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Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.
Nucleic Acids Res
May 2025
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, these sites must be in proximity. Inverted repeat sequences, such as Alu elements, if positioned in the upstream and downstream introns, can base pair and represent one mechanism for inducing proximity.
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Nat Commun
May 2025
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
The human genome contains millions of copies of retrotransposons that are silenced but many of these copies have potential to become active if mutated, having phenotypic consequences, including disease. However, it is not thoroughly understood how nucleotide changes in retrotransposons affect their jumping activity. Here, we develop a massively parallel jumping assay (MPJA) that tests the jumping potential of thousands of transposons en masse.
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Annu Rev Neurosci
August 2024
Department of Anesthesiology and Department of Neurobiology and Behavior, Stony Brook School of Medicine, Stony Brook, New York, USA; email:
Over 40% of the human genome is composed of retrotransposons, DNA species that hold the potential to replicate via an RNA intermediate and are evolutionarily related to retroviruses. Retrotransposons are most studied for their ability to jump within a genome, which can cause DNA damage and novel insertional mutations. Retrotransposon-encoded products, including viral-like proteins, double-stranded RNAs, and extrachromosomal circular DNAs, can also be potent activators of the innate immune system.
View Article and Find Full Text PDFMassively parallel jumping assay decodes retrotransposition activity.
bioRxiv
April 2024
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
The human genome contains millions of retrotransposons, several of which could become active due to somatic mutations having phenotypic consequences, including disease. However, it is not thoroughly understood how nucleotide changes in retrotransposons affect their jumping activity. Here, we developed a novel massively parallel jumping assay (MPJA) that can test the jumping potential of thousands of transposons .
View Article and Find Full Text PDFDetecting Horizontal Transfer of Transposons.
Methods Mol Biol
December 2022
School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
Transposable elements (TEs) are prevalent genomic components which can replicate as a function of mobilization in eukaryotes. Not only do they alter genome structure, they also play regulatory functions or organize chromatin structure. In addition to vertical parent-to-offspring inheritance, TEs can also horizontally "jump" between species, known as horizontal transposon transfer (HTT).
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