Biochemistry Graduate Program

About Mengting Han

Research

Spatial RNA localization regulates the spatiotemporal organization of RNAs and proteins. This is particularly important in neurons and is disrupted in some neurological disorders including ALS, FTD, FXS, and SMA. However, the regulatory mechanisms, functional roles, and pathological relevance of spatial RNA localization are not well understood, largely due to limited tools. The Han lab is interested in answering these questions by developing cutting-edge synthetic biology, chemical biology, and CRISPR tools to profile and engineer the spatial transcriptome. The long-term goal is to explore novel therapeutic strategies for treating neurodegenerative diseases from the perspective of spatial transcriptome.

Research arears

• Engineering the RNA-targeting CRISPR systems for better performance to study RNA biology.

• Mechanistic study of spatial RNA localization, particularly focusing on how posttranslational modifications of RNA and RNA-binding proteins regulate spatial RNA localization.

• Functional interpretation of the spatial transcriptome using CRISPR-mediated high-throughput screening in neurons and cancer cells.

• Investigating the pathological relevance of aberrant spatial transcriptome in neurological disorders.

• Exploring novel therapeutic strategies for treating neurodegenerative diseases (e.g., amyotrophic lateral sclerosis (ALS)) by engineering the spatial transcriptome.

Publications

1. Han, M., Fu, M. L., Zhu, Y., Choi, A. A., Li, E., Bezney, J., Cai, S., Miles, L., Ma, Y. & Qi, L. S. Programmable control of spatial transcriptome in live cells and neurons. Nature 643(8070): 241-251 (2025). 
   Highlighted by Nature Biotechnology: Marchal, I. CRISPR-TO directs RNA to defined intracellular locations. Nat. Biotechnol. 43(6): 864 (2025). 
2. Han, M.* CRISPR-TO: a versatile tool for programmable control of the spatial transcriptome. Nat. Rev. Neurosci. Accepted. (*Corresponding author) 
3. Andronov, L.#, Han, M.#, Zhu, Y., Roy, A. R., Barentine, A. E. S., Garhyan, J., Qi, L. S. & Moerner, W. E. Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. Nat. Commun. 15(1): 4644 (2024). (#Co-first author) 
4. Wang, J.#, Han, M.#, Roy, A. R., Wang, H., Möckl L., Zeng, L., Moerner, W. E. & Qi, L. S. Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. Cell Rep. Methods 2(2): 100170 (2022). (#Co-first author) 
5. Wang, H.#, Han, M.# & Qi, L. S. Engineering 3D genome organization. Nat. Rev. Genet. 22(6): 343-360 (2021). (#Co-first author) 
6. Huang, R.#, Han, M.#, Meng, L. & Chen, X. Transcriptome-wide discovery of coding and noncoding RNA-binding proteins. Proc. Natl. Acad. Sci. USA 115(17): E3879-E3887 (2018). (#Co-first author) 
7. Huang, R.#, Han, M.#, Meng, L. & Chen, X. Capture and identification of RNA-binding proteins by using click chemistry-assisted RNA-interactome capture (CARIC) strategy. J. Vis. Exp. 140(140): e58580 (2018). (#Co-first author) 
8. Zhu, Y., Balaji, A., Han, M., Andronov, L., Roy, A. R., Wei, Z., Chen, C., Miles, L., Cai, S., Gu, Z., Tse, A., Yu, B. C., Uenaka, T., Lin, X., Spakowitz, A. J., Moerner, W. E. & Qi, L. S. High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH. Cell 188(12): 3310-3328 e3327 (2025). 
9. Gao, Y., Han, M., Shang, S., Wang, H. & Qi, L. S. Interrogation of the dynamic properties of higher-order heterochromatin using CRISPR-dCas9. Mol. Cell 81(20): 4287-4299 e4285 (2021). 
10. Zeng, L., Liu, Y., Nguyenla, X. H., Abbott, T. R., Han, M., Zhu, Y., Chemparathy, A., Lin, X., Chen, X., Wang, H., Rane, D. A., Spatz, J. M., Jain, S., Rustagi, A., Pinsky, B., Zepeda, A. E., Kadina, A. P., Walker, J. A., 3rd, Holden, K., Temperton, N., Cochran, J. R., Barron, A. E., Connolly, M. D., Blish, C. A., Lewis, D. B., Stanley, S. A., La Russa, M. F., Qi, L. S. Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro. Nat. Commun. 13(1): 2766 (2022). 
11. Qin, W., Qin, K., Fan, X., Peng, L., Hong, W., Zhu Y., Lv, P., Du, Y., Huang, R., Han, M., Chen, B., Liu, Y., Zhou, W., Wang, C. & Chen, X. Artificial cysteine S-glycosylation induced by per-O-acetylated unnatural monosaccharides during metabolic glycan labeling. Angew. Chem. Int. Ed., 57(7): 1817-1820 (2018). 

Patents

Qi L. S., Han, M. “United States Patent US provisional patent application No. 63/594,147 Manipulating spatial RNA localization”, Leland Stanford Junior University, October 30, 2023

Awards

School of Medicine Dean's Postdoctoral Fellowship, Stanford University, 2022-2023