James Nuñez

Assistant Professor of Biochemistry, Biophysics and Structural Biology

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Research Interests

The core interest of our group is to understand the regulatory principles of the human genome. Specifically, we investigate the molecular principles underlying epigenetic memory and inheritance in mammalian cells: how do cells establish the ‘epigenome’ to dictate gene expression programs and genome organization; how is the epigenome maintained and remodeled as cells divide and differentiate; and how do defects in these pathways lead to disease? We combine functional genomics CRISPR screens, cell biology, and biochemistry to answer our research questions. 

Concurrently, we develop and apply CRISPR-based programmable technologies for editing the epigenome by writing/erasing DNA and histone modifications at any genomic locus, allowing us to perturb gene expression programs without changing the underlying DNA sequence.

Current Projects

Epigenetic memory and inheritance

The ‘epigenetic code’ is complex and often requires the orchestration of multiple DNA and histone modifications to result in a biological output such as transcriptional repression or activation. During early mammalian development, DNA methylation and histone modifications are remodeled dramatically, leading to the establishment of many gene expression programs that are subsequently remembered by cells through embryogenesis and mammalian development. We seek to understand the interplay between DNA methylation and histone modifications that allow for epigenetic memory and discover the factors that mediate these processes in mammalian cells. How is epigenetic memory established and how are the chromatin marks spread from the establishment site and maintained durably?

CRISPR-based epigenome editing

Programmable epigenome editing technologies remodel the epigenetic landscape in mammalian cells without the need to induce DNA breaks, leading to the fine tuning of transcription at a desired level (repression/activation). As an example, we engineered the CRISPRoff technology for editing DNA methylation and histone modifications at gene promoters. Transient expression of CRISPRoff in mammalian cells leads to heritable gene silencing that is memorized by cells through cell division and differentiation from stem cells to neurons. We seek to develop new CRISPR-based epigenome editing technologies by fusing catalytically dead Cas9 to chromatin writer/eraser/reader proteins and apply these technologies genome-wide. These tools enable fine-tuned programming of gene expression for cell and tissue engineering and in vivo therapeutic applications.

DNA methylation biology and disease

DNA methylation is an essential epigenetic modification that can regulate gene expression, such as repressing transposable elements and establishing genomic imprinting. Mutations of DNA methyltransferases, demethylases, and DNA methylation ‘reader’ proteins are implicated in cancer and neurological diseases. By studying the fundamental functions of these proteins at the systems-wide, cell biology, and biochemical levels, we seek to understand how aberrant writing, erasing, and reading of DNA methylation modifications can directly lead to disease.

Selected Publications

Nuñez, J.K., Chen, J., Pommier, G.C., Cogan, J.Z., Replogle, J.M., Adriaens, C., Ramadoss, G.N., Shi, Q., Hung, K.L., Samelson, A.J., Pogson, A.N., Kim, J.Y.S., Chung, A., Leonetti, M.D., Chang, H.Y., Kampmann, M., Bernstein, B.E., Hovestadt, V., Gilbert, L.A., Weissman, J.S. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell 184 (2021).

Chen, J., Brunner, A., Cogan, J.Z., Nuñez, J.K., Fields, A.P., Adamson, B., Mann, M., Leonetti, M.D., Weissman, J.S. Pervasive functional micropeptides in humans encoded by non-canonical open reading frames. Science 367 (2020).

Tak, Y.E., Kleinstiver, B.P., Nuñez, J.K., Hsu, J.Y., Horng, J.E., Gong, J., Weissman, J.S., Joung, J.K. Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors. Nature Methods 14 (2017).

Adamson B., Norman, T.M., Jost, M., Cho, M.Y., Nuñez, J.K., Chen, Y., Villalta, J.E., Gilbert, L.A., Horlbeck, M.A., Hein, M.Y., Pak, R.A., Gray, A.N., Gross, C.A., Dixit, A., Parnas, O., Regev, A., Weissman, J.S. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell 167 (2016).

Nuñez, J.K., Bai, L., Harrington, L.B., Hinder, T.L., Doudna, J.A. CRISPR immunological memory requires a host factor for specificity. Molecular Cell 62 (2016).

Nuñez, J.K.*, Harrington, L.B.*, Kranzusch, P.J., Engelman, A.N., Doudna, J.A. Foreign DNA capture during CRISPR–Cas adaptive immunity. Nature 527 (2015b). *Equal contribution.

Nuñez, J.K., Lee, A.S.Y., Engelman, A.N., Doudna, J.A. Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity. Nature 519 (2015a).

Nuñez, J.K., Kranzusch, P.J., Noeske, J., Wright, A.V., Davies, C.W., Doudna, J.A. Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity. Nature Structural & Molecular Biology 21 (2014).

Last Updated 2021-06-17