title: Serial number tagging reveals a prominent sequence preference of retrotransposon integration.
abstract: Transposable elements (TE) have both negative and positive impact on the biology of their host. As a result, a balance is struck between the host and the TE that relies on directing integration to specific genome territories. The extraordinary capacity of DNA sequencing can create ultra dense maps of integration that are being used to study the mechanisms that position integration. Unfortunately, the great increase in the numbers of insertion sites detected comes with the cost of not knowing which positions are rare targets and which sustain high numbers of insertions. To address this problem we developed the serial number system, a TE tagging method that measures the frequency of integration at single nucleotide positions. We sequenced 1 million insertions of retrotransposon Tf1 in the genome of Schizosaccharomyces pombe and obtained the first profile of integration with frequencies for each individual position. Integration levels at individual nucleotides varied over two orders of magnitude and revealed that sequence recognition plays a key role in positioning integration. The serial number system is a general method that can be applied to determine precise integration maps for retroviruses and gene therapy vectors.
authors.affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Atreyi Ghatak
authors.initials: AG
authors.lastname: Chatterjee
authors.affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Caroline
authors.initials: C
authors.lastname: Esnault
authors.affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Yabin
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Stevephen
authors.initials: S
authors.lastname: Hung
authors.affiliation: Mathematical & Statistical Computing Laboratory, Division of Computational, Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Philip G
authors.initials: PG
authors.lastname: McQueen
authors.affiliation: Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA henry_levin@nih.gov.
authors.forename: Henry L
authors.initials: HL
authors.lastname: Levin
mesh_terms: D002874:Chromosome Mapping; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D011401:Promoter Regions, Genetic; D018626:Retroelements; D012568:Schizosaccharomyces / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D016324:Sequence Tagged Sites
chemical_list: D018626:Retroelements