Franklin Lab

Matt Franklin

Group Leader

Dr. Matt Franklin started his scientific career in biochemical engineering (Michigan State University, University of Washington) and structural biology (EMBL-Hamburg). He earned his PhD in Chemical Engineering at Stanford University under the mentorship of Jan Liphardt, with support from the National Science Foundation Graduate Research Fellowship. During his graduate work, Matt investigated multiple biological questions from a physical perspective. While studying the dynamics of Hippo pathway signaling, Matt unexpectedly discovered that the Hippo pathway transcription factor family TEAD directly binds one of the major satellite repeats, Human Satellite 3 (HSat3). Intrigued by this observation, Matt went all-in to understand why such a highly conserved transcription factor targets the largest elements in the genome.

During his multi-lab postdoctoral journey at University of California San Diego, Stowers Institute for Medical Research, and Stanford University, Matt unveiled two core discoveries: [1] the Hippo transcription effectors YAP/TEAD accumulate on satellites inside the nucleolus, allowing YAP to directly activate RNA Polymerase-I, and [2] human satellite repeats encode binding platforms for dozens of transcription factors, including those of highly-conserved signaling pathways. Using experimental and computational approaches, the Franklin Lab aims to uncover how satellite repeats shape genome regulation in health and disease.

Franklin Lab about

Matt Franklin

Group Leader

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Functions of repetitive DNA in human health and disease

The Franklin lab investigates the roles of massive repetitive DNA elements (a.k.a. satellite repeats) in the contexts of developmental signaling and disease states.

Tandemly repeated DNA sequences make up the largest elements of eukaryotic genomes and can span tens of megabases. These so-called “satellite” repeats were identified in the 1960s, yet we have not fully explored their roles in regulating the genome. At NIMSB, the Franklin Lab will conduct multi-omics profiling of these mysterious repeats to understand how they influence core cell processes in early development signaling and human disease states. The lab will also utilize the unique properties of satellite repeats for biotechnology applications, such as drug screening.

To serve the greater chromatin community, our lab developed a database to centralize functional research on repetitive DNA, called the “repeatome”. We hope to publicly release this resource soon – please reach out if you would like to contribute!

Full list of publications

Franklin Lab team

Meet Our Team

Matt Franklin

Group Leader

Franklin Lab Selected Publications

Franklin, J.M., Dubocanin, D., Chittenden, C., Barillas, A., Jooyoung Lee, R., Ghosh, R.P., Gerton, L. J., Guan, K-L.,* Altemose, N*. Human Satellite3 DNA encodes megabase-scale transcription factor binding platforms. BioRxiv (2025) (doi:10.1101/2024.10.22.616524v2)
Franklin, J.M., Wu, Z. & Guan, KL. Insights into recent findings and clinical application of YAP and TAZ in cancer. Nat Rev Cancer 23, 512–525 (2023). https://doi.org/10.1038/s41568-023-00579-1
Franklin, J.M., Ghosh, R.P., Shi, Q. et al. Concerted localization-resets precede YAP-dependent transcription. Nat Commun (2020) (doi:10.1038/s41467-020-18368-x)
Ghosh, R.P., Franklin, J.M., Draper, W.E. et al. A fluorogenic array for temporally unlimited single-molecule tracking. Nat Chem Biol (2019) (doi:10.1038/s41589-019-0241-6)
Ban, E., Franklin, J.M., Nam, S., Smith, R.L., Wang, H., Wells, G.R., Chaudhuri, O., Liphardt, T.J., and Vivek B. Shenoy, B.V. Mechanisms of Plastic Deformation in Collagen Networks Induced by Cellular Forces. Biophysical Journal (2018) (doi:10.1016/j.bpj.2017.11.3739)