Lab Publications

[Note on accessing publications: Click on paper title to be linked to the PubMed abstract and on figure to be linked to the PDF version of the paper]


John D. Blair, Dirk Hockemeyer, and Helen S. Bateup. (2018) Genetically engineered human cortical spheroid models of tuberous sclerosis. Nature Medicine.



Daphné Dambournet, Kem A. Sochacki, Aaron T. Cheng, Matthew Akamatsu, Justin W. Taraska, Dirk Hockemeyer, and David G. Drubin. (2018) Genome-edited human stem cells expressing fluorescently labeled endocytic markers allow quantitative analysis of clathrin-mediated endocytosis during differentiation. JCB 217(9).


Mustafa Mir, Armando Reimer, Michael Stadler, Astou Tangara, Anders S. Hansen, Dirk Hockemeyer, Michael B. Eisen, Hernan Garcia, and Xavier Darzacq. (2018) Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. Nanoscale Imaging: Methods and Protocols, Methods in Molecular Biology (1814).



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. (2018) Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Science 360(284).



Blair JD, Hockemeyer DDoudna JABateup HSFloor SN. (2017) Widespread Translational Remodeling during Human Neuronal Differentiation. Cell Reports 21(7):2005-2016.




Chiba KLorbeer FShain AMcSwiggen DSchruf EOh ARyu JDarzacq XBastain BHockemeyer D. (2017) Mutations in the promoter of the telomerase gene TERT contribute to tumorigenesis by a two-step mechanism. Science, 357: 1416-1420.




GMC, Gaj T, Adil MM, Wahba J, Rao AT, Lorbeer FKKulkarni RU, Diogo MM, Cabral JMS, Miller EW, Hockemeyer Dand Schaffer DV. (2017) Defined and Scalable Differentiation of Human Oligodendrocyte Precursors from Pluripotent Stem Cells in a 3D Culture System. Stem Cell Reports 8(6):1770-1783.



Chiba K, Vogan JM, Wu RA, Gill MS, Zhang X, Collins K, Hockemeyer D. (2016) Endogenous TERT N-terminal tagging affects human telomerase function at telomeres in vivoMolecular and Cell Biology 37:e00541-16.



Link to PDF

Vogan JM, Zhang X, Youmans DT, Regalado SG, Johnson JZ, Hockemeyer D, Collins K. (2016) Minimized human telomerase maintains telomeres and resolves endogenous roles of H/ACA proteins, TCAB1, and Cajal bodies. eLife 5: e18221



Hockemeyer D, Jaenisch R. (2016) Induced Pluripotent Stem Cells Meet Genome Editing. Cell Stem Cell 18(5) 573-586Link to PDF




Link to PDFBlair JD, Bateup H, Hockemeyer D. (2016) Establishment of Genome-edited Human Pluripotent Stem Cell Lines: From Targeting to Isolation. J Vis Exp. 2016; (108): 53583.




Johnson JZ, Hockemeyer D. (2015) Human stem cell-based disease modeling: prospects and challenges. Curr. Opin. Cell. Biol. 37: 84-90




Hockemeyer D, Collins, K. (2015) Control of telomerase action at human telomeres. Nat. Struct. Mol. Biol. 22(11) 848-852



Chiba K, Johnson JZ, Vogan JM, Wagner T, Boyle JM, Hockemeyer D. (2015) Cancer-associated TERT promoter mutations abrogate telomerase silencing. eLIFE 4:e07918


Chiba K, Hockemeyer D. (2015) Genome Editing in Human Pluripotent Stem Cells Using Site-Specific Nucleases. Methods Mol. Biol. 1239:267-280




Kabir S, Hockemeyer D, de Lange T. (2014) TALEN Gene Knockouts Reveal No Requirement for the Conserved Human Shelterin Protein Rap1 in Telomere Protection and Length Regulation. Cell Reports. Cell Reports 9(4):1273-80


Sexton AN, Regalado SG, Lai CS, Cost GJ, O'Neil CM, Urnov FD, Gregory PD, Jaenisch R, Collins K, Hockemeyer D. (2014) Genetic and molecular identification of three human TPP1 functions in telomerase action: recruitment, activation, and homeostasis set point regulation. Genes and Development 28(17)


Link to PDFForster 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. (2014) Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells. Cell Stem Cell Reports 2(6):838-52


Link to PDF Forster R, Hockemeyer D (2014) Genome editing 101: Let's go digital. Nature methods 11, 248-249



Dr. Hockemeyer's Doctoral and Post-doctoral Publications


Graphical Abstract 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.  (2013) Global transciptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons. Cell Stem Cell 13(4):446-58




Link to PDFGao Q, Steine E, Barrasa M, Hockemeyer D, Pawlak M, Fu D, Reddy S, Bell G, Jaenisch R. (2011) Deletion of the de novo methyltransferase Dnmt3a promotes lung tumor progression. Proceedings of the National Academy of Sciences of the United States of America.


Link to PDFMajor T, Menon J, Auyeung G, Soldner F, Hockemeyer D, Jaenisch R, Tabar V. (2011) Transgene Excision Has No Impact on In Vivo Integration of Human iPS Derived Neural Precursors. PLoS ONE 6: e24687



Graphical AbstractSoldner 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. (2011) Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell 146: 318-31



Link to PDFHockemeyer 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. (2011) Genetic engineering of human pluripotent cells using TALE nucleases. Nature biotechnology 29: 731-4 *equal contribution



Link to PDFHockemeyer D, Jaenisch R. (2010) Gene targeting in human pluripotent cells. Cold Spring Harbor symposia on quantitative biology 75: 201-9



Link to PDFHargus 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. (2010) Differentiated Parkinson patient-derived induced pluripotent stem cells grow in the adult rodent brain and reduce motor asymmetry in Parkinsonian rats. Proceedings of the National Academy of Sciences of the United States of America 107: 15921-6


Link to PDFGuenther 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



Link to PDFDeKelver 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. (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. Genome Research 20: 1133-42



Link to PDFSoldner F*, Hockemeyer D*, Beard C, Gao Q, Bell GW, Cook EG, Hargus G, Blak A, Cooper O, Mitalipova M, Isacson O, Jaenisch R. (2009) Parkinson's disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Cell 136: 964-77 *equal contribution


Link to PDFSfeir A, Kosiyatrakul ST, Hockemeyer D, MacRae SL, Karlseder J, Schildkraut CL, de Lange T. (2009) Mammalian telomeres resemble fragile sites and require TRF1 for efficient replication. Cell 138: 90-103


Link to PDFPalm W, Hockemeyer D, Kibe T, de Lange T. (2009) Functional dissection of human and mouse POT1 proteins. Molecular and Cellular Biology 29: 471-82



Link to PDFHockemeyer 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. (2009) Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nature Biotechnology 27: 851-7 *equal contribution


Link to PDFHockemeyer D, Soldner, F., Jaenisch, R. (2009) Direct reprogramming of somatic cells to a pluripotent state. 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




Link to PDFHockemeyer D*, Soldner F*, Cook EG, Gao Q, Mitalipova M, Jaenisch R. (2008) A drug-inducible system for direct reprogramming of human somatic cells to pluripotency. Cell Stem Cell 3: 346-53 *equal contribution


Link to PDFHockemeyer D, Palm W, Wang RC, Couto SS, de Lange T. (2008) Engineered telomere degradation models dyskeratosis congenita. Genes & Development 22: 1773-85




Link to PDFHockemeyer D, Palm W, Else T, Daniels JP, Takai KK, Ye JZ, Keegan CE, de Lange T, Hammer GD. (2007) Telomere protection by mammalian Pot1 requires interaction with Tpp1. Nature Structural & Molecular Biology 14: 754-61


Link to PDFHockemeyer D, Daniels JP, Takai H, de Lange T. (2006) Recent expansion of the telomeric complex in rodents: Two distinct POT1 proteins protect mouse telomeres. Cell 126: 63-77


Link to PDFHockemeyer D, Sfeir AJ, Shay JW, Wright WE, de Lange T. (2005) POT1 protects telomeres from a transient DNA damage response and determines how human chromosomes end. The EMBO journal 24: 2667-78




Link to PDFYe JZ, Hockemeyer D, Krutchinsky AN, Loayza D, Hooper SM, Chait BT, de Lange T. (2004) POT1-interacting protein PIP1: a telomere length regulator that recruits POT1 to the TIN2/TRF1 complex. Genes & Development 18: 1649-54


Link to PDFWang Z, Wang DZ, Hockemeyer D, McAnally J, Nordheim A, Olson EN. (2004) Myocardin and ternary complex factors compete for SRF to control smooth muscle gene expression. Nature 428: 185-9


 Link to PDFSchratt G, Philippar U, Hockemeyer D, Schwarz H, Alberti S, Nordheim A. (2004) SRF regulates Bcl-2 expression and promotes cell survival during murine embryonic development. The EMBO Journal 23: 1834-44



Link to PDFWang DZ, Li S, Hockemeyer D, Sutherland L, Wang Z, Schratt G, Richardson JA, Nordheim A, Olson EN. (2002) Potentiation of serum response factor activity by a family of myocardin-related transcription factors. Proceedings of the National Academy of Sciences of the United States of America 99: 14855-60