RT Journal Article
SR Electronic
T1 MPRAnator: a web-based tool for the design of Massively Parallel Reporter Assay experiments
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 035444
DO 10.1101/035444
A1 Ilias Georgakopoulos-Soares
A1 Naman Jain
A1 Jesse Gray
A1 Martin Hemberg
YR 2015
UL http://biorxiv.org/content/early/2015/12/28/035444.abstract
AB 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 introducing multiple random mutations in the input sequences or motifs.