Research Summary

The Ahituv lab is focused on identifying gene regulatory elements and linking nucleotide variation within them to various phenotypes including morphological differences between species, drug response and human disease. It develops and uses massively parallel reporter assays (MPRAs) that allow for high-throughput functional characterization of gene regulatory elements. In addition, the lab pioneered cis-regulation therapy (CRT), the use of gene regulatory elements as therapeutic targets for haploinsufficient disorders, and adipose modulation transplantation (AMT), a novel cancer cell therapy.

Research Funding

  • September 1, 2021 - May 31, 2026 - Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: UM1HG011966
  • July 1, 2020 - June 30, 2025 - From Obesity GWAS to therapeutic targets , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01DK124769
  • August 1, 2013 - June 30, 2023 - The Airway Functional Genomics of Bronchodilator Drug Response in Minority Children with Asthma , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01HL117004
  • July 6, 2018 - March 31, 2023 - Massively parallel characterization of psychiatric disease associated regulatory elements in defined cell types , Principal Investigator . Sponsor: NIH, Sponsor Award ID: U01MH116438
  • July 1, 1982 - June 30, 2022 - Pharmaceutical Sciences and Pharmacogenomics , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: T32GM007175
  • February 1, 2017 - January 31, 2022 - Massively parallel reporter assays and genome editing of ENCODE predicted regulatory elements , Principal Investigator . Sponsor: NIH, Sponsor Award ID: UM1HG009408
  • September 15, 2018 - August 31, 2021 - Genetic Etiology of Abdominal Hernia Susceptibility , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01DK116738
  • August 16, 2019 - July 31, 2021 - Technologies for simultaneous characterization of regulatory activity and protein binding , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R21HG010683
  • September 1, 2016 - June 30, 2021 - Developmental Mechanisms of Human Idiopathic Scoliosis , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: P01HD084387
  • May 1, 2016 - February 28, 2021 - Massively parallel dissection of psychiatric regulatory networks , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01MH109907
  • May 1, 2018 - April 30, 2020 - Development of massively parallel reporter assays that use cognate promoters , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R21HG010065
  • May 1, 2012 - March 31, 2016 - Identification & functional characterization of SIM1 obesity-associated variants , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01DK090382
  • April 1, 2012 - March 31, 2016 - Characterization of neuronal gene regulatory elements associated with epilepsy , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01NS079231
  • April 24, 2012 - June 30, 2015 - Massively parallel, in vivo functional testing of regulatory elements , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01HG006768
  • April 1, 2000 - June 30, 2015 - Pharmacogenomics of Membrane Transporters , Co-Investigator . Sponsor: NIH, Sponsor Award ID: U19GM061390
  • April 1, 2009 - March 31, 2015 - Characterization of regulatory elements leading to human limb malformations , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01HD059862
  • September 29, 2009 - July 31, 2014 - Computational & Functional Annotation of the Zebrafish Genome Regulatory Toolbox , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01HG005058

Honors & Awards

  • 2014
    ASCPT Leon I. Goldberg Young Investigator Award
  • 2002
    Ph.D. with distinction
  • 2024
    American Society of Human Genetics (ASHG) Scientific Achievement Award

Selected Publications

  1. Tamura S, Nelson AD, Spratt PWE, Hamada EC, Zhou X, Kyoung H, Li Z, Arnould C, Barskyi V, Krupkin B, Young K, Zhao J, Holden SS, Sahagun A, Keeshen CM, Lu C, Ben-Shalom R, Taloma SE, Schamiloglu S, Li YC, Min L, Jenkins PM, Pan JQ, Paz JT, Sanders SJ, Matharu N, Ahituv N, Bender KJ. CRISPR activation for SCN2A-related neurodevelopmental disorders. View on PubMed
  2. Golan Y, Nyquist SK, Liu Z, Ennis D, Zhao J, Blair E, Khan AR, Prahl M, Gaw SL, Yassour M, Engelhardt BE, Flaherman VJ, Ahituv N. Genomic characterization of normal and aberrant human milk production. View on PubMed
  3. Georgakopoulos-Soares I, Yizhar-Barnea O, Mouratidis I, Chan CSY, Patsakis M, Nayak A, Bradley R, Mahajan M, Sims J, Cintron DL, Easterlin R, Kim JS, Chen E, Pineda G, Parada GE, Witte JS, Maher CA, Feng F, Vathiotis I, Syrigos N, Panagiotou E, Charpidou A, Syrigos K, Chapman J, Kvale M, Hemberg M, Ahituv N. Leveraging sequences missing from the human genome to diagnose cancer. View on PubMed
  4. An K, Ito Y, Ahituv N. Reprogramming White Fat Cells for Adipose Manipulation Transplantation (AMT) Therapy. View on PubMed
  5. Sepich DS, Gray RS, Ahituv N, Gurnett CA, Rios JJ, Solnica-Krezel L, Wise CA. The importance of imperfect pre-clinical models in adolescent idiopathic scoliosis. View on PubMed
  6. Li Z, Fischbein N, Jin F, Nyquist S, O'Brien K, Ahituv N, Flaherman V, Golan Y. Methods for Preserving Cellular and Milk Fat Globules RNA from Human Milk Samples. View on PubMed
  7. Zhang Z, Georgakopoulos-Soares I, Bourque G, Ahituv N, Inoue F. Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA. View on PubMed
  8. Golan Y, Nyquist SK, Liu Z, Ennis D, Zhao J, Blair E, Rahim Khan A, Prahl M, Gaw SL, Yassour M, Engelhardt BE, Flaherman VJ, Ahituv N. Genomic characterization of normal and aberrant human milk production. View on PubMed
  9. Easterlin R, Ahituv N. Lineage-specific regulatory evolution: insights from massively parallel reporter assays. View on PubMed
  10. Kosicki M, Laboy Cintrón D, Keukeleire P, Schubach M, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Kircher M, Pennacchio LA, Ahituv N. Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity. Nat Commun. 2025 May 23; 16(1):4786. View on PubMed
  11. Matharu N, Zhao J, Sohota A, Deng L, Hung Y, Li Z, An K, Sims J, Rattanasopha S, Meyer TJ, Carbone L, Kircher M, Ahituv N. Massively parallel jumping assay decodes Alu retrotransposition activity. Nat Commun. 2025 May 09; 16(1):4310. View on PubMed
  12. Yarden Golan Maor, Nicole G Fischbein, Flora G Jin, Kelli G Faiai, Kerri G Bertrand, Christina G Chambers, Nadav G Ahituv, Valerie Flaherman. Breast Milk Composition in the First Month for Health Dyads: Relationship to Infant Growth and Maternal Experience of Receiving Results. View on PubMed
  13. Zhao J, Baltoumas FA, Konnaris MA, Mouratidis I, Liu Z, Sims J, Agarwal V, Pavlopoulos GA, Georgakopoulos-Soares I, Ahituv N. MPRAbase a Massively Parallel Reporter Assay database. Genome Res. 2025 Apr 22. View on PubMed
  14. Chaar DL, Jiang C, Cowan B, Patel S, Kvale M, Yin J, Mostaedi R, Ahituv N, Jorgenson E, Hoffmann TJ, Choquet H. Multi-tissue transcriptome-wide association study identifies novel candidate genes and pleiotropy effects across four abdominal hernia subtypes. HGG Adv. 2025 Apr 09; 6(3):100436. View on PubMed
  15. Laboy Cintrón D, Sheng RR, Ahituv N. Functional characterization of OXTR-associated enhancers. Hum Mol Genet. 2025 Feb 17. View on PubMed
  16. Devinsky O, Coller J, Ahrens-Nicklas R, Liu XS, Ahituv N, Davidson BL, Bishop KM, Weiss Y, Mingorance A. Gene therapies for neurogenetic disorders. Trends Mol Med. 2025 Feb 17. View on PubMed
  17. Lima AC, Okhovat M, Stendahl AM, Yang R, VanCampen J, Nevonen KA, Herrera J, Li W, Harshman L, Fedorov LM, Vigh-Conrad KA, Ahituv N, Conrad DF, Carbone L. Deletion of an evolutionarily conserved TAD boundary impacts spermatogenesis in mice†. Biol Reprod. 2025 Feb 04. View on PubMed
  18. Nguyen HP, An K, Ito Y, Kharbikar BN, Sheng R, Paredes B, Murray E, Pham K, Bruck M, Zhou X, Biellak C, Ushiki A, Nobuhara M, Fong SL, Bernards DA, Lynce F, Dillon DA, Magbanua MJM, Huppert LA, Hammerlindl H, Klein JA, Valdiviez L, Fiehn O, Esserman L, Desai TA, Yee SW, Rosenbluth JM, Ahituv N. Implantation of engineered adipocytes suppresses tumor progression in cancer models. Nat Biotechnol. 2025 Feb 04. View on PubMed
  19. Agarwal V, Inoue F, Schubach M, Penzar D, Martin BK, Dash PM, Keukeleire P, Zhang Z, Sohota A, Zhao J, Georgakopoulos-Soares I, Noble WS, Yardimci GG, Kulakovskiy IV, Kircher M, Shendure J, Ahituv N. Massively parallel characterization of transcriptional regulatory elements. Nature. 2025 Mar; 639(8054):411-420. View on PubMed
  20. Chan CSY, Mouratidis I, Montgomery A, Tsiatsianis GC, Chantzi N, Hemberg M, Ahituv N, Georgakopoulos-Soares I. The topography of nullomer-emerging mutations and their relevance to human disease. Comput Struct Biotechnol J. 2025; 30:1-11. View on PubMed

Go to UCSF Profiles, powered by CTSI