Dissertation Research: Probing Retrotransposon Extinctions Grant uri icon



  • As much as 50% of the typical mammalian genome consists of retrotransposed sequences, dominated by LINE-1 and various types of SINE retrotransposons. LINE-1 encodes genes for its own retrotransposition, but is also parasitized by SINEs for their movement. LINE-1 has been co-evolving with its mammalian hosts for at least 170 million years and has had major impacts on their evolution. However, two LINE-1 extinction events have been documented, affecting 9% of mammalian species. Shutting down LINE-1 activity should result in a simultaneous silencing of SINEs. However, in a LINE-1 extinction event in South American rodents, the extinction of the B1 family of SINEs was unexpectedly found to precede the extinction of LINE-1. Reconstruction of the common ancestor of the extinct LINE-1 and B1 and analysis of their interactions in a tissue culture assay will be used to explore the mechanism underlying their extinction.

    Although retrotransposons like LINEs and SINEs have had large impacts on mammalian evolution, our knowledge of them is limited to the study of sequenced genomes and work in model organisms. The arms race between LINE-1 and B1, or autonomous and the corresponding non-autonomous transposons in a broader sense, has been investigated by computational simulations, but empirical data are scarce. Tools developed to understand the mechanism of transpositions in humans and model organisms will be extended to a non-model system with a unique evolutionary history. This proposal will contribute to the larger picture of mammalian genome evolution and transposable element regulation.

date/time interval

  • June 1, 2012 - May 31, 2013

total award amount

  • 14,508