title: Using TRIP for genome-wide position effect analysis in cultured cells.
abstract: The influence of local chromatin context on gene expression can be explored by integrating a transcription reporter at different locations in the genome as a sensor. Here we provide a detailed protocol for analyzing thousands of reporters integrated in parallel (TRIP) at a genome-wide level. TRIP is based on tagging each reporter with a unique barcode, which is used for independent reporter expression analysis and integration site mapping. Compared with previous methods for studying position effects, TRIP offers a 100-1,000-fold higher throughput in a faster and less-labor-intensive manner. The entire experimental protocol takes ∼42 d to complete, with high-throughput sequencing and data analysis requiring an additional ∼11 d. TRIP was developed by using transcription reporters in mouse embryonic stem (mES) cells, but because of its flexibility the method can be used to probe the influence of chromatin context on a variety of molecular processes in any transfectable cell line.
authors.affiliation: 1] Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands. [2].
authors.forename: Waseem
authors.initials: W
authors.lastname: Akhtar
authors.affiliation: 1] Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands. [2] Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia. [3].
authors.forename: Alexey V
authors.initials: AV
authors.lastname: Pindyurin
authors.affiliation: Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: Johann
authors.initials: J
authors.lastname: de Jong
authors.affiliation: Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: Ludo
authors.initials: L
authors.lastname: Pagie
authors.affiliation: Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: Jelle
authors.initials: J
authors.lastname: Ten Hoeve
authors.affiliation: 1] Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands. [2] Skoltech Center for Stem Cell Research, Skolkovo Institute for Science and Technology, Skolkovo, Russia.
authors.forename: Anton
authors.initials: A
authors.lastname: Berns
authors.affiliation: 1] Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands. [2] Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
authors.forename: Lodewyk F A
authors.initials: LF
authors.lastname: Wessels
authors.affiliation: Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: Bas
authors.initials: B
authors.lastname: van Steensel
authors.affiliation: 1] Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands. [2] Cancer Genomics Centre, The Netherlands.
authors.forename: Maarten
authors.initials: M
authors.lastname: van Lohuizen
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D002843:Chromatin / Q000378:metabolism*; D055012:Chromosomal Position Effects / Q000235:genetics*; D004251:DNA Transposable Elements; D017930:Genes, Reporter / Q000235:genetics*; D005822:Genetic Vectors / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D051379:Mice; D011119:Polynucleotides / Q000235:genetics
chemical_list: D002843:Chromatin; D004251:DNA Transposable Elements; D011119:Polynucleotides