title: Genome-wide mapping of autonomous promoter activity in human cells.
abstract: Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of the sequences that could be tested. Here we present 'survey of regulatory elements' (SuRE), a method that assays more than 108DNA fragments, each 0.2-2 kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library of random genomic fragments upstream of a 20-bp barcode is constructed, and decoded by paired-end sequencing. This library is used to transfect cells, and barcodes in transcribed RNA are quantified by high-throughput sequencing. When applied to the human genome, we achieve 55-fold genome coverage, allowing us to map autonomous promoter activity genome-wide in K562 cells. By computational modeling we delineate subregions within promoters that are relevant for their activity. We show that antisense promoter transcription is generally dependent on the sense core promoter sequences, and that most enhancers and several families of repetitive elements act as autonomous transcription initiation sites.
authors.affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
authors.forename: Joris
authors.initials: J
authors.lastname: van Arensbergen
authors.affiliation: Department of Biological Sciences, Columbia University, New York, New York, USA.|Department of Systems Biology, Columbia University Medical Center, New York, New York, USA.
authors.forename: Vincent D
authors.initials: VD
authors.lastname: FitzPatrick
authors.affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
authors.forename: Marcel
authors.initials: M
authors.lastname: de Haas
authors.affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
authors.forename: Ludo
authors.initials: L
authors.lastname: Pagie
authors.affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
authors.forename: Jasper
authors.initials: J
authors.lastname: Sluimer
authors.affiliation: Department of Biological Sciences, Columbia University, New York, New York, USA.|Department of Systems Biology, Columbia University Medical Center, New York, New York, USA.
authors.forename: Harmen J
authors.identifier: 0000-0002-7274-5277
authors.initials: HJ
authors.lastname: Bussemaker
authors.affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
authors.forename: Bas
authors.initials: B
authors.lastname: van Steensel
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D004247:DNA / Q000235:genetics; D015723:Gene Library; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D020014:K562 Cells; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D061785:Transcription Initiation, Genetic; D015533:Transcriptional Activation / Q000235:genetics*
chemical_list: D004247:DNA