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Genomics. 2015 Sep;106(3):145-150. doi: 10.1016/j.ygeno.2015.06.001. Epub 2015 Jun 11.

STARR-seq - principles and applications.

Author information

1
Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria. Electronic address: felix.muerdter@imp.ac.at.
2
Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria.
3
Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria. Electronic address: cosmas.arnold@imp.ac.at.

Abstract

Differential gene expression is the basis for cell type diversity in multicellular organisms and the driving force of development and differentiation. It is achieved by cell type-specific transcriptional enhancers, which are genomic DNA sequences that activate the transcription of their target genes. Their identification and characterization is fundamental to our understanding of gene regulation. Features that are associated with enhancer activity, such as regulatory factor binding or histone modifications can predict the location of enhancers. Nonetheless, enhancer activity can only be assessed by transcriptional reporter assays. Over the past years massively parallel reporter assays have been developed for large scale testing of enhancers. In this review we focus on the principles and applications of STARR-seq, a functional assay that quantifies enhancer strengths in complex candidate libraries and thus allows activity-based enhancer identification in entire genomes. We explain how STARR-seq works, discuss current uses and give an outlook to future applications.

KEYWORDS:

Enhancer; High-throughput; Reporter; Reporter assay; STARR-seq; Transcription

PMID:
26072434
DOI:
10.1016/j.ygeno.2015.06.001
[Indexed for MEDLINE]
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