scholarly journals A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assays

2019 ◽  
Author(s):  
Jason Klein ◽  
Vikram Agarwal ◽  
Fumitaka Inoue ◽  
Aidan Keith ◽  
Beth Martin ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Experimental Design ◽  
Massively Parallel ◽  
Systematic Evaluation ◽  
Regulatory Activity ◽  
Sequence Context ◽  
Enhancer Activity ◽  
Extended Sequence ◽  
Reporter Assays ◽  
Novel Method

ABSTRACTMassively parallel reporter assays (MPRAs) functionally screen thousands of sequences for regulatory activity in parallel. Although MPRAs have been applied to address diverse questions in gene regulation, there has been no systematic comparison of how differences in experimental design influence findings. Here, we screen a library of 2,440 sequences, representing candidate liver enhancers and controls, in HepG2 cells for regulatory activity using nine different approaches (including conventional episomal, STARR-seq, and lentiviral MPRA designs). We identify subtle but significant differences in the resulting measurements that correlate with epigenetic and sequence-level features. We also test this library in both orientations with respect to the promoter, validatingen massethat enhancer activity is robustly independent of orientation. Finally, we develop and apply a novel method to assemble and functionally test libraries of the same putative enhancers as 192-mers, 354-mers, and 678-mers, and observe surprisingly large differences in functional activity. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements, and to a lesser degree the precise assay, influence MPRA results.

scholarly journals A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assays

2020 ◽  
Author(s):  
Jason Klein ◽  
Vikram Agarwal ◽  
Fumitaka Inoue ◽  
Aidan Keith ◽  
Beth Martin ◽  
...  
Keyword(s):  
Experimental Design ◽  
High Throughput ◽  
Functional Activity ◽  
Massively Parallel ◽  
Systematic Evaluation ◽  
Regulatory Activity ◽  
Sequence Context ◽  
Extended Sequence ◽  
Reporter Assays ◽  
Novel Method

Abstract Massively parallel reporter assays (MPRAs) functionally screen thousands of sequences for regulatory activity in parallel. Here, we further develop and apply a novel method to assemble and functionally test libraries of greater than 2000 of the same putative enhancers as 192-mers, 354-mers, and 678-mers. We achieved a yield of 95% for 354-mers and 84% for 678-mers. Importantly, we observe surprisingly large differences in functional activity. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements, and to a lesser degree the precise assay, influence MPRA results.

scholarly journals TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers

2020 ◽  
Author(s):  
Diego Calderon ◽  
Andria Ellis ◽  
Riza M. Daza ◽  
Beth Martin ◽  
Jacob M. Tome ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factors ◽  
Regulatory Elements ◽  
Massively Parallel ◽  
Reporter Assay ◽  
Regulatory Activity ◽  
Large Numbers ◽  
Reporter Assays ◽  
Regulatory Potential

AbstractGene regulation occurs through trans-acting factors (e.g. transcription factors) acting on cis-regulatory elements (e.g. enhancers). Massively parallel reporter assays (MPRAs) functionally survey large numbers of cis-regulatory elements for regulatory potential, but do not identify the trans-acting factors that mediate any observed effects. Here we describe transMPRA — a reporter assay that efficiently combines multiplex CRISPR-mediated perturbation and MPRAs to identify trans-acting factors that modulate the regulatory activity of specific enhancers.

scholarly journals Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

2018 ◽  
Author(s):  
Rajiv Movva ◽  
Peyton Greenside ◽  
Georgi K. Marinov ◽  
Surag Nair ◽  
Avanti Shrikumar ◽  
...  
Keyword(s):  
Neural Network ◽  
Dna Sequences ◽  
Genetic Variants ◽  
Massively Parallel ◽  
Regulatory Sequence ◽  
Regulatory Activity ◽  
Neural Network Models ◽  
Regulatory Dna Sequences ◽  
Reporter Assays ◽  
Regulatory Dna

AbstractThe relationship between noncoding DNA sequence and gene expression is not well-understood. Massively parallel reporter assays (MPRAs), which quantify the regulatory activity of large libraries of DNA sequences in parallel, are a powerful approach to characterize this relationship. We present MPRA-DragoNN, a convolutional neural network (CNN)-based framework to predict and interpret the regulatory activity of DNA sequences as measured by MPRAs. While our method is generally applicable to a variety of MPRA designs, here we trained our model on the Sharpr-MPRA dataset that measures the activity of ~500,000 constructs tiling 15,720 regulatory regions in human K562 and HepG2 cell lines. MPRA-DragoNN predictions were moderately correlated (Spearman ρ = 0.28) with measured activity and were within range of replicate concordance of the assay. State-of-the-art model interpretation methods revealed high-resolution predictive regulatory sequence features that overlapped transcription factor (TF) binding motifs. We used the model to investigate the cell type and chromatin state preferences of predictive TF motifs. We explored the ability of our model to predict the allelic effects of regulatory variants in an independent MPRA experiment and fine map putative functional SNPs in loci associated with lipid traits. Our results suggest that interpretable deep learning models trained on MPRA data have the potential to reveal meaningful patterns in regulatory DNA sequences and prioritize regulatory genetic variants, especially as larger, higher-quality datasets are produced.

Deciphering Gene Regulation Using Massively Parallel Reporter Assays

2020 ◽  
Vol 45 (1) ◽  
pp. 90-91
Author(s):  
Max Trauernicht ◽  
Miguel Martinez-Ara ◽  
Bas van Steensel
Keyword(s):  
Gene Regulation ◽  
Massively Parallel ◽  
Reporter Assays

scholarly journals A systematic evaluation of the design and context dependencies of massively parallel reporter assays

2020 ◽  
Vol 17 (11) ◽  
pp. 1083-1091 ◽  
Author(s):  
Jason C. Klein ◽  
Vikram Agarwal ◽  
Fumitaka Inoue ◽  
Aidan Keith ◽  
Beth Martin ◽  
...  
Keyword(s):  
Massively Parallel ◽  
Systematic Evaluation ◽  
Reporter Assays

scholarly journals Analysis of long and short enhancers in melanoma cell states

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
David Mauduit ◽  
Ibrahim Ihsan Taskiran ◽  
Liesbeth Minnoye ◽  
Maxime de Waegeneer ◽  
Valerie Christiaens ◽  
...  
Keyword(s):  
Melanoma Cell ◽  
Massively Parallel ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Enhancer Activity ◽  
Reporter Assays ◽  
Enhancer Function ◽  
The Relationship ◽  
Deep Learning Model ◽  
Shed Light

Understanding how enhancers drive cell type specificity and efficiently identifying them is essential for the development of innovative therapeutic strategies. In melanoma, the melanocytic (MEL) and the mesenchymal-like (MES) states present themselves with different responses to therapy, making the identification of specific enhancers highly relevant. Using massively parallel reporter assays (MPRA) in a panel of patient-derived melanoma lines (MM lines), we set to identify and decipher melanoma enhancers by first focusing on regions with state specific H3K27 acetylation close to differentially expressed genes. An in-depth evaluation of those regions was then pursued by investigating the activity of overlapping ATAC-seq peaks along with a full tiling of the acetylated regions with 190 bp sequences. Activity was observed in more than 60% of the selected regions and we were able to precisely locate the active enhancers within ATAC-seq peaks. Comparison of sequence content with activity, using the deep learning model DeepMEL2, revealed that AP-1 alone is responsible for the MES enhancer activity. In contrast, SOX10 and MITF both influence MEL enhancer function with SOX10 being required to achieve high levels of activity. Overall, our MPRAs shed light on the relationship between long and short sequences in terms of their sequence content, enhancer activity, and specificity across melanoma cell states.

scholarly journals Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

2021 ◽  
Vol 49 (7) ◽  
pp. 3856-3875
Author(s):  
Marina Kulik ◽  
Melissa Bothe ◽  
Gözde Kibar ◽  
Alisa Fuchs ◽  
Stefanie Schöne ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Dna Binding ◽  
Receptor Binding ◽  
Binding Sites ◽  
Specific Gene ◽  
Functional Diversification ◽  
Enhancer Activity ◽  
Sequence Composition

Abstract The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the result of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.

scholarly journals Development of a novel method for the in-situ dechlorination of immovable iron elements: optimization of Cl− extraction yield through experimental design

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marco Veneranda ◽  
Nagore Prieto-Taboada ◽  
Jose Antonio Carrero ◽  
Ilaria Costantini ◽  
Aitor Larrañaga ◽  
...  
Keyword(s):  
Experimental Design ◽  
Optimization Design ◽  
Degradation Process ◽  
Extraction Yield ◽  
Alkaline Solutions ◽  
Iron Core ◽  
Total Consumption ◽  
Iron Leaching ◽  
Novel Method

AbstractThe conservation of iron objects exposed to marine aerosol is threatened by the formation of akaganeite, a highly unstable Cl-bearing corrosion phase. As akaganeite formation is responsible of the exfoliation of the rust layer, chlorides trigger a cyclic alteration phenomenon that often ends with the total consumption of the iron core. To prevent this degradation process, movable iron elements (e.g. archaeometallurgical artefacts) are generally immersed in alkaline dechlorination baths. Aiming to transfer this successful method to the treatment of immovable iron objects, we propose the in-situ application of alkaline solutions through the use of highly absorbent wraps. As first step of this novel research line, the present work defines the best desalination solution to be used and optimizes its extraction yield. After literature review, a screening experimental design was performed to understand the single and synergic effects of common additives used for NaOH baths. Once the most effective variables were selected, an optimization design was carried out to determine the optimal conditions to be set during treatment. According to the experimental work here presented, the use of 0.7 M NaOH solutions applied at high temperatures (above 50 °C) is recommended. Indeed, these conditions enhance chloride extraction and iron leaching inhibition, while promoting corrosion stabilization.

Abstract 18374: Targeted Sequencing and Massively Parallel Reporter Assay Identify the Functional Variation Underlying the 4q25 Locus for Atrial Fibrillation

Circulation ◽  
2015 ◽  
Vol 132 (suppl_3) ◽  
Author(s):  
Nathan R Tucker ◽  
Jiangchuan Ye ◽  
Honghuang Lin ◽  
Michael A McLellan ◽  
Emelia J Benjamin ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Association Studies ◽  
Targeted Sequencing ◽  
Massively Parallel ◽  
Genome Wide Association Studies ◽  
Sequencing Analysis ◽  
Reporter Assay ◽  
Enhancer Activity ◽  
Functional Variants ◽  
Massively Parallel Reporter Assay

Introduction: Genome-wide association studies have identified 14 independent loci for atrial fibrillation (AF). The 4q25 locus upstream of the left-right asymmetry gene PITX2 is, by far, the strongest association signal for AF. However, as with most GWAS loci, the functional variants are noncoding, presumed to be regulatory, and remain unknown. We therefore sought to rapidly identify the functional variants at an AF locus by combining high throughput sequencing and massively parallel reporter assays. Methods and Results: We sequenced a ~750kb region encompassing the PITX2 locus in 462 individuals with early-onset AF from the MGH AF Study and 464 referents from the Framingham Heart Study. The SNP most significantly associated with AF in our sequenced sample was rs2129983, which is 140kb from PITX2 (OR=2.43, P =8.9X10 -16 ). rs2129983 is approximately 1.7kb from the most significantly associated SNP in a prior AF GWAS, rs6817105 (r 2 =0.52). From the targeted sequencing analysis, we identified 262 SNVs with a MAF >0.5% within a genomic region bounded by SNPs with an r2 greater than 0.4 with the top variant. To identify functional variants, we then utilized a massively parallel reporter assay (MPRA) in order to measure enhancer activity at each SNP across the entire AF locus. In both HL-1 and C2C12 myoblasts, MPRA identified many distinct SNP regions with differential enhancer activity. Using AF-association status as a standard, we were able to identify a series of variants that have both differential activity in either cell line tested and also a high level of association (rs17042076, rs4469143). Mechanistically, these functional SNPs are predicted to alter transcription factor binding. Conclusions: We have comprehensively identified the AF-associated variation at 4q25 and determined which of these variants are functional through differential enhancer activity. Here, in addition to identifying the causative variation for AF at 4q25, we provide a generalizable pathway for translating this work to other loci, a method that could expedite the identification of causative genetic variants at other disease loci.

scholarly journals Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

PLoS ONE ◽  
2019 ◽  
Vol 14 (6) ◽  
pp. e0218073 ◽  
Author(s):  
Rajiv Movva ◽  
Peyton Greenside ◽  
Georgi K. Marinov ◽  
Surag Nair ◽  
Avanti Shrikumar ◽  
...  
Keyword(s):  
Neural Network ◽  
Dna Sequences ◽  
Genetic Variants ◽  
Network Models ◽  
Massively Parallel ◽  
Neural Network Models ◽  
Regulatory Dna Sequences ◽  
Reporter Assays ◽  
Regulatory Dna
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