Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome

Jared P. Steranka, Zuojian Tang, Mark Grivainis, Cheng Ran Lisa Huang, Lindsay M. Payer, Fernanda O.R. Rego, Thiago Luiz Araujo Miller, Pedro A.F. Galante, Sitharam Ramaswami, Adriana Heguy, David Fenyö, Jef D. Boeke, Kathleen Burns

Research output: Contribution to journalArticle

Abstract

Background: Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To this end, laboratories have developed strategies to selectively amplify or otherwise enrich transposable element insertion sites in genomic DNA. Results: Here we describe a technique, Transposon Insertion Profiling by sequencing (TIPseq), to map Long INterspersed Element 1 (LINE-1, L1) retrotransposon insertions in the human genome. This method uses vectorette PCR to amplify species-specific L1 (L1PA1) insertion sites followed by paired-end Illumina sequencing. In addition to providing a step-by-step molecular biology protocol, we offer users a guide to our pipeline for data analysis, TIPseqHunter. Our recent studies in pancreatic and ovarian cancer demonstrate the ability of TIPseq to identify invariant (fixed), polymorphic (inherited variants), as well as somatically-acquired L1 insertions that distinguish cancer genomes from a patient's constitutional make-up. Conclusions: TIPseq provides an approach for amplifying evolutionarily young, active transposable element insertion sites from genomic DNA. Our rationale and variations on this protocol may be useful to those mapping L1 and other mobile elements in complex genomes.

Original languageEnglish (US)
Article number8
JournalMobile DNA
Volume10
Issue number1
DOIs
StatePublished - Mar 8 2019

Fingerprint

DNA Transposable Elements
Human Genome
DNA
Long Interspersed Nucleotide Elements
Genome
Retroelements
Pancreatic Neoplasms
Ovarian Neoplasms
Molecular Biology
Polymerase Chain Reaction
Mutation
Neoplasms

Keywords

  • LINE-1
  • Next generation sequencing
  • Targeted PCR

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome. / Steranka, Jared P.; Tang, Zuojian; Grivainis, Mark; Huang, Cheng Ran Lisa; Payer, Lindsay M.; Rego, Fernanda O.R.; Miller, Thiago Luiz Araujo; Galante, Pedro A.F.; Ramaswami, Sitharam; Heguy, Adriana; Fenyö, David; Boeke, Jef D.; Burns, Kathleen.

In: Mobile DNA, Vol. 10, No. 1, 8, 08.03.2019.

Research output: Contribution to journalArticle

Steranka, JP, Tang, Z, Grivainis, M, Huang, CRL, Payer, LM, Rego, FOR, Miller, TLA, Galante, PAF, Ramaswami, S, Heguy, A, Fenyö, D, Boeke, JD & Burns, K 2019, 'Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome', Mobile DNA, vol. 10, no. 1, 8. https://doi.org/10.1186/s13100-019-0148-5
Steranka, Jared P. ; Tang, Zuojian ; Grivainis, Mark ; Huang, Cheng Ran Lisa ; Payer, Lindsay M. ; Rego, Fernanda O.R. ; Miller, Thiago Luiz Araujo ; Galante, Pedro A.F. ; Ramaswami, Sitharam ; Heguy, Adriana ; Fenyö, David ; Boeke, Jef D. ; Burns, Kathleen. / Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome. In: Mobile DNA. 2019 ; Vol. 10, No. 1.
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