Ci Ji Lim

Department of Biochemistry Assistant Professor Lab Website 265-4690

315C HF DeLuca Biochemistry Laboratories
433 Babcock Drive
Madison, WI 53706-1544


B.Sc., Nanyang Technological University, Singapore
Ph.D., National University of Singapore, Singapore
Postdoctoral, University of Colorado Boulder (Cech lab)

Mechanism of telomere maintenance; Structure-function studies of biological machines by cryo-EM and single-molecule imaging

Telomere Maintenance Molecular Mechanism: A multiscale interdisciplinary approach
Telomeres are repetitive DNA and associated proteins at the ends of linear chromosomes. They protect our chromosome ends from being misread as broken ends, underlining the importance of telomeres for genome stability, and they also serve as a “clock” for our biological lifespan. Our lab seeks to investigate the molecular mechanisms of human telomere maintenance using an interdisciplinary approach. This includes structural studies using cryo-electron microscopy (cryo-EM) and spatial/temporal studies using single-molecule imaging techniques. Specially, our lab focuses on two major areas – 1) Telomere chromatin organization and 2) Telomere replication mechanism

Illustration of Telomere maintenance molecular mechanism

Telomere Chromatin Organization
Key to understanding how telomeric proteins perform their functions at telomeres is to determine how they organize telomeres to various functional chromatin states. A leading and widely popular inhibitory model is the shelterin-mediated telomere loop, but its underlying mechanism is not well understood. A simpler model would be an end-capping model. Using an array of biochemical and biophysical techniques, we seek to understand how different compositions of telomeric protein complexes organize long telomeric DNA into various architectures, and further determine their ability to prime telomere elongation by telomerase and to regulate DNA damage repair pathways.

Photos illustrating telomere chromatin organization

Telomere Replication Mechanism
We are interested in how telomeric protein complexes shelterin, CST, telomerase and DNA polymerase assemble and coordinate the replication of telomere. Key stages of this process are 1) telomerase recruitment by shelterin, 2) telomere extension by telomerase, 3) termination of telomere extension and 4) conversion of the newly synthesized telomeric single-stranded DNA to double-stranded form by DNA polymerase machinery. Our lab aims to dissect molecular mechanisms of these individual steps using cryo-EM single-particle analysis and single-molecule imaging techniques, with the eventual goal of building a structural roadmap of telomere replication at the ends of chromosomes.

Cryo-EM model of human CST defamer with telomeric ssDNA

Photo of Ci Ji Lim

Areas of Expertise

  • RNA/DNA Biophysics
  • Spectroscopy Microscopy Imaging
  • Structural Biology