Dec 28, 2015

MPRAnator: a web-based tool for the design of Massively Parallel Reporter Assay experiments.

BioRxiv : the Preprint Server for Biology
Ilias Georgakopoulos-SoaresMartin Hemberg

Abstract

DNA regulatory elements contain short motifs where transcription factors (TFs) can bind to modulate gene expression. Although the broad principles of TF regulation are well understood, the rules that dictate how combinatorial TF binding translates into transcriptional activity remain largely unknown. With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-throughput reporter assay experiments such as Massively Parallel Reporter Assays (MPRAs) and similar methods remains challenging. We introduce MPRAnator, a set of tools that facilitate rapid design of MPRA experiments. With MPRA Motif design, a set of variables provides fine control of how motifs are placed into sequences therefore allowing the user to investigate the rules that govern TF occupancy. MPRA SNP design can be used to investigate the functional effects of single or combinations of SNPs at regulatory sequences. Finally, the Transmutation tool allows for the design of negative controls by permitting scrambling, reversing, complementing or ...Continue Reading

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Mentioned in this Paper

MprA protein, E coli
PAQR7 gene
High Throughput Screening
Transcription, Genetic
Gene Expression
Sequencing
Transcription Factor Binding
Protein Domain
Oligonucleotides
Molecular Genetic Technique

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