2024
iSCORE-PD: an isogenic stem cell collection to research Parkinson’s Disease. Oriol Busquets, Hanqin Li, Khaja Mohieddin Syed, Pilar Alvarez Jerez, Jesse Dunnack, Riana Lo Bu, Yogendra Verma, Gabriella R. Pangilinan, Annika Martin, Jannes Straub, YuXin Du, Vivien M. Simon, Steven Poser, Zipporiah Bush, Jessica Diaz, Atehsa Sahagun, Jianpu Gao, Dena G. Hernandez, Kristin S. Levine, Ezgi O. Booth, Helen S.Bateup, Donald C. Rio, Dirk Hockemeyer, Cornelis Blauwendraat, Frank Soldner. bioRxiv 2024.02.12.579917; doi: https://doi.org/10.1101/2024.02.12.579917. Preprint.
Distinct senescence mechanisms restrain progression of dysplastic nevi. Franziska K Lorbeer, Gabrielle Rieser, Aditya Goel, Meng Wang, Areum Oh, Iwei Yeh, Boris C Bastian, Dirk Hockemeyer, Distinct senescence mechanisms restrain progression of dysplastic nevi, PNAS Nexus, Volume 3, Issue 2, February 2024, pgae041, https://doi.org/10.1093/pnasnexus/pgae041
Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Nat Commun. 2024 Jan 17;15(1):579. doi: 10.1038/s41467-023-43012-9. PMID: 38233380
2023
STAT3 regulates the generation of astroglia in human brain organoids with high mTORC1 activity. Deb, B, Li T, Blair J, Hockemeyer D, Bateup H. bioRxiv. 2023 Dec 21: 2023.12.21.572786. doi: https://doi.org/10.1101/2023.12.21.572786. Preprint. PMID:
Digital telomere measurement by long-read sequencing distinguishes healthy aging from disease. Sanchez SE, Gu J, Golla A, Martin A, Shomali W, Hockemeyer D, Savage SA, Artandi SE. bioRxiv. 2023 Dec 1:2023.11.29.569263. doi: 10.1101/2023.11.29.569263. Preprint. PMID: 38077053.
Tracing cancer evolution and heterogeneity using Hi-C. Erdmann-Pham DD, Batra SS, Turkalo TK, Durbin J, Blanchette M, Yeh I, Shain H, Bastian BC, Song YS, Rokhsar DS, Hockemeyer D. Nat Commun. 2023 Nov 6;14(1):7111. doi: 10.1038/s41467-023-42651-2. PMID: 37932252; PMCID: PMC10628133.
Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells. Li H, Bartke R, Zhao L, Verma Y, Horacek A, Rechav Ben-Natan A, Pangilinan GR, Krishnappa N, Nielsen R, Hockemeyer D. Nat Biomed Eng. 2023 Jul 24. doi: 10.1038/s41551-023-01065-7. PMID: 37488236.
A non-genetic switch triggers alternative telomere lengthening and cellular immortalization in ATRX deficient cells. Turkalo, T.K., Maffia, A., Schabort, J.J., Regalado, S.G., Bhakta, M., Blanchette, M., Spierings, D.C., Lansdorp, P.M. and Hockemeyer, D., 2023. Nature Communications, 14(1), p.939.
2022
Highly efficient generation of isogenic pluripotent stem cell models using prime editing. Li H, Busquets O, Verma Y, Syed KM, Kutnowski N, Pangilinan GR, Gilbert LA, Bateup HS, Rio DC, Hockemeyer D, Soldner F. Elife. 2022 Sep 7;11:e79208. doi: 10.7554/eLife.79208. PMID: 36069759; PMCID: PMC9584603.
Editing TINF2 as a potential therapeutic approach to restore telomere length in dyskeratosis congenita. Choo S, Lorbeer FK, Regalado SG, Short SB, Wu S, Rieser G, Bertuch AA, Hockemeyer D. Blood. 2022 Aug 11;140(6):608-618. doi: 10.1182/blood.2021013750. PMID: 35421215.
2021
A multimodal cell census and atlas of the mammalian primary motor cortex. BRAIN Initiative Cell Census Network (BICCN). Nature. 2021
Generation of a DAT-P2A-Flpo mouse line for intersectional genetic targeting of dopamine neuron subpopulations. Kramer DJ, Aisenberg EE, Kosillo P, Friedmann D, Stafford DA, Lee AY, Luo L, Hockemeyer D, Ngai J, Bateup HS. Cell Rep. 2021.
Cancer-associated POT1 mutations lead to telomere elongation without induction of a DNA damage response. Kim WT, Hennick K, Johnson J, Finnerty B, Choo S, Short SB, Drubin C, Forster R, McMaster ML, Hockemeyer D. The Embo Journal. 2021.
Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus. IGI SARS-CoV-2 Testing consortium. medRxiv. 2021.
2020
TINF2 is a haploinsufficient tumor suppressor that limits telomere length. Schmutz I, Mensenkamp AR, Takai KK, Haadsma M, Spruijt L, de Voer RM, Choo SS, Lorbeer FK, van Grinsven EJ, Hockemeyer D, Jongmans MC, de Lange T. Elife. 2020.
Telomere length set point regulation in human pluripotent stem cells critically depends on the shelterin protein TPP1. Boyle JM, Hennick KM, Regalado SG, Vogan JM, Zhang X, Collins K, Hockemeyer D. Mol Biol Cell. 2020.
Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells. Shin JJ, Schröder MS, Caiado F, Wyman SK, Bray NL, Bordi M, Dewitt MA, Vu JT, Kim WT, Hockemeyer D, Manz MG, Corn JE. Cell Rep. 2020.
TERT promoter mutations and telomeres during tumorigenesis. Lorbeer FK, Hockemeyer D. Curr Opin Genet Dev. 60:56-62. 2020.
Blueprint for a pop-up SARS-CoV-2 testing lab. IGI Testing Consortium:Alexandra M Amen, Kerrie W Barry,John M Boyle, Cara E Brook, Seunga Choo, L T Cornmesser, David J Dilworth, Jennifer A Doudna, Alexander J Ehrenberg, Indro Fedrigo, Skyler E Friedline, Thomas G W Graham, Ralph Green, Jennifer R Hamilton, Ariana Hirsh, Megan L Hochstrasser, Dirk Hockemeyer, Netravathi Krishnappa, Azra Lari, Hanqin Li, Enrique Lin-Shiao, Tianlin Lu, Elijah F Lyons, Kevin G Mark, Lisa Argento Martell, A Raquel O Martins, Shana L McDevitt, Patrick S Mitchell, Erica A Moehle, Christine Naca, Divya Nandakumar, Elizabeth O’Brien, Derek J Pappas, Kathleen Pestal, Diana L Quach, Benjamin E Rubin, Rohan Sachdeva, Elizabeth C Stahl, Abdullah Muhammad Syed, I-Li Tan, Amy L Tollner, Connor A Tsuchida, C Kimberly Tsui, Timothy K Turkalo, Fyodor D Urnov, M Bryan Warf, Oscar N, Whitney, Lea B Witkowsky (2020) Nat Biotechnol. 38(7):791-797. 2020.
Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution. Mudd AB, Bredeson JV, Baum R, Hockemeyer D, Rokhsar DS. Commun Biol. 3(1):480. 2020.
2019
Transient activation of the UPRER is an essential step in the acquisition of pluripotency during reprogramming. Milos S. Simic, Erica A. Moehle, Robert T. Schinzel, Franziska K. Lorbeer, Jonathan J. Halloran, Kartoosh Heydari, Melissa Sanchez, Damien Jullié, Dirk Hockemeyer, and Andrew Dillin. Sci Adv. 5(4). 2019
2018
Genetically engineered human cortical spheroid models of tuberous sclerosis. John D. Blair, Dirk Hockemeyer, and Helen S. Bateup. Nature Medicine. 2018
Genome-edited human stem cells expressing fluorescently labeled endocytic markers allow quantitative analysis of clathrin-mediated endocytosis during differentiation. Daphné Dambournet, Kem A. Sochacki, Aaron T. Cheng, Matthew Akamatsu, Justin W. Taraska, Dirk Hockemeyer, and David G. Drubin. JCB 217(9). 2018
Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. Mustafa Mir, Armando Reimer, Michael Stadler, Astou Tangara, Anders S. Hansen, Dirk Hockemeyer, Michael B. Eisen, Hernan Garcia, and Xavier Darzacq. Nanoscale Imaging: Methods and Protocols, Methods in Molecular Biology (1814). 2018
Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Tsung-Li Liu1, Srigokul Upadhyayula, Daniel E. Milkie, Ved Singh, Kai Wang, Ian A. Swinburne, Kishore R. Mosaliganti, Zach M. Collins, Tom W. Hiscock, Jamien Shea, Abraham Q. Kohrman, Taylor N. Medwig, Daphne Dambournet, Ryan Forster, Brian Cunniff, Yuan Ruan, Hanako Yashiro, Steffen Scholpp, Elliot M. Meyerowitz, Dirk Hockemeyer, David G. Drubin, Benjamin L. Martin, David Q. Matus, Minoru Koyama, Sean G. Megason, Tom Kirchhausen, Eric Betzig. Science 360(284). 2018
2017
Widespread Translational Remodeling during Human Neuronal Differentiation. Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN. Cell Reports 21(7):2005-2016. 2017.
Mutations in the promoter of the telomerase gene TERT contribute to tumorigenesis by a two-step mechanism. Chiba K, Lorbeer F, Shain A, McSwiggen D, Schruf E, Oh A, Ryu J, Darzacq X, Bastain B, Hockemeyer D. Science, 357: 1416-1420. 2017.
Defined and Scalable Differentiation of Human Oligodendrocyte Precursors from Pluripotent Stem Cells in a 3D Culture System. GMC, Gaj T, Adil MM, Wahba J, Rao AT, Lorbeer FK, Kulkarni RU, Diogo MM, Cabral JMS, Miller EW, Hockemeyer D, and Schaffer DV. Stem Cell Reports 8(6):1770-1783. 2017.
2016
Endogenous TERT N-terminal tagging affects human telomerase function at telomeres in vivo. Chiba K, Vogan JM, Wu RA, Gill MS, Zhang X, Collins K, Hockemeyer D. Molecular and Cell Biology 37:e00541-16. 2016.
Minimized human telomerase maintains telomeres and resolves endogenous roles of H/ACA proteins, TCAB1, and Cajal bodies. Vogan JM, Zhang X, Youmans DT, Regalado SG, Johnson JZ, Hockemeyer D, Collins K. eLife 5: e18221. 2016.
Induced Pluripotent Stem Cells Meet Genome Editing. Hockemeyer D, Jaenisch R. Cell Stem Cell 18(5) 573-586. 2016.
Establishment of Genome-edited Human Pluripotent Stem Cell Lines: From Targeting to Isolation. Blair JD, Bateup H, Hockemeyer D. J VisExp. 2016; (108): 53583. 2016.
2015
Human stem cell-based disease modeling: prospects and challenges. Johnson JZ, Hockemeyer D. Curr. Opin. Cell. Biol. 37: 84-90. 2015.
Control of telomerase action at human telomeres. Hockemeyer D, Collins, K. Nat. Struct. Mol. Biol. 22(11) 848-852. 2015.
Chiba K, Johnson JZ, Vogan JM, Wagner T, Boyle JM, Hockemeyer D. (2015) Cancer-associated TERT promoter mutations abrogate telomerase silencing. Chiba K, Johnson JZ, Vogan JM, Wagner T, Boyle JM, Hockemeyer D. eLIFE 4:e07918. 2015.
Genome Editing in Human Pluripotent Stem Cells Using Site-Specific Nucleases. Chiba K, Hockemeyer D. Methods Mol. Biol. 1239:267-280. 2015.
2014
TALEN Gene Knockouts Reveal No Requirement for the Conserved Human Shelterin Protein Rap1 in Telomere Protection and Length Regulation. Cell Reports. Kabir S, Hockemeyer D, de Lange T. Cell Reports 9(4):1273-80. 2014.
Genetic and molecular identification of three human TPP1 functions in telomerase action: recruitment, activation, and homeostasis set point regulation. Sexton AN, Regalado SG, Lai CS, Cost GJ, O’Neil CM, Urnov FD, Gregory PD, Jaenisch R, Collins K, Hockemeyer D. Genes and Development 28(17). 2014.
Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells. Forster R, Chiba K, Schaeffer L, Regalado SG, Lai C, Gao Qing, Kiana S, Farin HF, Clevers H, Cost GJ, Chan A, Rebar EJ, Urnov FD, Gregory PD, Pachter L, Jaenisch R, Hockemeyer D. Cell Stem Cell Reports 2(6):838-52. 2014.
Forster R, Hockemeyer D (2014) Genome editing 101: Let’s go digital. Nature methods 11, 248-249. 2014.
2013
Global transciptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons. Li Y, Wang H, Muffat J, Cheng AW, Orlando DA, Lovén J, Kwok SM, Feldman DA, Bateup HS, Gao Q, Hockemeyer D, Mitalipova M, Lewis CA, Vander Heiden MG, Sur M, Young RA, Jaenisch R. Cell Stem Cell 13(4):446-58. 2013
2011
Deletion of the de novo methyltransferase Dnmt3a promotes lung tumor progression. Gao Q, Steine E, Barrasa M, Hockemeyer D, Pawlak M, Fu D, Reddy S, Bell G, Jaenisch R. Proceedings of the National Academy of Sciences of the United States of America. 2011.
Transgene Excision Has No Impact on In Vivo Integration of Human iPS Derived Neural Precursors. Major T, Menon J, Auyeung G, Soldner F, Hockemeyer D, Jaenisch R, Tabar V. PLoS ONE 6: e24687. 2011.
Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Soldner F, Laganiere J, Cheng AW, Hockemeyer D, Gao Q, Alagappan R, Khurana V, Golbe LI, Myers RH, Lindquist S, Zhang L, Guschin D, Fong LK, Vu BJ, Meng X, Urnov FD, Rebar EJ, Gregory PD, Zhang HS, Jaenisch R. Cell 146: 318-31. 2011.
Genetic engineering of human pluripotent cells using TALE nucleases. Hockemeyer D, Wang H, Kiani S, Lai CS, Gao Q, Cassady JP, Cost GJ, Zhang L, Santiago Y, Miller JC, Zeitler B, Cherone JM, Meng X, Hinkley SJ, Rebar EJ, Gregory PD, Urnov FD, Jaenisch R. Nature biotechnology 29: 731-4 *equal contribution. 2011.
2010
Gene targeting in human pluripotent cells. Hockemeyer D, Jaenisch R. Cold Spring Harbor symposia on quantitative biology 75: 201-9. 2010.
Differentiated Parkinson patient-derived induced pluripotent stem cells grow in the adult rodent brain and reduce motor asymmetry in Parkinsonian rats. Hargus G, Cooper O, Deleidi M, Levy A, Lee K, Marlow E, Yow A, Soldner F, Hockemeyer D, Hallett PJ, Osborn T, Jaenisch R, Isacson O. Proceedings of the National Academy of Sciences of the United States of America 107: 15921-6. 2010.
Guenther MG, Frampton GM, Soldner F, Hockemeyer D, Mitalipova M, Jaenisch R, Young RA. (2010) Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 7: 249-57. 2010.
Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. DeKelver RC, Choi VM, Moehle EA, Paschon DE, Hockemeyer D, Meijsing SH, Sancak Y, Cui X, Steine EJ, Miller JC, Tam P, Bartsevich VV, Meng X, Rupniewski I, Gopalan SM, Sun HC, Pitz KJ, Rock JM, Zhang L, Davis GD, Rebar EJ, Cheeseman IM, Yamamoto KR, Sabatini DM, Jaenisch R, Gregory PD, Urnov FD. Genome Research 20: 1133-42. 2010.
2009
Parkinson’s disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Soldner F, Hockemeyer D, Beard C, Gao Q, Bell GW, Cook EG, Hargus G, Blak A, Cooper O, Mitalipova M, Isacson O, Jaenisch R. Cell 136: 964-77 *equal contribution. 2009.
Mammalian telomeres resemble fragile sites and require TRF1 for efficient replication. Sfeir A, Kosiyatrakul ST, Hockemeyer D, MacRae SL, Karlseder J, Schildkraut CL, de Lange T. Cell 138: 90-103. 2009.
Functional dissection of human and mouse POT1 proteins. Palm W, Hockemeyer D, Kibe T, de Lange T. Molecular and Cellular Biology 29: 471-82. 2009.
Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Hockemeyer D, Soldner F, Beard C, Gao Q, Mitalipova M, DeKelver RC, Katibah GE, Amora R, Boydston EA, Zeitler B, Meng X, Miller JC, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Jaenisch R. Nature Biotechnology 27: 851-7 *equal contribution. 2009.
Direct reprogramming of somatic cells to a pluripotent state. Hockemeyer D, Soldner, F., Jaenisch, R. Essentials of Stem Cell Biology, Second edition, pp. pp. 29-32. (San Diego, USA, Academic Press, Elsevier): Robert Lanza, John Gearhart, Brigid Hogan, Douglas Melton, Roger Pederson, E. Donnall Thomas, James Thomson, and Sir Ian Wilmut. 2009.
2008
A drug-inducible system for direct reprogramming of human somatic cells to pluripotency. Hockemeyer D, Soldner F, Cook EG, Gao Q, Mitalipova M, Jaenisch R. Cell Stem Cell 3: 346-53 *equal contribution. 2008
Engineered telomere degradation models dyskeratosis congenita. Hockemeyer D, Palm W, Wang RC, Couto SS, de Lange T. Genes & Development 22: 1773-85. 2008.
2007
Telomere protection by mammalian Pot1 requires interaction with Tpp1. Hockemeyer D, Palm W, Else T, Daniels JP, Takai KK, Ye JZ, Keegan CE, de Lange T, Hammer GD. Nature Structural & Molecular Biology 14: 754-61. 2007.
2006
Recent expansion of the telomeric complex in rodents: Two distinct POT1 proteins protect mouse telomeres. Hockemeyer D, Daniels JP, Takai H, de Lange T. Cell 126: 63-77. 2006
2005
POT1 protects telomeres from a transient DNA damage response and determines how human chromosomes end. Hockemeyer D, Sfeir AJ, Shay JW, Wright WE, de Lange T. The EMBO journal 24: 2667-78. 2005.
2004
POT1-interacting protein PIP1: a telomere length regulator that recruits POT1 to the TIN2/TRF1 complex. Ye JZ, Hockemeyer D, Krutchinsky AN, Loayza D, Hooper SM, Chait BT, de Lange T. Genes & Development 18: 1649-54. 2004.
Myocardin and ternary complex factors compete for SRF to control smooth muscle gene expression. Wang Z, Wang DZ, Hockemeyer D, McAnally J, Nordheim A, Olson EN. Nature 428: 185-9. 2004
SRF regulates Bcl-2 expression and promotes cell survival during murine embryonic development. Schratt G, Philippar U, Hockemeyer D, Schwarz H, Alberti S, Nordheim A. The EMBO Journal 23: 1834-44. 2004.
2002
Potentiation of serum response factor activity by a family of myocardin-related transcription factors. Wang DZ, Li S, Hockemeyer D, Sutherland L, Wang Z, Schratt G, Richardson JA, Nordheim A, Olson EN. Proceedings of the National Academy of Sciences of the United States of America 99: 14855-60. 2002.