267075 | GEO
Project description:comparison of liver tumors, surrounding liver tissue and empty vector (EV) injected control mouse livers
2022-10-21 | GSE216200 | GEO
Project description:Motivation:The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRAs), have been used to functionally validate non-coding variants. However, we are still missing high-quality and robust data analysis tools for these datasets. Results:We have further developed our method for allele-specific analysis QuASAR (quantitative allele-specific analysis of reads) to analyze allele-specific signals in barcoded read counts data from MPRA. Using this approach, we can take into account the uncertainty on the original plasmid proportions, over-dispersion, and sequencing errors. The provided allelic skew estimate and its standard error also simplifies meta-analysis of replicate experiments. Additionally, we show that a beta-binomial distribution better models the variability present in the allelic imbalance of these synthetic reporters and results in a test that is statistically well calibrated under the null. Applying this approach to the MPRA data, we found 602 SNPs with significant (false discovery rate 10%) allele-specific regulatory function in LCLs. We also show that we can combine MPRA with QuASAR estimates to validate existing experimental and computational annotations of regulatory variants. Our study shows that with appropriate data analysis tools, we can improve the power to detect allelic effects in high-throughput reporter assays. Availability and implementation:http://github.com/piquelab/QuASAR/tree/master/mpra. Contact:fluca@wayne.edu or rpique@wayne.edu. Supplementary information:Supplementary data are available online at Bioinformatics.
| S-EPMC6049023 | biostudies-literature
Project description:Mitochondrial gene therapy and diagnosis have the potential to provide substantial medical benefits. However, the utility of this approach has not yet been realized because the technology available for mitochondrial gene delivery continues to be a bottleneck. We previously reported on mitochondrial gene delivery in skeletal muscle using hydrodynamic limb vein (HLV) injection. HLV injection, a useful method for nuclear transgene expression, involves the rapid injection of a large volume of naked plasmid DNA (pDNA). Moreover, the use of a condensed form of pDNA enhances the nuclear transgene expression by the HLV injection. The purpose of this study was to compare naked pDNA and condensed pDNA for mitochondrial association in skeletal muscle, when used in conjunction with HLV injection. PCR analysis showed that the use of condensed pDNA rather than naked pDNA resulted in a more effective mitochondrial association with pDNA, suggesting that the physicochemical state of pDNA plays a key role. Moreover, no mitochondrial toxicities in skeletal muscle following the HLV injection of condensed pDNA were confirmed, as evidenced by cytochrome c oxidase activity and mitochondrial membrane potential. These findings have the potential to contribute to the development for in vivo mitochondrial gene delivery system.
| S-EPMC4167204 | biostudies-literature
Project description:We designed an oligonucleotide libraries containing a potential frameshifting site, cloned the library variants into a dedicated reporter construct, transfected and integrated these constructs in the genome of K562 cells, and performed FACSseq (as well as targeted RNA sequencing) to determine if and to what extent frameshifting occurs.
2020-02-22 | GSE145684 | GEO
Project description:The hemodynamics during a hydrodynamic injection were evaluated using cone beam computed tomography (CBCT) and fluoroscopic imaging. The impacts of hydrodynamic (5 seconds) and slow (60 seconds) injections into the tail veins of mice were compared using 9% body weight of a phase-contrast medium. Hydrodynamically injected solution traveled to the heart and drew back to the hepatic veins (HV), which led to liver expansion and a trace amount of spillover into the portal vein (PV). The liver volumes peaked at 165.6 ± 13.3% and 165.5 ± 11.9% of the original liver volumes in the hydrodynamic and slow injections, respectively. Judging by the intensity of the CBCT images at the PV, HV, right atrium, liver parenchyma (LP), and the inferior vena cava (IVC) distal to the HV conjunction, the slow injection resulted in the higher intensity at PV than at LP. In contrast, a significantly higher intensity was observed in LP after hydrodynamic injection in comparison with that of PV, suggesting that the liver took up the iodine from the blood flow. These results suggest that the enlargement speed of the liver, rather than the expanded volume, primarily determines the efficiency of hydrodynamic delivery to the liver.
| S-EPMC4362352 | biostudies-literature
Project description:NRAS hydrodynamic tail vein injection
| PRJNA892576 | ENA