title: Chromatin position effects assayed by thousands of reporters integrated in parallel.
abstract: Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here, we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ∼1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for crosstalk between neighboring genes and estimate that enhancers can influence gene expression on average over ∼20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation.
authors: Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
authors: Waseem
authors: W
authors: Akhtar
authors: Johann
authors: J
authors: de Jong
authors: Alexey V
authors: AV
authors: Pindyurin
authors: Ludo
authors: L
authors: Pagie
authors: Wouter
authors: W
authors: Meuleman
authors: Jeroen
authors: J
authors: de Ridder
authors: Anton
authors: A
authors: Berns
authors: Lodewyk F A
authors: LF
authors: Wessels
authors: Maarten
authors: M
authors: van Lohuizen
authors: Bas
authors: B
authors: van Steensel
mesh_terms: D000818:Animals; D002843:Chromatin / Q000378:metabolism; D055012:Chromosomal Position Effects; D053595:Embryonic Stem Cells / Q000378:metabolism; D017930:Genes, Reporter; D005821:Genetic Techniques; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D011401:Promoter Regions, Genetic
chemical_list: D002843:Chromatin