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Juan Carlos Rivera-Mulia

Assistant Professor

Research Lab:

DNA replication timing and nuclear architecture

Lab website:


The human genome is organized in functional compartments that align with the temporal order of DNA replication (Replication Timing). Research in the Rivera-Mulia lab focusses in understanding the how DNA replication timing and large-scale chromosome organization are regulated and maintained in distinct cell types and remodeled during development as well as how alterations in nuclear architecture disrupt gene function in human disease.








We exploit exploit human embryonic stem cells (hESCs) and optimized differentiation systems to model development and track the changes in RT, gene expression and 3D genome organization. In our lab, we use genome-wide characterization of nuclear architecture, replication timing and gene expression as well as computational approaches to construct integrative models of nuclear function.







Recent publications:


  • Rivera-Mulia, J. C., Sasaki, T., Trevilla-Garcia, C., Nakamichi, N., Knapp, D., Hammond, C., et al. (2019). Replication timing alterations in leukemia affect clinically-relevant chromosome domains. Blood Advances. 3(21):3201-3213.
  • Rivera-Mulia, J. C., Kim, S., Gabr, H., Chakraborty, A., Ay, F., Kahveci, T., Gilbert, D. M. (2019). Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. Genome Research. 29(9):1415-1428.
  • Sarni, D., Sasaki, T., Miron, K., Tur-Sinai, M. I., Rivera-Mulia, J. C., Magnuson, B., et al. (2019). Replication Timing and Transcription Identifies a Novel Fragility Signature Under Replication Stress. bioRxiv, 150, 716951.
  • Dileep, V., Wilson, K., Marchal, C., Lyu, X., Zhao, P., Li, B., Poulet, A., Bartlett, D., Rivera-Mulia, J. C., et al. (2019). Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment. Stem Cell Reports.
  • Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner J., Rivera-Mulia, J. C., et al. (2019) Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell. Feb 7;176(4):816–8.
  • Poulet, A., Li, B., Rivera-Mulia, J. C., Dubos, T., Gilbert, D. M., Quin, Z. S. (2019). RT States: systematic annotation of the human genome using cell type-specific replication timing programs. Bioinformatics. 35(13), 2019, 2167–2176.
  • Zhang, J., Lee, D., Dhiman, V., Jiang, P., Xu, J., McGillivray, P., Yang, H., Liu, J., Meyerson, W., Clarke, D., Gu, M., Li, S., Lou, S., Xu, J., Lochovsky, L., Ma, L., Harmanci, A., Yan, K., Sethi, A., Cao, Q., Wang, D., Gursoy, G., Liu, J., Li, X., Rutenberg, M., Rozowsky, J., Reich, L., Rivera-Mulia, J. C., et al. (2019). An integrative ENCODE resource for cancer genomics. bioRxiv, 2, 706424.
  • Rivera-Mulia, J. C., Dimond, A., Vera, D., Trevilla-Garcia, C., Sasaki, T., Zimmerman, J., Dupont, C., Gribnau, J., Fraser, P., Gilbert D. M. (2018). Allele-specific control of replication timing and genome organization during development. Genome Research. 28(6), 800–811.
  • Rivera-Mulia, J. C., Schwerer, H., Besnard, E., Desprat, R., Trevilla-García, C., Sima, J., Bensadoun, P., Zouaoui, A,. Gilbert, D. M. Lemaitre, J. M. (2018). Cellular senescence induces replication stress with almost no affect on DNA replication timing. Cell Cycle. 17(13), 1667–1681.
  • Dixon, J., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V.T., Yardimci, G., Chakraborty, A., Bann, D., Wang Y., Clark, R., Zhang, L., Yang, H., Liu, T., Lyyanki, S., An, L., Pool, C., Sasaki, T., Rivera-Mulia, J. C., Ozadam, H., et al. (2018). Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. 4(10), 1–1398.
  • Marchal, C., Sasaki, T., Vera, D., Wilson, K., Sima, J., Rivera-Mulia, J. C., et al. (2018). Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nature Protocols. 13(5), 819–839.
  • Rivera-Mulia, J. C., Desprat, R., Trevilla-Garcia, C., Cornacchia, D., Schwerer, H., Sasaki, T., Sima, J., Fells, T., Studer, L., Lemaitre, J. M., Gilbert, D. M. (2017). DNA replication timing alterations as a novel marker of progeroid diseases. Proc Natl Acad Sci USA. 114(51): E10972-E10980.




7-212 Molecular and Cellular Biology Building
420 Washington Ave. S.E.
Minneapolis, MN 55455