title: Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus.
abstract: DNA transposons and retroviruses are versatile tools in functional genomics and gene therapy. To facilitate their application, we conducted a genome-wide insertion site profiling of the piggyBac (PB), Tol2 and Sleeping Beauty (SB) transposons and the murine leukemia virus (MLV) in mouse embryonic stem cells (ESCs). PB and MLV preferred highly expressed genes, whereas Tol2 and SB preferred weakly expressed genes. However, correlations with DNase I hypersensitive sites were different for all vectors, indicating that chromatin accessibility is not the sole determinant. Therefore, we analysed various chromatin states. PB and MLV highly correlated with Cohesin, Mediator and ESC-specific transcription factors. Notably, CTCF sites were correlated with PB but not with MLV, suggesting MLV prefers smaller promoter-enhancer loops, whereas PB insertion encompasses larger chromatin loops termed topologically associating domains. Tol2 also correlated with Cohesin and CTCF. However, correlations with ESC-specific transcription factors were weaker, suggesting that Tol2 prefers transcriptionally weak chromatin loops. Consistently, Tol2 insertions were associated with bivalent histone modifications characteristic of silent and inducible loci. SB showed minimum preference to all chromatin states, suggesting the least adverse effect on adjacent genes. These results will be useful for vector selection for various applications.
authors.affiliation: Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan.|Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Junko
authors.initials: J
authors.lastname: Yoshida
authors.affiliation: Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA.
authors.forename: Keiko
authors.initials: K
authors.lastname: Akagi
authors.affiliation: Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Misawa
authors.affiliation: Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Chikara
authors.initials: C
authors.lastname: Kokubu
authors.affiliation: Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Junji
authors.initials: J
authors.lastname: Takeda
authors.affiliation: Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan.|Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.|Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.
authors.forename: Kyoji
authors.initials: K
authors.lastname: Horie
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics*; D042002:Chromatin Assembly and Disassembly; D004251:DNA Transposable Elements; D015870:Gene Expression; D005786:Gene Expression Regulation; D023061:Gene Order; D005822:Genetic Vectors / Q000235:genetics*; D016678:Genome; D023281:Genomics / Q000379:methods; D006657:Histones / Q000378:metabolism; D009052:Leukemia Virus, Murine / Q000502:physiology*; D051379:Mice; D008954:Models, Biological; D000066450:Mouse Embryonic Stem Cells / Q000378:metabolism; D016254:Mutagenesis, Insertional; D011485:Protein Binding; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D016662:Virus Integration
chemical_list: D002843:Chromatin; D004251:DNA Transposable Elements; D006657:Histones; D014157:Transcription Factors