SuRE

Survey of Regulatory Elements is a massively parallel reporter assay. Some key differences compared to most other MPRAs are:

• It uses genomic DNA fragments rather than synthetic oligonucleotides. This makes it possible to query larger DNA elements.
• It can assay hundreds of millions of random DNA fragments, sufficient to obtain quantitative data for entire human genomes.
• It can detect transcriptional activity of both promoters and enhancers.
• It can be used to determine the impact of millions of human SNPs on the activity of regulatory elements.
• When combined with epigenomics data, it can be used to infer the regulatory impact of chromatin states such as LADs.

Publications

Genome-wide mapping of autonomous promoter activity in human cells.
Van Arensbergen J*, FitzPatrick VD, de Haas M, Pagie L, Sluimer J, Bussemaker HJ*, van Steensel B*. Nature Biotechnol. 2017.

Systematic identification of human SNPs affecting regulatory element activity.
Van Arensbergen J, Pagie L, FitzPatrick V, de Haas M, Baltissen M, Comoglio F, van der Weide R, Teunissen H, Võsa U, Franke U, de Wit E, Vermeulen M, Bussemaker HJ, van Steensel B.  Nature Genetics 2019

Promoter-intrinsic and local chromatin features determine gene repression in LADs.
Leemans C, van der Zwalm MCH, Brueckner L, Comoglio F, van Schaik T, Pagie L, van Arensbergen J, van Steensel B. Cell 2019

Deciphering Gene Regulation Using Massively Parallel Reporter Assays.
Trauernicht M, Martinez-Ara M, van Steensel B. Trends Biochem Sci 2020