Recent Publications
Sher F, Hossain M, Seruggia D, Schoonenberg VAC, Yao Q, Cifani P, Dassama LMK, Cole MA, Ren C, Vinjamur DS, Macias-Trevino C, Luk K, McGuckin C, Schupp PG, Canver MC, Kurita R, Nakamura Y, Fujiwara Y, Wolfe SA, Pinello L, Maeda T, Kentsis A, Orkin SH, Bauer DE. Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Nat Genet. 2019 Jul;51(7):1149-1159. PMID: 31253978
Iyer S, Suresh S, Guo D, Daman K, Chen JCJ, Liu P, Zieger M, Luk K, Roscoe BP, Mueller C, King OD, Emerson CP & Wolfe SA. Precise therapeutic gene correction by a simple nuclease-induced double-strand break. Nature 2019 568(7753):561-565. PMID30944467 PMCID:6483862
Liu, P., Luk, K., Shin, M., Idrizi, F., Kwok, S., Roscoe, B., Mintzer, E., Suresh, S., Morrison, K., Frazão, J.B., Bolukbasi, M.F., Ponnienselvan, K., Luban, J., Zhu, L.J., Lawson, N.D.*, Wolfe S.A.* Enhanced Cas12a editing in mammalian cells and zebrafish.Nucleic Acids Res. 2019 47(8):4169-4180 PMID 30892626 PMCID: PMC6486634
Wu Y, Zeng J, Roscoe BP, Liu P, Yao Q, Lazzarrotto CR, Clement MK, Cole MA, Luk K, Baricordi C, Shen A, Ren C, Esrick EB, Manis JP, Dorfman DM, Williams DA, Biffi A, Brugnara C, Biasco L, Brendel C, Pinello L, Tsai SQ, Wolfe SA, Bauer DE. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nature Med. 2019 25(5), 776-783. PMID 30911135. PMCID: PMC6512986
Xu S, Luk K, Yao Q, Shen AH, Zeng J, Wu Y, LuoH-Y, Brendel C, Pinello L, ChuiDHK, Wolfe SA*, Bauer DE*. Editing aberrant splice sites efficiently restores b-globin expression in b-thalassemia. Blood2019 133(21), 2255-2262. PMID 30704988PMCID:PMC6533605. Article highlight: http://www.bloodjournal.org/content/133/21/2245
Amrani N, Gao XD, Liu P, Edraki A, Mir A, Ibraheim R, Gupta A, Sasaki KE, Wu T, Donohoue PD, Settle AH, Lied AM, McGovern K, Fuller CK, Cameron P, Fazzio TG, Zhu LJ, Wolfe SA, Sontheimer EJ. NmeCas9 is an intrinsically high-fidelity genome-editing platform. Genome Biol.2018 19(1):214. PMID: 30518407PMCID: PMC6282386
Swygert, S.G., Senapati, S., Bolukbasi, M.F., Wolfe, S.A., Lindsay, S., Peterson, C.L. SIR proteins create compact heterochromatin fibers. Proc Natl Acad Sci U S A. 2018 Nov 19. pii: 201810647. doi: 10.1073/pnas.1810647115. PMID30455303
Bolukbasi, M.F., Liu, P., Luk, K., Kwok, S.F., Gupta, A., Amrani, N., Sontheimer, E.J., Zhu, L.J., Wolfe, S.A.*. Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing. Nature Communications 2018 Nov 19;9(1):4856. PMID30451839
Pulikkan, J.A., Hegde, M., Ahmad, H.M., Belaghzal, H., Illendula, A., Yu, J., O'Hagan, K., Ou, J., Muller-Tidow, C., Wolfe, S.A., Zhu, L.J., Dekker, J., Bushweller, J.H., Castilla, L.H. CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. 2018, Cell. Jun 28;174(1):172-186 PMID29958106
Gao, X. D., Tu, L.-C., Mir, A., Rodriguez, T., Ding, Y., Leszyk, J., Dekker, J., Shaffer, S. A., Zhu, L. J., Wolfe, S. A., and Sontheimer, E. J. C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. 2018, Nature Methods, 15(6):433-436. PMC6202229
Ou, J., Wolfe, S.A., Brodsky, M.H., Zhu, L.J. motifStack for the analysis of transcription factor binding site evolution. 2018 Nat Methods. 15(1):8-9. PMID29298290
Yin H, Song CQ, Suresh S, Kwan SY, Wu Q, Walsh S, Ding J, Bogorad RL, Zhu LJ, Wolfe SA, Koteliansky V, Xue W, Langer R, Anderson DG. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Nat Chem Biol. 2018, 14(3):311-316. PMC5902734
Yin, H., Song, C.Q., Suresh, S., Wu, Q., Walsh, S., Rhym, L.H., Mintzer, E., Bolukbasi, M.F., Zhu, L.J., Kauffman, K., Mou, H., Oberholzer, A., Ding, J., Kwan, S.Y., Bogorad, R.L., Zatsepin, T., Koteliansky, V., Wolfe, S.A., Xue, W., Langer, R., Anderson, D.G.”Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing” Nat Biotechnol. 2017, 35(12):1179-1187 PMID29131148
Ma, L., Boucher, J.I., Paulsen, J., Matuszewski, S., Eide, C.A., Ou, J., Eickelberg, G., Press, R.D., Zhu, L.J., Druker, B.J., Branford, S., Wolfe, S.A., Jensen, J.D., Schiffer, C.A., Green, M.R., Bolon, D.N. “CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy” Proc Natl Acad Sci U S A. 2017, 114(44):11751-11756. PMC5676903
Leonard, J.L., Leonard, D.M., Wolfe, S.A., Liu, J., Rivera, J., Yang, M., Leonard, R.T., Johnson, J.P.S., Kumar, P., Liebmann, K.L., Tutto, A.A., Mou, Z., Simin, K.J. “The Dkk3 gene encodes a vital intracellular regulator of cell proliferation” PLoS One. 2017;12(7):e0181724. PMC5524345
Zhu, L.J., Lawrence, M., Gupta, A., Pagès, H., Kucukural, A., Garber, M., Wolfe, S.A. “GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases” BMC Genomics. 2017, 18(1):379. PMC5433024
Markert, M.J., Zhang, Y., Enuameh, M.S., Reppert, S.M., Wolfe, S.A., Merlin, C. “Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis” G3 (Bethesda). 2016, 6(4), 905-15. PMC4825660
Yin, H., Song, C., Dorkin, J.R., Zhu, L.J., Li, Y., Wu, Q., Park, A., Yang. J., Suresh, S., Bizhanova, A., Gupta, A., Bolukbasi, M.F. Walsh, S., Bogorad, R., Gao, G., Weng, Z., Dong, Y., Koteliansky, V., Wolfe, S.A., Langer, R. Xue, W., Anderson, D.G., “Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo” Nat. Biotechnology 2016, 34(3), 328-33. PMC5423356
Bolukbasi, M.F., Gupta, A., Oikemus, S., Derr, A.G., Garber, M., Brodsky, M.H., Zhu, L.J., Wolfe, S.A.. "DNA-binding-domain fusions enhance the targeting range and precision of Cas9". Nature Methods , 12:1150-1156 (2015). PMC4679368
Ma, H., Naseri, A., Reyes-Gutierrez, P., Wolfe, S.A., Zhang, S. and Pederson, T. “Multicolor CRISPR Labeling of Chromosomal Loci in Human Cells” PNAS 2015, 112(10), 3002-3007. PMC4364232
Kok, F. O., Shin, M., Ni, C-W., Gupta, A., Grosse, A. S., van Impel, A., Kirchmaier, B., Peterson-Meduro, J., Kourkoulis, G., Male, I., DeSantis, D.F., Sheppard-Tindell, S., Ebarasi, L., Betsholtz, C., Schulte-Merker, S., Wolfe, S.A., Lawson, N.D. “Reverse genetic screening reveals poor correlation between Morpholino-induced and mutant phenotypes in zebrafish” Dev Cell 2015, 32(1), 97-108. PMC4487878
Weicksel, S.E., Gupta, A., Zannino, D.A., Wolfe, S.A., Sagerström, C.G. “Targeted germ line disruptions reveal general and species-specific roles for paralog group 1 hox genes in zebrafish.” BMC Dev Biol. 2014 Jun 5;14(1):25. PMC4061917
Gupta, A., Christensen, R.G., Bell, H.A., Goodwin, M., Patel, R.Y., Pandey, M., Enuameh, M.S., Rayla, A.L., Zhu, C., Thibodeau-Beganny, S., Brodsky, M.H., Joung, J.K. Wolfe, S.A.*, Stormo, G.D.* “An improved predictive recognition model for Cys2-His2 zinc finger proteins” Nucleic Acids Res. 2014 42(8):4800-12. PMC4005693 *Co-corresponding author
Kearns, N.A., Genga, R.M.J, Enuameh, M.S., Garber, M., Wolfe, S.A.*, Maehr, R*. “Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells” Development 2014, 141(1):219-23. PMC3865759 *Co-corresponding author
Kazemian, M., Pham, H., Wolfe, S.A., Brodsky, M.H., Sinha, S., “Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.” Nucleic Acids Res 2013, 41(17):8237-52. PMC3783179
Cheng, Q., Kazemian, M., Pham, H., Blatti, C., Celniker, S.E., Wolfe, S.A., Brodsky, M.H., Sinha, S., “Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy.” PLoS Genetics 2013, 9(8) e1003571. PMC3731213
Enuameh, M.S., Asriyan, Y., Richards, A., Christensen, R.G., Hall, V.L., Kazemian, M., Zhu, C., Pham, H., Cheng, Q., Blatti, C., Brasefield, J.A., Basciotta, M.D., Ou, J., McNulty, J.C., Zhu, L.J., Celniker, S.E., Sinha, S., Stormo, G.D., Brodsky, M.H., Wolfe, S.A., “Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.” Genome Research. 2013, 23(6), 928-40. PMC3668361.
Gupta, A., Hall, V.L., Kok, F.O., Shin, M., McNulty, J.C., Lawson, N.D., Wolfe, S.A., “Targeted Chromosomal Deletions and Inversions in Zebrafish.” Genome Research. 2013, 23(6),1008-17. PMC3668355.
Zhu, C., Gupta, A., Hall, V.L., Rayla, A.L., Christensen, R.G., Dake, B., Lakshmanan, A., Kuperwasser, C., Stormo, G.D., Wolfe, S.A. “Using Defined Finger-Finger Interfaces as Units of Assembly for Constructing Zinc Finger Nucleases” Nucleic Acids Res. 2013, 41(4), 2455-65. PMC3575815
Merlin, C., Beaver, L.E., Taylor, O.R., Wolfe, S.A., Reppert, S.M. “Efficient targeted mutagenesis in the monarch butterfly using zinc finger nucleases.” Genome Res. 2013 23(1), 159-68. PMC3530676
Anderson, D.M., George, R., Noyes, M.B., Rowton, M., Liu, W., Jiang, R., Wolfe, S.A., Wilson-Rawls, J., Rawls, A. “Characterization of the DNA-Binding Properties of the Mohawk (Mkx) Homeobox Transcription Factor.” J Biol Chem, 2012, 287(42), 35351-9. PMC3471766
Shin, J., Padmanabhan, A., de Groh, E.D., Lee, J.S., Haidar, S., Dahlberg, S., Guo, F., He, S., Wolman, M.A., Granato, M., Lawson, N.D., Wolfe, S.A., Kim, S.H., Solnica-Krezel, L., Kanki, J.P., Ligon, K.L., Epstein, J.A., Look, A.T. “Zebrafish neurofibromatosis type 1 genes have redundant functions in tumorigenesis and embryonic development.” Dis Model Mech, 2012, 5(6),881-94. PMC3484870
Chu, S.W., Noyes, M.B., Christensen, R.G., Pierce, B.G., Zhu, L.J., Weng, Z., Stormo, G.D., Wolfe, S.A. “Exploring the DNA-recognition potential of homeodomains” Genome Res. 2012, 22(10),1889-98. PMC3460184.
Gupta, A., Christensen, R.G., Rayla, A.L., Lakshmanan, A., Stormo, G.D., Wolfe, S.A. “An optimized two-finger archive for ZFN-mediated gene targeting” Nat Methods. 2012, 9, 588–590. PMC3443678
Christensen, R.G., Enuameh, M.S., Noyes, M.B., Brodsky, M.H., Wolfe, S.A., Stormo, G.D. “Recognition models to predict DNA-binding specificities of homeodomain proteins” Bioinformatics. 2012, 28(12), i84-i89. PMC3371834
Lawson, N.D. & Wolfe, S.A. “Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish.” Dev Cell. 2011, 21(1), 48-64. (Review)
Zhu, C., Smith, T., McNulty, J., Rayla, A.L., Lakshmanan, A., Siekmann, A.F., Buffardi, M., Meng, X.; Shin, J., Padmadanhan, A., Cifuentes, D.,Giraldez, G.; Look, A.T., Epstein, J.A.; Lawson, N. D., Wolfe, S.A., “Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish.” Development, 2011,138, 4555-64. PMC3177320
Christensen, R.G., Gupta, A., Zuo, Z., Schriefer, L.A., Wolfe, S.A., Stormo, G.D. “A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity” Nucleic Acids Res. 2011, 39(12),e83. PMC3130293
Bussmann, J., Wolfe, S.A., Siekmann, A.F., “Arterial-venous network formation during brain vascularization involves hemodynamic regulation of chemokine signaling” Development 2011, 138, 1717-26. PMC3074448
Zhu, L.J., Christensen, R.G., Kazemian, M., Hull, C.J., Enuameh, M.S., Basciotta, M.D., Brasefield, J.A., Zhu, C., Asriyan, Y., Lapointe, D.S., Sinha, S., Wolfe, S.A.*, Brodsky, M.H.*, “FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system.” Nucleic Acids Res. 2011, 39, D111-7. PMC3013762 *Co-corresponding author
Gupta, A., Meng, X., Zhu, L.J., Lawson, N.D., Wolfe, S.A., ”Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases.” Nucleic Acids Res. 2011, 39, 381-92. PMC3017618
Kazemian, M., Blatti, C., Richards, A., McCutchan, M., Wakabayashi-Ito, N., Hammonds, A.S., Celniker, S.E., Kumar, S., Wolfe, S.A., Brodsky, M.H., Sinha, S., “Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials.” PLoS Biol. 2010 8(8) e1000456. PMC2923081
Cifuentes, D., Xue, H., Taylor, D.W., Patnode, H., Mishima, Y., Cheloufi, S., Ma, E., Mane, S., Hannon, G.J., Lawson, N.D., Wolfe, S.A., Giraldez, A.J., “A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity” Science, 2010, 328,1694-8. PMC3093307
Siekmann, A.F., Standley, C., Fogarty, K.E., Wolfe, S.A., Lawson, N.D. “Chemokine signaling guides regional patterning of the first embryonic artery” Genes Dev, 2009, 23, 2272-2277. Pubmed
Noyes, M.B., Christensen, R.G., Wakabayashi, A., Stormo, G.D., Brodsky, M.H.; Wolfe, S.A. (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell, 133, 1277-1289. (Preview Cell, 2008, 133, 1133 & Editor’s Choice Science 2008, 321, 16.) PubMed
Meng, X., Noyes, M.B., Zhu, L.J., Lawson, N.D., Wolfe, S.A. (2008) Targeted gene inactivation in zebrafish using engineered zinc finger nucleases. Nat Biotechnol, 26, 695-701. (Research Highlight in Nature 2008, 453, 700 & Nat. Methods 2008, 5, 579.) PubMed
Noyes, M.B., Meng, X., Wakabayashi, A., Sinha, S., Brodsky, M.H.; Wolfe, S.A. (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Research, 36, 2547-2560. PubMed
Meng, X., Thibodeau-Beganny, S., Jiang, T., Joung, J. K., and Wolfe, S. A. (2007) Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method. Nucleic Acids Research, 35(11), e81.
Meng, X., Wolfe, S.A. (2006) Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nature Protocols 1, 30.
Meng, X., Brodsky, M.H., and Wolfe, S.A. (2005) A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat. Biotechnol., 23: 988-994.
Wolfe, S.A., Grant, R.A., and Pabo, C.O. (2003) Structure of a designed dimeric zinc finger protein bound to DNA. Biochemistry, 42: 13401-13409.
Wolfe, S.A., Grant, R.A., Elrod-Erickson, M., and Pabo, C.O. (2001) Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure, 9: 717-723.
Wolfe, S.A, Ramm, E.I., and Pabo, C.O. (2000) Combining structure-based design with phage display to create new Cys2His2 zinc finger dimers. Structure, 8: 739-750.
Wolfe, S.A., Nekludova, L., and Pabo, C.O. (2000) DNA recognition by Cys2His2 zinc finger proteins. Ann. Rev. Biophys. Biomol. Struct., 29: 183-212.
Wolfe, S.A., Greisman, H.A., Ramm, E.I., and Pabo, C. O. (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J. Mol. Biol., 285: 1917-1934.
Pomerantz, J.P., Wolfe, S.A., and Pabo, C.O. (1998) Structure-based design of a dimeric zinc finger protein. Biochemistry, 37: 965-970.
Erlanson, D.A., Wolfe, S.A., Chen, L., and Verdine, G.L. (1997) Selective base-pair destabilization enhances binding of a DNA methyltransferase. Tetrahedron, 53: 12041-12056.
Wolfe, S.A., Zhou, P., Dtsch, V., Chen, L., You, A., Ho, S.H., Crabtree, G.R., Wagner, G., and Verdine, G.L. (1997) Unusual Rel-like architecture in the DNA-binding domain of the transcription factor NFATc. Nature, 385: 172-176.
Wolfe, S.A., Ferentz, A.E., Grantcharova, V., Churchill, M.E.A.,and Verdine, G.L. (1995) Modifying the helical structure of DNA by design: recruitment of an architecture-specific protein to an enforced DNA bend. Chem. Biol., 2: 213-221.
Wolfe, S.A. and Verdine, G.L. (1993) Ratcheting torsional stress in duplex DNA. J. Am. Chem. Soc., 115: 12585-12586.