Natural genome editing of ciliates

Estienne Swart

EstienneSwart FacPage Nov17
  • PhD 2006-2012, Princeton University
  • Postdoctoral fellow 2012-2017, University of Bern
  • Group leader at the MPI for Developmental Biology since 2017

Research Interest

Currently my lab is focused on determining the key molecules involved during genome-wide DNA elimination in ciliates, a diverse and ancient group of microbial eukaryotes. This DNA elimination process transforms germline genomes into somatic ones during development. Domesticated transposases are responsible for the excision of the DNA, and are assisted by additional proteins and RNAs. Over the past years a number of new molecules involved in ciliate genome editing have been discovered. The main challenges are to determine the interactions among these molecules and to identify and functionally characterize potential additional ones that may be required.

To investigate genome reorganisation/editing my lab uses functional genomic approaches in the model ciliate Paramecium, including analyses of the consequences of gene knockdown on DNA excision that are revealed by high-throughput sequencing. The thrust of this work is to determine the key interactions between molecules whose silencing suggests possible involvement in genome editing. We also use comparative genomic approaches between model and non-model ciliates to identify which molecular components involved in the DNA elimination are functionally conserved and how they came to be.

  • Fig1 Swart
    click to enlarge

Fig 1. Ciliates have dimorphic nuclei within each cell. Extensive DNA elimination, and, sometimes, also reordering occurs when a germline nucleus develops into a new somatic nucleus in ciliates. Image copyright: 3Swart et al. 2013 (CC BY).

Available PhD Projects

Functional genomic investigation of genome editing in Paramecium.

Selected Reading

Swart EC, Denby Wilkes C, Sandoval PY, Hoehener C, Singh A, et al. (2017) Identification and analysis of functional associations among natural eukaryotic genome editing components. F1000Research. doi: 10.12688/f1000research.12121.1

Sandoval PY*, Swart EC*, Arambasic M and Nowacki M (2014) Functional diversification of Dicer-like proteins and small RNAs required for genome sculpting. Developmental Cell. 28: 1-15. doi: 10.1016/j.devcel. 2013.12.010. * Equal contributions.

Swart EC, Bracht J, Magrini V, Minx P, Chen X, et al. (2013) The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLOS Biology. 11(1): e1001473. doi: 10.1371/journal.pbio.1001473