Xiaoyang Zhang

Xiaoyang Zhang, PhD

Languages spoken: Chinese

Academic Information

Departments Primary - Oncological Sciences

Academic Office Information

u6021337@utah.edu

Research Statement

The Zhang Lab applies 3D genomics approaches to investigate the interplay between cancer genome and epigenome. We are interested in how genetic alterations cause epigenetic and transcriptional dysregulations that promote tumorigenesis, with a long-term goal of discovering novel therapeutic targets. Our group utilizes genomics and epigenomics analyses to generate hypotheses that we test using cutting-edge CRISPR technologies. Our research uniquely spans the interface between computational and experimental biology. The research directions include:




  • Identifying and characterizing recurrent noncoding genomic and epigenomic alterations in cancer.


  • Investigating the function of oncogenic transcription factors in cancer, particularly in 3D genome context.


Selected Publications

Journal Article

  1. Scholz P, Thompson J, Crosby KT, Fauth T, Krah NM, Schlauderaff G, Back R, Berkheimer ZA, Jolley A, Sombroek D, Medert R, Zurek C, Dmytrenko O, Wilson E, Schut FT, Rutter J, Zhang X, Krohn M, Jackson RN, Beisel CL, Liu (2026). RNA-triggered cell killing with CRISPR-Cas12a2. Nature, 655(8121), 230-239.
  2. Li J, Nelson ML, Li L, Xia X, Stephan C, Modzelewska K, Yu G, Mulford I, Srinivas H, Ge X, McCollum S, Jones ER, Guo Y, Chen X, Hollingworth G, Zoller T, Halilovic E, Clapier CR, Whittaker-Tademy AF, Faheem, Abrams T, Harrington E, Gkountela S, Galli GG, Voshol H, Thomas J, Carte N, Zhang X, Diehl KL, Lum DH, Hirst M, Yap JT, Forrester W, Cairns BR, Jones K (2026). BRD9 Degraders Unleash GBAF Chromatin Remodeling Activity in Synovial Sarcoma. Cancer research,
  3. Yang Y, Wang TY, Fry J, Li Y, Meng Q, Guo Q, Patchen NE, White KH, Ramakrishnan A, Ren Y, Li Q, Zhang X, Ali T, Dawes C, Fragkogianni S, Irvin P, Alam SK, Hoeppner LH, Zhang X, Yee D, Weiner AB, Schaeffer EM, Liu Y, Zhang X, Dehm SM, Cao Q, Yang (2026). Tumor-specific lncRNA IGF1R-AS1 trans-regulates chromatin interactions associated with oncogenic MYC signaling. Nature communications, 17(1),
  4. Abewe H, Richey A, Vahrenkamp JM, Ginley-Hidinger M, Rush CM, Kitchen N, Zhang X, Gertz (2025). Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements. Genome research, 35(3), 393-403.
  5. Gillis K, Orellana WA, Wilson E, Parnell TJ, Fort G, Fang P, Essel Dadzie H, Murphy BM, Zhang X, Snyder E (2025). FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma. Developmental cell, 60(3), 472-489.e8.
  6. Mortenson KL, Dawes C, Wilson ER, Patchen NE, Johnson HE, Gertz J, Bailey SD, Liu Y, Varley KE, Zhang (2024). 3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression. Nature communications, 15(1), 6130.
  7. Gnanapragasam A, Kirbizakis E, Li A, White KH, Mortenson KL, Cavalcante de Moura J, Jawhar W, Yan Y, Falter R, Russett C, Giannias B, Camilleri-Broët S, Bertos N, Cools-Lartigue J, Garzia L, Sangwan V, Ferri L, Zhang X, Bailey S (2024). HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer. Cancer research, 84(14), 2377-2389.
  8. Ginley-Hidinger M, Abewe H, Osborne K, Richey A, Kitchen N, Mortenson KL, Wissink EM, Lis J, Zhang X, Gertz (2024). Cis-regulatory control of transcriptional timing and noise in response to estrogen. Cell genomics, 4(5), 100542.
  9. Song Y, Li F, Wang S, Wang Y, Lai C, Chen L, Jiang N, Li J, Chen X, Bailey SD, Zhang (2024). Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer. Genome research, 34(10), 1514-1527.
  10. Zhao Z, Chen Y, Cheng X, Huang L, Wen H, Xu Q, Zhou X, Zhang X, Chen J, Ni (2023). The landscape of cryptic antisense transcription in human cancers reveals an oncogenic noncoding RNA in lung cancer. Science advances, 9(14), eadf3264.
  11. Pan Y, Han H, Hu H, Wang H, Song Y, Hao Y, Tong X, Patel AS, Misirlioglu S, Tang S, Huang HY, Geng K, Chen T, Karatza A, Sherman F, Labbe KE, Yang F, Chafitz A, Peng C, Guo C, Moreira AL, Velcheti V, Lau SCM, Sui P, Chen H, Diehl JA, Rustgi AK, Bass AJ, Poirier JT, Zhang X, Ji H, Zhang H, Wong K (2023). KMT2D deficiency drives lung squamous cell carcinoma and hypersensitivity to RTK-RAS inhibition. Cancer cell, 41(1), 88-105.e8.
  12. Tang S, Sethunath V, Metaferia NY, Nogueira MF, Gallant DS, Garner ER, Lairson LA, Penney CM, Li J, Gelbard MK, Alaiwi SA, Seo JH, Hwang JH, Strathdee CA, Baca SC, AbuHammad S, Zhang X, Doench JG, Hahn WC, Takeda DY, Freedman ML, Choi PS, Viswanathan S (2022). A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer. Cell reports, 38(8), 110417.
  13. Chu Z, Gu L, Hu Y, Zhang X, Li M, Chen J, Teng D, Huang M, Shen CH, Cai L, Yoshida T, Qi Y, Niu Z, Feng A, Geng S, Frederick DT, Specht E, Piris A, Sullivan RJ, Flaherty KT, Boland GM, Georgopoulos K, Liu D, Shi Y, Zheng (2022). STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming. Nature communications, 13(1), 1859.
  14. Liu Y, Wu Z, Zhou J, Ramadurai DKA, Mortenson KL, Aguilera-Jimenez E, Yan Y, Yang X, Taylor AM, Varley KE, Gertz J, Choi PS, Cherniack AD, Chen X, Bass AJ, Bailey SD, Zhang (2021). A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer. Nature communications, 12(1), 7139.
  15. Llabata P, Torres-Diz M, Gomez A, Tomas-Daza L, Romero OA, Grego-Bessa J, Llinas-Arias P, Valencia A, Esteller M, Javierre BM, Zhang X, Sanchez-Cespedes (2021). MAX mutant small-cell lung cancers exhibit impaired activities of MGA-dependent noncanonical polycomb repressive complex. Proceedings of the National Academy of Sciences of the United States of America, 118(37),
  16. Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, Meyerson M, Zhang (2020). Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma. Molecular cancer research, 18(4), 574-584.
  17. Liu Y, Guo B, Aguilera-Jimenez E, Chu VS, Zhou J, Wu Z, Francis JM, Yang X, Choi PS, Bailey SD, Zhang (2020). Chromatin Looping Shapes KLF5-Dependent Transcriptional Programs in Human Epithelial Cancers. Cancer research, 80(24), 5464-5477.

Review

  1. Wilson ER, Zhang (2025). Enhancers, silencers, and attenuators: A dynamic and reversible regulatory code. Developmental cell, 60(18), 2381-2382.
  2. Zhang X, Meyerson (2020). Illuminating the noncoding genome in cancer. Nature cancer, 1(9), 864-872.