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@ARTICLE{Misak:304992,
      author       = {M. Misak and A. Basu and C. Niehrs$^*$},
      title        = {{S}ubfamily-selective {PCR} primers for the human {LINE}1
                      {L}1{PA} lineage.},
      journal      = {Scientific reports},
      volume       = {15},
      number       = {1},
      issn         = {2045-2322},
      address      = {[London]},
      publisher    = {Springer Nature},
      reportid     = {DKFZ-2025-01983},
      pages        = {32499},
      year         = {2025},
      note         = {#LA:A050# / DKFZ-ZMBH Alliance},
      abstract     = {Long interspersed nuclear element-1 (LINE1)
                      retrotransposons are classified into different subfamilies
                      based on evolutionary history. For human biology, the L1PA
                      lineage of LINE1s is particularly significant. This lineage
                      contains both retrotransposition-competent and inactive
                      subfamilies. PCR-based methods are widely used to monitor
                      LINE1s in genomic DNA. However, PCR analysis distinguishing
                      between L1PA lineage subfamilies of different evolutionary
                      age is thus far challenging due to the difficulty to design
                      primers that are sufficiently specific. Here, we developed
                      and applied a workflow to design PCR primers that
                      discriminate between different subfamilies of the L1PA
                      lineage. Amplicon sequencing after PCR amplification of
                      genomic DNA confirmed that the primers differentiate between
                      groups of L1PA subfamilies of different evolutionary age. We
                      validated the primers using RT-qPCR and verified consistency
                      with publicly available RNA-seq data. Moreover, inhibition
                      of DNA methyltransferase dose-dependently increased LINE1
                      expression for younger L1PA subfamilies, consistent with
                      transcriptional de-repression. Thus, our primers enable
                      PCR-based surveys that can stratify expression, copy number
                      or epigenetic modification for L1PA subfamilies of differing
                      evolutionary age.},
      keywords     = {Long Interspersed Nucleotide Elements: genetics / Humans /
                      DNA Primers: genetics / Polymerase Chain Reaction: methods /
                      Evolution, Molecular / L1PA (Other) / LINE1 (Other) / PCR
                      (Other) / Primer (Other) / Subfamily (Other) / DNA Primers
                      (NLM Chemicals)},
      cin          = {A050},
      ddc          = {600},
      cid          = {I:(DE-He78)A050-20160331},
      pnm          = {311 - Zellbiologie und Tumorbiologie (POF4-311)},
      pid          = {G:(DE-HGF)POF4-311},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:40940398},
      pmc          = {pmc:PMC12432230},
      doi          = {10.1038/s41598-025-17649-z},
      url          = {https://inrepo02.dkfz.de/record/304992},
}