Jesse Dixon

Assistant Professor

Gene Expression Laboratory

Jesse Dixon
Salk Institute for Biological Studies - Publications

all Publications


Reid, D.A., Reed, P.J., Schlachetzki, J.C.M., Nitulescu, I.I., Chou, G., Tsui, Chandran, S., Jones, J.R., Lu, A.T., McClain, C.A., Ooi, J.H., Wang, T.W., Lana, Linker, S.B., Ricciardulli, A.S., Lau, S., Schafer, S., Horvath, S., Dixon, J.R., Hah, N., Glass, C.K., Gage, F.H. Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons. (2021) Science. 372(6537):91-94. DOI: 10.1126/science.abb9032

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Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J.D., Conte, M., Gorkin, D., Yu, M., Li, B., Dixon, J.R., Hu, M., Nicodemi, M., Zhao, H., Ren, B. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. (2021) Nature Structural & Molecular Biology. DOI: 10.1038/s41594-020-00539-5

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Akdemir, K.C., Le, V.T., Kim, J.M., Killcoyne, S., King, D.A., Lin, Y.P., Tian, Y., Inoue, A., Amin, S.B., Robinson, F.S., Nimmakayalu, M., Herrera, R.E., Lynn, E.J., Chan, K., Seth, S., Klimczak, L.J., Gerstung, M., Gordenin, D.A., O'Brien, J., Li, L., Deribe, Y.L., Verhaak, R.G., Campbell, P.J., Fitzgerald, R., Morrison, A.J., Dixon, J.R., Andrew Futreal, P. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. (2020) Nature Genetics. DOI: 10.1038/s41588-020-0708-0

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Kang, H., Shokhirev, M.N., Xu, Z., Chandran, S., Dixon, J.R., Hetzer, M.W. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. (2020) Genes & Development. DOI: 10.1101/gad.335794.119

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Akdemir, K.C., Le, V.T., Chandran, S., Li, Y., Verhaak, R.G., Beroukhim, R., Campbell, P.J., Chin, L., Dixon, J.R., Futreal, P.A. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. (2020) Nature Genetics. DOI: 10.1038/s41588-019-0564-y

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Dixon, J.R. TADs for Life: Chromatin Domain Organization Regulates Lifespan in C. elegans. (2019) Developmental Cell. 51(2):131-132. DOI: 10.1016/j.devcel.2019.09.021

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Lee, D.S., Luo, C., Zhou, J., Chandran, S., Rivkin, A., Bartlett, A., Nery, J.R., Fitzpatrick, C., O'Connor, C., Dixon, J.R., Ecker, J.R. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. (2019) Nature Methods. DOI: 10.1038/s41592-019-0547-z

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Song, M., Yang, X., Ren, X., Maliskova, L., Li, B., Jones, I.R., Wang, C., Jacob, F., Wu, K., Traglia, M., Tam, T.W., Jamieson, K., Lu, S.Y., Ming, G.L., Li, Y., Yao, J., Weiss, L.A., Dixon, J.R., Judge, L.M., Conklin, B.R., Song, H., Gan, L., Shen, Y. Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. (2019) Nature Genetics. 51(8):1252-1262. DOI: 10.1038/s41588-019-0472-1

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Yang, Y., Zhang, Y., Ren, B., Dixon, J.R., Ma, J. Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. (2019) Cell Systems. DOI: 10.1016/j.cels.2019.05.011

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Zhou, J., Ma, J., Chen, Y., Cheng, C., Bao, B., Peng, J., Sejnowski, T.J., Dixon, J.R., Ecker, J.R. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation. (2019) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1901423116

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Barbosa, K., Deshpande, A., Chen, B.R., Ghosh, A., Sun, Y., Dutta, S., Weetall, M., Dixon, J., Armstrong, S.A., Bohlander, S.K., Deshpande, A.J. Acute Myeloid Leukemia Driven by the CALM-AF10 Fusion Gene is Dependent on BMI1. (2019) Experimental Hematology. DOI: 10.1016/j.exphem.2019.04.003

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Gatchalian, J., Malik, S., Ho, J., Lee, D.S., Kelso, T.W.R., Shokhirev, M.N., Dixon, J.R., Hargreaves, D.C. A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells. (2018) Nature Communications. 9(1):5139. DOI: 10.1038/s41467-018-07528-9

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Dixon, J.R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V.T., Yardımcı, G.G., Chakraborty, A., Bann, D.V., Wang, Y., Clark, R., Zhang, L., Yang, H., Liu, T., Iyyanki, S., An, L., Pool, C., Sasaki, T., Rivera-Mulia, J.C., Ozadam, H., Lajoie, B.R., Kaul, R., Buckley, M., Lee, K., Diegel, M., Pezic, D., Ernst, C., Hadjur, S., Odom, D.T., Stamatoyannopoulos, J.A., Broach, J.R., Hardison, R.C., Ay, F., Noble, W.S., Dekker, J., Gilbert, D.M., Yue, F. Integrative detection and analysis of structural variation in cancer genomes. (2018) Nature Genetics. DOI: 10.1038/s41588-018-0195-8

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Du, Z., Zheng, H., Huang, B., Ma, R., Wu, J., Zhang, X., He, J., Xiang, Y., Wang, Q., Li, Y., Ma, J., Zhang, X., Zhang, K., Wang, Y., Zhang, M.Q., Gao, J., Dixon, J.R., Wang, X., Zeng, J., Xie, W. Allelic reprogramming of 3D chromatin architecture during early mammalian development. (2017) Nature. 547(7662):232-235. DOI: 10.1038/nature23263

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Dixon, J.R., Gorkin, D.U., Ren, B. Chromatin Domains: The Unit of Chromosome Organization. (2016) Molecular Cell. 62(5):668-80. DOI: 10.1016/j.molcel.2016.05.018

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Diao, Y., Li, B., Meng, Z., Jung, I., Lee, A.Y., Dixon, J., Maliskova, L., Guan, K.L., Shen, Y., Ren, B. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. (2016) Genome Research. 26(3):397-405. DOI: 10.1101/gr.197152.115

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Selvaraj, S., Schmitt, A.D., Dixon, J.R., Ren, B. Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. (2015) BMC Genomics. 16:900. DOI: 10.1186/s12864-015-1949-7

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Ren, B., Dixon, J.R. A CRISPR Connection between Chromatin Topology and Genetic Disorders. (2015) Cell. 161(5):955-957. DOI: 10.1016/j.cell.2015.04.047

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Dixon, J.R.*, Jung, I.*, Selvaraj, S.*, Shen, Y., Antosiewicz-Bourget, J.E., Lee, A.Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., Diao, Y., Liang, J., Zhao, H., Lobanenkov, V.V., Ecker, J.R., Thomson, J.A., Ren, B. Chromatin architecture reorganization during stem cell differentiation. (2015) Nature. 518(7539):331-6. DOI: 10.1038/nature14222

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Li, Y., Rivera, C.M., Ishii, H., Jin, F., Selvaraj, S., Lee, A.Y., Dixon, J.R., Ren, B. CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. (2014) PLOS One. 9(12):e114485. DOI: 10.1371/journal.pone.0114485

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Attanasio, C., Nord, A.S., Zhu, Y., Blow, M.J., Biddie, S.C., Mendenhall, E.M., Dixon, J., Wright, C., Hosseini, R., Akiyama, J.A., Holt, A., Plajzer-Frick, I., Shoukry, M., Afzal, V., Ren, B., Bernstein, B.E., Rubin, E.M., Visel, A., Pennacchio, L.A. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. (2014) Genome Research. 24(6):920-9. DOI: 10.1101/gr.168930.113

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Zuin, J.*, Dixon, J.R.*, van der Reijden, M.I., Ye, Z., Kolovos, P., Brouwer, R.W., van de Corput, M.P., van de Werken, H.J., Knoch, T.A., van IJcken, W.F., Grosveld, F.G., Ren, B., Wendt, K.S. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(3):996-1001. DOI: 10.1073/pnas.1317788111

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Selvaraj, S.*, Dixon, J.R.*, Bansal, V., Ren, B. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. (2013) Nature Biotechnology. 31(12):1111-8. DOI: 10.1038/nbt.2728

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Jin, F., Li, Y., Dixon, J.R., Selvaraj, S., Ye, Z., Lee, A.Y., Yen, C.A., Schmitt, A.D., Espinoza, C.A., Ren, B. A high-resolution map of the three-dimensional chromatin interactome in human cells. (2013) Nature. 503(7475):290-4. DOI: 10.1038/nature12644

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Hu, M., Deng, K., Qin, Z., Dixon, J., Selvaraj, S., Fang, J., Ren, B., Liu, J.S. Bayesian inference of spatial organizations of chromosomes. (2013) PLOS Computational Biology. 9(1):e1002893. DOI: 10.1371/journal.pcbi.1002893

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Shen, Y., Yue, F., McCleary, D.F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V.V., Ren, B. A map of the cis-regulatory sequences in the mouse genome. (2012) Nature. 488(7409):116-20. DOI: 10.1038/nature11243

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Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S., Ren, B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. (2012) Nature. 485(7398):376-80. DOI: 10.1038/nature11082

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Barish, G.D., Yu, R.T., Karunasiri, M., Ocampo, C.B., Dixon, J., Benner, C., Dent, A.L., Tangirala, R.K., Evans, R.M. Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. (2010) Genes & Development. 24(24):2760-5. DOI: 10.1101/gad.1998010

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Pagliarini, D.J., Wiley, S.E., Kimple, M.E., Dixon, J.R., Kelly, P., Worby, C.A., Casey, P.J., Dixon, J.E. Involvement of a mitochondrial phosphatase in the regulation of ATP production and insulin secretion in pancreatic beta cells. (2005) Molecular Cell. 19(2):197-207. DOI: 10.1016/j.molcel.2005.06.008

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Education

AB, Princeton University
PhD, University of California San Diego
MD, University of California San Diego
Helmsley-Salk Fellow, Salk Institute for Biological Studies


Awards & Honors

  • NIH Early Independence Award (DP5), 2016-2021
  • University of California San Diego Chancellor’s Dissertation Medal for Biological Studies, 2014
  • University of California San Diego Department of Biomedical Science Outstanding Dissertation Award, 2013
  • California Institute for Regenerative Medicine Pre-Doctoral Fellowship, 2010-2012