John Kim

Our Research

We study how microRNAs regulate fundamental biological processes including regulation of post-embryonic and germline development, transposon silencing to preserve genome integrity, and oncogenic cell proliferation.

The RNA interference (RNAi) and microRNA pathways regulate these diverse activities through sequence-specific gene silencing mechanisms mediated by small RNAs.

About John Kim

  • Epigenetics
  • MicroRNAs
  • Germline biology

John Kim is interested in deciphering the biological function of microRNAs and other small RNAs expressed in the genome. To do so, he takes a multidisciplinary approach, from deep sequencing to identify novel microRNAs and small RNAs, to detailed analysis of a number of microRNAs that are conserved from worm to human.

Research highlight

The Kim lab recently published a study on the global binding of mRNA binding proteins in budding yeast, titled "Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae." Though the interactions between proteins and RNA are integral components of everything from gene expression to disease, relatively little is known about them. The Kim lab's paper studies the dynamics of protein-RNA interactions in response to environmental stress conditions, an aspect of protein-RNA interactions that is even less understood.

The paper was published in February 2013 in Genome Biology.

Recent Publications

Billi, A.C., Freeberg, M.A., Day, A.M., Chun, S.Y., Khivansara, V., and Kim, J.K. A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genetics 9(3): e1003392 (2013).

Freeberg, M.A., Han, T., Moresco, J.J., Kong, A., Yang, Y-C., Lu, Z.J., Yates III, J.R., and Kim, J.K. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology 14(2):R13 (2013).