Seung Kuk Park

All Publications

• Enhancer activation from transposable elements in extrachromosomal DNA. Nature cell biology Kraft, K., Murphy, S. E., Jones, M. G., Shi, Q., Bhargava-Shah, A., Luong, C., Hung, K. L., He, B. J., Li, R., Park, S. K., Montgomery, M. T., Weiser, N. E., Wang, Y., Luebeck, J., Bafna, V., Boeke, J. D., Mischel, P. S., Boettiger, A. N., Chang, H. Y. 2025

  Abstract

  Extrachromosomal DNA (ecDNA) drives oncogene amplification and intratumoural heterogeneity in aggressive cancers. While transposable element reactivation is common in cancer, its role on ecDNA remains unexplored. Here we map the 3D architecture of MYC-amplified ecDNA in colorectal cancer cells and identify 68 ecDNA-interacting elements-genomic loci enriched for transposable elements that are frequently integrated onto ecDNA. We focus on an L1M4a1#LINE/L1 fragment co-amplified with MYC, which functions only in the ecDNA-amplified context. Using CRISPR-CATCH, CRISPR interference and reporter assays, we confirm its presence on ecDNA, enhancer activity and essentiality for cancer cell fitness. These findings reveal that repetitive elements can be reactivated and co-opted as functional rather than inactive sequences on ecDNA, potentially driving oncogene expression and tumour evolution. Our study uncovers a mechanism by which ecDNA harnesses repetitive elements to shape cancer phenotypes, with implications for diagnosis and therapy.

  View details for DOI 10.1038/s41556-025-01788-6

  View details for PubMedID 41120733

  View details for PubMedCentralID 7484012

• Structural basis for the evolution of a domesticated group II intron-like reverse transcriptase to function in host cell DNA repair PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Park, S., Guo, M., Stamos, J. L., Kim, W., Lee, S., Zhang, Y., Lambowitz, A. M. 2025; 122 (31): e2504208122

  Abstract

  A previous study found that a bacterial group II intron-like reverse transcriptase (G2L4 RT) evolved to function in double-strand break repair (DSBR) via microhomology-mediated end-joining (MMEJ) and that a mobile group II intron-encoded RT has a basal DSBR activity that uses conserved structural features of non-long terminal repeat (non-LTR)-retroelement RTs. Here, we determined G2L4 RT apoenzyme and snap-back DNA synthesis structures revealing unique structural adaptations that optimized its cellular function in DSBR. These included an RT3a structure that stabilizes the apoenzyme in an inactive conformation until encountering a DNA substrate; a longer N-terminal extension/RT0-loop with conserved residues that together with a modified active site favors strand annealing; and a conserved dimer interface that localizes G2L4 RT homodimers to DSBR sites with both monomers positioned for MMEJ. Our findings reveal how an RT can function in DNA repair and suggest ways of optimizing related RTs for genome engineering applications.

  View details for DOI 10.1073/pnas.2504208122

  View details for Web of Science ID 001547126900001

  View details for PubMedID 40729381

  View details for PubMedCentralID PMC12337344

• Mechanisms used for cDNA synthesis and site-specific integration of RNA into DNA genomes by a reverse transcriptase-Cas1 fusion protein. Science advances Mohr, G., Yao, J., Park, S. K., Markham, L., Lambowitz, A. M. 2024; 10 (15): eadk8791

  Abstract

  Reverse transcriptase-Cas1 (RT-Cas1) fusion proteins found in some CRISPR systems enable spacer acquisition from both RNA and DNA, but the mechanism of RNA spacer acquisition has remained unclear. Here, we found that Marinomonas mediterranea RT-Cas1/Cas2 adds short 3'-DNA (dN) tails to RNA protospacers, enabling their direct integration into CRISPR arrays as 3'-dN-RNAs or 3'-dN-RNA/cDNA duplexes at rates comparable to similarly configured DNAs. Reverse transcription of RNA protospacers is initiated at 3' proximal sites by multiple mechanisms, including recently described de novo initiation, protein priming with any dNTP, and use of short exogenous or synthesized DNA oligomer primers, enabling synthesis of near full-length cDNAs of diverse RNAs without fixed sequence requirements. The integration of 3'-dN-RNAs or single-stranded DNAs (ssDNAs) is favored over duplexes at higher protospacer concentrations, potentially relevant to spacer acquisition from abundant pathogen RNAs or ssDNA fragments generated by phage defense nucleases. Our findings reveal mechanisms for site-specifically integrating RNA into DNA genomes with potential biotechnological applications.

  View details for DOI 10.1126/sciadv.adk8791

  View details for PubMedID 38608016

• Mechanisms used for cDNA synthesis and site-specific integration of RNA into DNA genomes by a reverse transcriptase-Cas1 fusion protein. bioRxiv : the preprint server for biology Mohr, G., Yao, J., Park, S. K., Markham, L. M., Lambowitz, A. M. 2023

  Abstract

  Reverse transcriptase-Cas1 (RT-Cas1) fusion proteins found in some CRISPR systems enable spacer acquisition from both RNA and DNA, but the mechanism of RNA spacer acquisition has remained unclear. Here, we found Marinomonas mediterranea RT-Cas1/Cas2 adds short 3'-DNA (dN) tails to RNA protospacers enabling their direct integration into CRISPR arrays as 3'-dN-RNA/cDNA duplexes or 3'-dN-RNAs at rates comparable to similarly configured DNAs. Reverse transcription of RNA protospacers occurs by multiple mechanisms, including recently described de novo initiation, protein priming with any dNTP, and use of short exogenous or synthesized DNA oligomer primers, enabling synthesis of cDNAs from diverse RNAs without fixed sequence requirements. The integration of 3'-dN-RNAs or single-stranded (ss) DNAs is favored over duplexes at higher protospacer concentrations, potentially relevant to spacer acquisition from abundant pathogen RNAs or ssDNA fragments generated by phage-defense nucleases. Our findings reveal novel mechanisms for site-specifically integrating RNA into DNA genomes with potential biotechnological applications.

  View details for DOI 10.1101/2023.09.01.555893

  View details for PubMedID 37693417

• Group II intron-like reverse transcriptases function in double-strand break repair. Cell Park, S. K., Mohr, G., Yao, J., Russell, R., Lambowitz, A. M. 2022; 185 (20): 3671-3688.e23

  Abstract

  Bacteria encode reverse transcriptases (RTs) of unknown function that are closely related to group II intron-encoded RTs. We found that a Pseudomonas aeruginosa group II intron-like RT (G2L4 RT) with YIDD instead of YADD at its active site functions in DNA repair in its native host and when expressed in Escherichia coli. G2L4 RT has biochemical activities strikingly similar to those of human DNA repair polymerase θ and uses them for translesion DNA synthesis and double-strand break repair (DSBR) via microhomology-mediated end-joining (MMEJ). We also found that a group II intron RT can function similarly in DNA repair, with reciprocal active-site substitutions showing isoleucine favors MMEJ and alanine favors primer extension in both enzymes. These DNA repair functions utilize conserved structural features of non-LTR-retroelement RTs, including human LINE-1 and other eukaryotic non-LTR-retrotransposon RTs, suggesting such enzymes may have inherent ability to function in DSBR in a wide range of organisms.

  View details for DOI 10.1016/j.cell.2022.08.014

  View details for PubMedID 36113466

  View details for PubMedCentralID PMC9530004