Publications
Liu, B., Dong, X., Zheng, C., Keener, D., Chen, Z., Cheng, H., Watts, J. K., Xue, W., Sontheimer, E. J.(2024) Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. Nature Biotechnology 42(7), 1039-1045. (PMID: 37709915)
Rodríguez, T. C., Yurkovetskiy, L., Nagalekshmi, K., Lam, C. H. O., Jazbec, E., Maitland, S. A., Wolfe, S. A., Sontheimer, E. J., and Luban, J. (2024) PRC1.6 localizes on chromatin with the human silencing hub (HUSH) complex for promoter-specific silencing. bioRxiv 2024.07.12.603173. (doi: 10.1101/2024.07.12.603173)
Adler, B. A., Trinidad, M. I., Bellieny-Rabelo, D., Zhang, E., Karp, H. M., Skopintsev, P., Thornton, B. W., Weissman, R. F., Yoon, P. H., Chen, L., Hessler, T., Eggers, A. R., Colognori, D., Boger, R., Doherty, E. E., Tsuchida, C. A., Tran, R. V., Hofman, L., Shi, H., Wasko, K. M., Zhou, Z., Xia, C., Al-Shimary, M. J., Patel, J. R., Thomas, V. C. J. X., Pattali, R., Kan, M. J., Vardapetyan, A., Yang, A., Lahiri, A., Maxwell, M. F., Murdock, A. G., Ramit, G. C., Henderson, H. R., Calvert, R. W., Bamert, R. S., Knott, G. J., Lapinaite, A., Pausch, P., Cofsky, J. C., Sontheimer, E. J., Wiedenheft, B., Fineran, P. C., Brouns, S. J. J., Sashital, D. G., Thomas, B. C., Brown, C. T., Goltsman, D. S. A., Barrangou, R., Siksnys, V., Banfield, J. F., Savage, D. F., Doudna, J. A. (2024) CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Research 52(D1), D590-D596. (PMID: 37889041)
Zhang, H., Kelly, K., Lee, J., Echeverria, D., Cooper, D., Panwala, R., Amrani, N., Chen, Z., Gaston, N., Wagh, A., Newby, G. A., Xie, J., Liu, D. R., Gao, G., Wolfe, S. A., Khvorova, A., Watts, J. K., Sontheimer, E. J. (2024) Self-delivering, chemically modified CRISPR RNAs for AAV co-delivery and genome editing in vivo. Nucleic Acids Research 52(2), 977-997. (PMID: 38033325)
Bamidele, N., Zhang, H., Dong, X., Cheng, H., Gaston, N., Feinzig, H., Cao, H., Kelly, K., Watts, J. K., Xie, J., Gao, G., Sontheimer, E. J. (2024) Domain-inlaid Nme2Cas9 adenine base editors with improved activity and targeting scope. Nature Communications 15(1), 1458. (PMID: 38368418)
McGee, A. V., Liu, Y. V., Griffith, A. L., Szegletes, Z. M., Wen, B., Kraus, C., Miller, N. W., Steger, R. J., Escude Velasco, B., Bosch, J. A., Zirin, J. D., Viswanatha, R., Sontheimer, E. J., Goodale, A., Greene, M. A., Green, T. M., Doench, J. G. (2024) Modular vector assembly enables rapid assessment of emerging CRISPR technologies. Cell Genomics 4(3), 100519. (PMID: 38484704)
Liu, P., Ponnienselvan, K., Nyalile, T., Oikemus, S., Joynt, A. T., Iyer, S., Kelly, K., Guo, D., Kyawe, P. P., Vanderleeden, E., Redick, S. D., Huang, L., Chen, Z., Lee, J. M., Schiffer, C. A., Harlan, D. M., Wang, J. P., Emerson, C. P. J., Lawson, N. D., Watts, J. K., Sontheimer, E. J., Luban, J., Wolfe, S. A. (2024) Increasing intracellular dNTP levels improves prime editing efficiency. Nature Biotechnology 6, 570-582. (PMID: 39322763)
Chen, Z.*, Kwan, S. Y.*, Mir, A., Hazeltine, M., Shin, M., Liang, S.-Q., Kelly, K., Ghanta, K. S., Gaston, N., Cao, Y., Xie, J., Gao, G., Xue, W., Sontheimer, E. J., and Watts, J. K. (2023) A fluorescent reporter mouse for in vivo assessment of genome editing with diverse Cas nucleases and prime editors. The CRISPR Journal 6, 570-582. (PMID: 38108517)
Chen, Z., Kelly, K., Cheng, H., Dong, X., Hedger, A. K., Li, L., Sontheimer, E. J., and Watts, J. K. (2023) In vivo prime editing by lipid nanoparticle co-delivery of chemically modified pegRNA and prime editor mRNA. GEN Biotechnology 2, 490-502.
McGee, A. V., Liu, Y. V., Griffith, A. L., Szegletes, Z. M., Wen, B., Kraus, C., Miller, N. W., Steger, R. J., Velasco, B. E., Bosch, J. A., Zirin, J. D., Viswanatha, R., Sontheimer, E. J., Goodale A., Greene, M. A., Green, T. M., and Doench, J. G. (2023) Modular vector assembly enables rapid assessment of emerging CRISPR technologies. Cell Genomics 4, 100519 (PMID: 37961518)
Ponnienselvan, K., Liu, P., Nyalile, T., Oikemus, S., Joynt, A. T., Kelly, K., Guo, D., Chen, Z., Lee, J. M., Schiffer, C. A., Emerson, C. P. Jr., Lawson, N. D., Watts, J. K., Sontheimer, E. J., Luban, J., and Wolfe, S. A. (2024) Addressing the dNTP bottleneck restricting prime editing activity. Manuscript in revision (preprint available at https://www.biorxiv.org/content/10.1101/2023.10.21.563443v2). (PMID:37904991)
Zhao, L.*, Koseki, S. R. T.*, Silverstein, R. A., Amrani, N., Peng, C., Kramme, C., Savic, N., Pacesa, M., Rodríguez, T. C., Stan, T., Tysinger, E., Hong, L., Yudistyra, V., Ponnapati, M. R., Jacobson, J. M., Church, G. M., Jakimo, N., Truant, R., Jinek, M., Kleinstiver, B. P., Sontheimer, E. J., and Chatterjee, P. (2023) PAM-flexible Genome Editing with an Engineered Chimeric Cas9. Nature Communications 14, 6175. (PMID: 37794046)
Kraus, C., and Sontheimer, E. J. (2023) Viruses use RNA decoys to thwart CRISPR defences. Nature, 623, 490-491. (PMID: 37853195)
Liu, B.*, Dong, X.*, Zheng, C.*, Keener, D., Chen, Z., Cheng, H., Watts, J. K., Xue, W., and Sontheimer, E. J. (2023). Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. Nature Biotechnology, in press (ePub ahead of print: https://www.nature.com/articles/s41587-023-01947-w). (PMID: 37709915)
Adler, B. A., Trinidad, M. I., Bellieny-Rabelo, D., Zhang, E., Karp, H. M., Skopintsev, P., Thornton, B. W., Weissman, R. F., Yoon, P. H., Chen, L. X., Hessler, T., Eggers, A. R., Colognori, D., Boger, R., Doherty, E. E., Tsuchida, C. A., Tran, R. V., Hofman, L., Shi, H., Wasko, K. M., Zhou, Z., Xia, C., Al-Shimary, M. J., Patel, J. R., Thomas, V. C. J. X., Pattali, R., Kan, M. J., Vardapetyan, A., Yang, A., Lahiri, A., Maxwell, M. F., Murdock, A. G., Ramit, G. C., Henderson, H. R., Calvert, R. W., Bamert, R. S., Knott, G. J., Lapinaite, A., Pausch, P., Cofsky, J. C., Sontheimer, E. J., Wiedenheft, B., Fineran, P. C., Brouns, S. J. J., Sashital, D. G., Thomas, B. C., Brown, C. T., Goltsman, D. S., Rodolphe Barrangou, R., Virginius Siksnys, V., Banfield, J. F., Savage, D. F., and Doudna, J. A. (2023). CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes. Nucleic Acids Research 52, D590-D596. (PMID: 37889041)
Zheng, C., Liu, B., Dong, X., Gaston, N., Sontheimer, E. J., Xue, W. (2023) Template-jumping prime editing enables large insertion and exon rewriting in vivo. Nature Communications 14 (PMID: 37291100)
Bamidele, N., Zhang, H., Dong, X., Gaston, N., Cheng, H., Kelly, K., Watts, J. K., Xie, J., Gao, G., and Sontheimer, E. J. (2023) Engineering Nme2Cas9 adenine base editors with improved activity and targeting scope. Nature Communications 15, 1458. (PMID: 37131611)
Zhang, H., Kelly, K., Lee, J., Eceverria, D., Cooper, D., Panwala, R., Chen, Z., Gaston, N., Newby, G., Zie, J., Liu, D. R., Gao, G., Wolfe, S. A., Khvorova, A., Watts, J. K., and Sontheimer, E. J. (2023) Self-delivering CRISPR RNAs for AAV co delivery and genome editing in vivo. Nucleic Acids Research 52, 977-997. (PMID: 36993169)
Liang, S-Q., Liu, P., Karthikeyan Ponnienselvan, K., Suresh, S., Chen, Z., Kramme, C., Chatterjee, P., Zhu, L. J., Sontheimer, E. J., Xue, W., and Wolfe, S. A. (2023) Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nature Methods, 20, 898-907 (PMID: 37156841)
Kraus, C., and Sontheimer, E. J. (2023) Applications of anti-CRISPR proteins in genome editing and biotechnology. Journal of Molecular Biology 435, 168120. (PMID: 37100169)
Meijboom, K.E., Abdallah, A., Fordham, N.P., Nagase, H., Rodriguez, T., Kraus, C., Gendron, T.F., Krishnan, G., Esanov, R., Andrade, N. S., Rybin, M. J., Ramic, M., Stephens, Z. D., Edraki, A., Blackwood, M. T., Kahriman, Al, Henniger, N., Kocher, J-P. A., Benatar, M., Brodsky, M. H., Petrucelli, L., Gao, F.-B., Sontheimer, E. J., Brown, R. H., Zeier, Z., and Mueller, C. (2022) CRISPR/Cas9-mediated excision of ALS/FTD-causing hexanucleotide repeat expansion in C90FR72 rescuses major disease mechanisms in vivo and in vitro. Nature Communications 13, 6286. (PMID: 36271076)
Barrangou, R., Sontheimer, E. J. and Marraffini, L. A., Editors (2022) CRISPR: Biology and Applications. American Society for Microbiology Press (ISBN: 978-1-683-67037-7).
Shin, M., Chan, I. L., Cao, Y., Gruntman, A. M., Lee, J., Sousa, J., Rodriguez, T. C., Echeverria, D., Devi, G., Debacker, A., Moazami, M., Krishnamurthy, P. M., Rembetsy-Brown, J., Kelly, K., Yukselen, O., Donnard, E., Parsons, T., Khvorova, A., Sontheimer, E. J., Maehr, R., Garber, M., and Watts, J. K. (2022) Intratracheally administered LNA gapmer antisense oligonucleotides induce robust gene silencing in mouse lung fibroblasts. Nucleic Acids Research 50, 8418-8430. (PMID: 35920332)
Rodríguez, T. R.*, Smith, J. L.*, Dadafarin, S., Kwan, S.-Y., Wu, C. H., Sontheimer, E. J., and Xue, W. (2022) Multi-omics characterization of mouse hepatoblastoma identifies novel YAP1 target genes. Hepatology 78, 58-71 (ePub: http://dx.doi.org/10.1002/ hep.32713).
Iyer, S., Mir, A., Vega-Badillo, J., Roscoe, B. P., Ibraheim, R., Zhu, L. J., Lee, J., Liu, P., Luk, K., Mintzer, E., Soares de Brito, J., Zamore, P. D., Sontheimer, E. J. and Wolfe, S. A. (2022) Efficient homology-directed repair with circular ssDNA donors. The CRISPR Journal 5, 685-701.
Chen, Z.*, Devi, G.*, Arif, A., Zamore, P. D., Sontheimer, E. J., and Watts, J. K. (2022) Tetrazine-ligated CRISPR sgRNAs for Efficient Genome Editing. ACS Chemical Biology, 17, 1045-1050. https://doi.org/10.1021/acschembio.2c00116). (PMID: 35446558).
Liu, B.*, Dong, X.*, Cheng, H., Zheng, C., Chen, Z., Rodríguez, T. C., Liang, S.-Q., Xue, W., and Sontheimer, E. J., (2022) A split prime editor with untethered reverse transcriptase and circular RNA template. Nature Biotechnology, 9, 1388-1393. (PMID: 35379962)
Zhang, H., Bamidele, N., Liu, P., Ojelabi, O., Gao, X. D., Rodríguez, T., Cheng, H., Kelly, K., Watts, J. K., Xie, J., Gao, G., Wolfe, S. A., Xue, W., Sontheimer, E. J. (2022) Adenine base editing in vivo with a single adeno-associated virus vector. GEN Biotechnology 1, 285-299. (PMID: 35811581)
Liang, S.-Q.*, Liu, P.*, Smith, J. L., Mintzer, E., Maitland, S., Dong, X., Yang, Q., Lee, J., Haynes, C. M., Zhu, L. J., Watts, J. K., Sontheimer E. J., Wolfe, S. A., and Xue, W. (2022) Genome-wide unbiased detection of CRISPR editing in vivo using GUIDE-tag. Nature Communications 13, 437. (PMID: 35064134)
Takasugi, P. R.*, Wang, S.*, Truong, K. T.*, Drage, E. P., Kanishka, S. N., Higbee, M. A., Bamidele, N., Ojelabi, O., Sontheimer, E. J., and Gagnon, J. A. (2022) Orthogonal CRISPR-Cas tools for genome editing, inhibition, and CRISPR recording in zebrafish embryos. Genetics, 220, 196. (PMID: 34735006)
Tsagkaraki, E., Nicoloro, S., De Souza, T., Solivan-Rivera, J., Desai, A., Shen, Y., Kelly, M., Guilherme, A., Henriques, F., Ibraheim, R., Amrani, N., Luk, K., Maitland, S., Friedline, R. H., Tauer, L., Hu, X., Kim, J. K., Wolfe, S. A., Sontheimer, E. J., Corvera, S., and Czech, M. P. (2021) CRISPR-enhanced human adipocyte browning as cell therapy for metabolic disease. Nature Communications 12, 6931. (PMID: 34836963)
Ghanta, K. S., Chen, Z., Mir, A., Dokshin, G. A., Krishnamurthy, P. M., Yoon, Y., Gallant, J., Xu, P., Zhang, X.-O., Ozturk, A., Shin, M., Idrizi, F., Liu, P., Gneid, H., Edraki, A., Lawson, N. D., Rivera-Pérez, J. A., Sontheimer, E. J., Watts, J., and Mello, C. C. (2021) 5’-Modifications improve potency and efficacy of DNA donors for precision genome editing. eLife 10, e72216. (PMID: 34665130)
Ibraheim, R., Tai, P. W. L., Mir, A., Javeed, N., Wang, J., Rodriguez, T., Nelson, S., Khokar, E., Mintzer, E., Maitland, S., Cao, Y., Tsagkaraki, E., Wolfe, S. A., Wang, D., Pai, A. A., Xue, W., Gao, G., and Sontheimer, E. J. (2021) Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo. Nature Communications 12, 6267. (PMID: 34725353)
Liu, P., Liang, S.-Q., Zheng, C., Mintzer, E., Zhao, Y. G., Ponnienselvan, K., Mir, A., Sontheimer, E. J., Flotte, T. R. Wolfe, S. A., and Xue, W. (2021) Improved prime editors enable pathogenic allele correction and cancer modeling in adult mice. Nature Communications 12, 2121. (PMID: 33837189)
Saha, K.,* Sontheimer, E. J.,* Brooks, P. J., Dwinell, M., Gersbach, C. A., Liu, D. R., Murray, S. A., Tsai, S. Q., Wilson, R. C., Anderson, D. G., Asokan, A., Banfield, J. F., Bankiewicz, K. S., Bao, G., Bulte, J. W. M., Bursac, N., Campbell, J. M., Carlson, D. F., Chaikof, E. L., Chen, Z.-Y., Cheng, R. H., Clark, K. J., Curiel, D. T., Dahlman, J. E., Deverman, B. E., Dickinson, M. E., Doudna, J. A., Ekker, S. C., Emborg, M. E., Feng, G., Freedman, B. S., Gamm, D. M., Gao, G., Ghiran, I. C., Glazer, P. M., Gong, S., Heaney, J. D., Hennebold, J. D., Hinson, J. T., Khvorova, A., Kiani, S., Lagor, W. R., Lam, K. S., Leong, K. W., Levine, J. E., Lewis, J. A., Lutz, C. M., Ly, D. H., Maragh, S., McCray, P. B. Jr., McDevitt, T. C., Mirochnitchenko, O., Morizane, R., Murthy, N., Prather, R. S., Ronald, J. A., Roy, S., Roy, S. Sabbisetti, V., Saltzman, W. M., Santangelo, P. J., Segal, D. J., Shimoyama, M., Skala, M. C., Tarantal, A. F., Tilton, J. C., Truskey, G. A., Vandsburger, M., Watts, J. K., Wells, K. D., Wolfe, S. A., Xu, Q., Xue,, W., Yi, G., Zhou, J. and the SCGE Consortium. (2021) The NIH Somatic Cell Genome Editing program. Nature 259, 195-204.
Smith, J., Rodriguez, T., Mou, H., Kwan, S-Y., Pratt, H., Zhang, X-O., Cao, Y., Liang, S., Ozata, D. M., Yu, T., Yin, Q., Hazeltine, M., Weng, Z., Sontheimer, E. J., Xue, W. (2020). YAP1 withdrawal in hepatoblastoma drives therapeutic differentiation of tumor cells to functional hepatocyte-like cells. Hepatology, 73, 1011-1027. (PMID: 32452550)
Chatterjee, P., Lee, J., Nip, L., Koseki, S. R. T., Tysinger, E., Sontheimer, E. J., Jacobson, J. M. and Jakimo, N. (2020). A Cas9 with PAM recognition for adenine dinucleotides. Nature Communications 11, 2474. (PMID: 32424114)
Chatterjee, P., Jakimo, N., Lee, J., Amrani, N., Rodriguez, T., Koseki, S. R. T., Tysinger, E., Qing, R., Sontheimer, E. J. and Jacobson, J. (2020) An engineered ScCas9 with broad PAM range and high specificity and activity. Nature Biotechnology, 38, 1154-1158. (PMID: 32393822)
Davidson, A. R., Lu, W.-T., Stanley, S.Y., Wang, J., Mejdani, M., Trost, C. N., Hicks, B.T., Lee, J. and Sontheimer, E. J. (2020) Anti-CRISPRs: Protein inhibitors of CRISPR-Cas systems. Annual Review of Biochemistry 89, 309-332. (PMID: 32186918)
Barrangou, R. and Sontheimer, E. J. (2020) CRISPR shields: Fending off diverse Cas nucleases with nucleus-like structures. Fending off diverse Cas nucleases with nucleus-like structures. Molecular Cell 77, 934-935. (PMID: 32142691)
Sun, W., Yang, J., Cheng, Z., Amrani, N., Liu, C., Wang, K., Ibraheim, R., Edraki, A., Huang, X., Wang, M., Wang, J., Liu, L., Sheng, G., Yang, Y., Liu, J., Sontheimer, E. J., and Wang, Y. (2019) Structures of Neisseria meningitidis Cas9 complexes in catalytically poised and anti-CRISPR-inhibited states. Molecular Cell 76, 938-952. (PMID: 31668930)
Garcia, B., Lee, J., Edraki, A., Hidalgo-Reyes, Y., Erwood, S., Mir, A., Trost, C., Seroussi, U., Stanley, S. Y., Cohn, R. D., Claycomb, J. M., Sontheimer, E. J., Maxwell, K. L. and Davidson, A. R. (2019) Anti-CRISPR AcrIIA5 potently inhibits all Cas9 homologs used for genome editing. Cell Reports 29, 1739-1746. (PMID: 31722192)
Lee, J., Mou, H., Ibraheim, R., Liang, S.-Q., Xue, W., and Sontheimer, E. J. (2019) Tissue-specific genome editing in vivo by microRNA-repressible anti-CRISPR proteins. RNA 25, 1421-1431. (PMID: 31439808)
Sontheimer, E. J. (2019) X-Tracting a new CRISPR-Cas genome-editing platform from metagenomic data sets. The CRISPR Journal 2, 148-150. (PMID: 31225753)
Thavalingam, A., Cheng, Z., Garcia, B., Huang, X., Shah, M., Sun, W., Wang, M., Harrington, L., Hwang, S., Hidalgo-Reyes, Y., Sontheimer, E. J., Doudna, J. A., Davidson, A. R., Moraes, T. F., Wang, Y., and Maxwell, K. L. (2019) Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anit-CRISPR AcrIIC2 Nature Communications 10, 2806. (PMID: 31243272)
Edraki, A., Mir, A., Ibraheim, R., Gainetdinov, I., Yoon, Y., Gallant, J., Song, C.-Q., Cao, Y., Xue, W., Rivera-Pérez, J. A., and Sontheimer, E. J. (2019) A compact, high-accuracy Cas9 with a dinucleotide PAM for in vivo genome editing. Molecular Cell 73, 714-726. (PMID: 30581144)
Gao, X. D., Rodriguez, T., and Sontheimer, E. J. (2018) Adapting dCas9-APEX2 for subnuclear proteomic profiling. Methods in Enzymology 616, 365-383. (PMID: 30691651)
Amrani, N., Gao, X. D., Liu, P., Edraki, A., Mir, A., Ibraheim, R., Gupta, A., Sasaki, K. E., Wu, T., Donohoue, P. D., Settle, A. H., Lied, A. M., McGovern, K., Fuller, C. K., Cameron, P., Fazzio, T. G., Zhu, L. J., Wolfe, S. A., and Sontheimer, E. J. (2018) NmeCas9 is an intrinsically high-fidelity genome editing platform. Genome Biology 19, 214. (PMID: 30518407)
Lee, J., Mir, A., Edraki, A., Garcia, B., Amrani, N., Lou, H. E., Gainetdinov, I., Pawluk, A., Ibraheim, R., Gao, X. D., Liu, P., Davidson, A. R., Maxwell, K. L., and Sontheimer, E. J. (2018) Potent Cas9 inhibition in bacterial and human cells by AcrIIC4 and AcrIIC5 anti-CRISPR proteins. mBio 9, e02321-18. (PMID: 30514786)
Bolukbasi, M. F., Liu, P., Luk, K., Kwok, S. F., Gupta, A., Amrani, N., Sontheimer, E. J., Zhu, L. J., and Wolfe, S. A. (2018) Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing. Nature Communications 9, 4856. (PMID: 30531933)
Bondy-Denomy, J., Davidson, A. R., Doudna, J. A., Fineran, P. C., Maxwell, K. L., Moineau, S., Peng, X., Sontheimer, E. J., and Weidenheft, B. (2018) A unified resource for tracking anti-CRISPR names. The CRISPR Journal 1, 304-305. (PMID: 31021273)
Ibraheim, R., Song, C.-Q., Mir, A., Amrani, N., Xue, W., and Sontheimer, E. J. (2018) All-in-one Adeno-associated Virus Delivery and Genome Editing by Neisseria meningitidis Cas9 in vivo. Genome Biology 19, 137. (PMID: 30231914)
Mir, A., Alterman, J. A., Hassler, M. R., Debacker, A. J., Hudgens, E., Echevarria, D., Brodsky, M. H., Khvorova, A., Watts, J. K., and Sontheimer, E. J. (2018) Heavily and fully modified RNAs guide efficient SpyCas9-mediated genome editing. Nature Communications 9, 2641. (PMID: 29980686)
Stone, N., Hilbert, B. J., Hidalgo, D., Halloran, K. T., Lee, J., Sontheimer, E. J., and Kelch, B. A. (2018) A hyperthermophilic phage decoration protein suggests common evolutionary origin with herpesvirus triplex proteins and an anti-CRISPR protein. Structure 26, 936-947. (PMID: 29779790)
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. (2018) C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. Nature Methods 15, 433-436. (PMID: 29735996)
Edraki, A., and Sontheimer, E. J. (2018) CRISPRs from scratch. Nature Microbiology 3, 261-262. (PMID: 29463924)
Mir, A., Edraki, A., Lee, J., and Sontheimer, E. J. (2018) Type II-C CRISPR-Cas9 biology, mechanism and application. ACS Chemical Biology 13, 357-365. (PMID: 29202216)
Harrington, L. B., Doxzen, K. W., Ma, E., Liu, J.-J., Knott, G. J., Edraki, A., Amrani, N., Chen, J. S., Cofsky, J. C., Kranzusch, P. J., Sontheimer, E. J., Davidson, A. R., Maxwell, K., and Doudna, J. A. (2017). A broad-spectrum inhibitor of CRISPR-Cas9. Cell 170, 1224-1233. (PMID: 28844692)
Sontheimer, E. J. and Davidson, A. R. (2017) Inhibition of CRISPR-Cas systems by mobile genetic elements. Current Opinion in Microbiology 37, 120-127. (PMID: 28668720)
Mou, H., Smith, J. L., Yin, H., Peng, L., Moore, J., Zhang, X.-O., Song, C.-Q., Sheel, A., Wu, Q., Ozata, D. M., Li, Y., Anderson, D. G., Emerson, C. P., Sontheimer, E. J., Moore, M. J., Weng, Z., and Xue, W. (2017) CRISPR-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biology 18, 108. (PMID: 28615073)
Pawluk, A., Amrani, N., Zhang, Y., Garcia, B., Hidalgo-Reyes, Y., Lee, J., Edraki, A., Shah, M., Sontheimer, E. J., Maxwell, K., and Davidson, A. R. (2016) Naturally occurring off-switches for CRISPR-Cas9. Cell 167, 1829-1838. (PMID: 27984730)
Sontheimer, E. J. and Marraffini, L. A. (2016) CRISPR goes retro. Science 351, 920-921. (PMID:26917756)
Sontheimer, E. J. and Wolfe, S. A. (2015) Cas9 gets a classmate. Nature Biotechnology 33, 1240-1241. (PMID: 26650011)
Zhang, Y., Rajan, R., Seifert, H. S., Mondragón, A. and Sontheimer, E. J. (2015) DNase H activity of Neisseria meningitidis Cas9. Molecular Cell 60, 242-255. (PMID: 26474066)
Wakefield, N., Rajan, R. and Sontheimer, E. J. (2015) Primary processing of CRISPR RNA by the endonuclease Cas6 in Staphylococcus epidermidis. FEBS Letters 589, 3197-3204. (PMID: 26364721)
Wang, D., Mou, H., Li, S., Li, Y., Hough, S., Tran, K., Li, J., Yin, H., Anderson, D. G., Sontheimer, E. J., Weng, Z., Gao, G. and Xue, W. (2015) Adenovirus-mediated somatic genome editing of Pten by CRISPR/Cas9 in mouse liver in spite of Cas9-specific immune responses. Human Gene Therapy 26, 432-442. (PMID: 26086867)
Sontheimer, E. J. and Barrangou, R. (2015) The bacterial origins of the CRISPR genome editing revolution. Human Gene Therapy 26, 413-424. (PMID: 26078042)
Doudna, J. A. and Sontheimer, E. J., Editors (2014) The use of CRISPR-Cas9, ZFNs, and TALENs in generating site-specific genome alterations. Methods in Enzymology, Volume 516. (PMID: 25398356)
Zhang, Y. and Sontheimer, E.J. (2014) Cascading into focus. Science 345, 1452-1453. (PMID: 25237089)
Hurtado, S. B., Kim Guisbert, K. S. and Sontheimer, E. J. (2014) SPO24 is a transcriptionally dynamic, small ORF-encoding locus required for efficient sporulation in S. cerevisiae. PLoS ONE 9(8), e105058. (PMID: 25127041)
Hou, Z., Zhang, Y., Propson, N. E., Howden, S. E., Chu, L.-F., Sontheimer, E. J. and Thomson, J. A. (2013) Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proceedings of the National Academy of Sciences U.S.A. 110, 15644-15649. (PMID: 23940360)
Zhang, Y., Heidrich, N., Joseph, B., Gunderson, C. Seifert, H. S., Schoen, C., Vogel, J. and Sontheimer, E. J. (2013) Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Molecular Cell 50, 488-503. (PMID: 23706818)
Kim Guisbert, K. S. and Sontheimer, E. J. (2013) Quit stalling or you’ll be silenced. Cell 152, 938-939. (PMID: 23452843)
Sontheimer, E. J. (2012) Small RNAs of opposite sign…but same absolute value. Cell 151, 1157-1158. (PMID: 23217700)
Kim Guisbert, K. S., Zhang, Y., Flatow, J., Hurtado, S., Staley, J. P., Lin, S. and Sontheimer, E. J. (2012) Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. RNA 18, 1142-1153. (PMID: 22539527)
Gerbasi, V. R., Preall, J. B., Golden, D. E., Powell, D. W., Cummins, T. D. and Sontheimer, E. J. (2011) Blanks, a nuclear siRNA/dsRNA binding complex component, is required for Drosophila spermiogenesis. Proceedings of the National Academy of Sciences U.S.A. 108, 3204-3209. (PMID: 21300896)
Sontheimer, E. J. and Marraffini, L. A. (2010) Microbiology: Slicer for DNA. Nature 468, 45-46. (PMID: 21048757)
Gerbasi, V. R., Golden, D. E., Hurtado, S. B. and Sontheimer, E. J. (2010) Proteomic identification of Drosophila siRNA-associated factors. Molecular & Cellular Proteomics 9, 1866-1872. (PMID: 20472918)
Marraffini, L. A. and Sontheimer, E. J. (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature Reviews Genetics 11, 181-190. (PMID: 20125085)
Marraffini, L. A. and Sontheimer, E. J. (2010) Self vs. non-self discrimination during CRISPR RNA-directed immunity. Nature 463, 568-571. (PMID: 20072129)
Marraffini, L. A. and Sontheimer, E. J. (2009) Invasive DNA, chopped and in the CRISPR. Structure 17, 786-787. (PMID: 19523896)
Lee, Y. S., Pressman, S., Andress, A. P., Kim, K., White, J. L., Cassidy, J. J., Li, X., Lubell, K., Lim, D. H., Cho, I. S., Nakahara, K., Preall, J. B., Bellare, P., Sontheimer, E. J. and Carthew, R. W. (2009) Silencing by small RNAs is linked to endosome trafficking. Nature Cell Biology 11, 1150-1156. (PMID: 19684574)
Carthew, R. W., and Sontheimer, E. J. (2009) Origins and mechanisms of siRNAs and miRNAs. Cell 136, 642-655. (PMID: 19239886)
Marraffini, L. A. and Sontheimer, E. J. (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843-1845. (PMID: 19095942)
Bellare, P., Small, E. C., Huang, X., Wohlschlegel, J. A., Staley, J. P. and Sontheimer, E. J. (2008) A role for ubiquitin in the spliceosome assembly pathway. Nature Structural & Molecular Biology 15, 444-451. (PMID: 18425143)
Golden, D. E., Gerbasi, V. R., and Sontheimer, E. J. (2008) An inside job for siRNAs. Molecular Cell 31, 309-312. (PMID: 18691963)
Bellare, P., and Sontheimer, E. J. (2007) A fork in the road for microRNAs. Nature Structural & Molecular Biology 14, 684-686. (PMID: 17676029)
Preall, J. B., He, Z., Gorra, J. and Sontheimer, E. J. (2006). Short interfering RNA strand selection is independent of double-stranded RNA processing polarity during RNA interference in Drosophila. Current Biology 16, 530-535. (PMID: 16527750)
Bellare, P., Kutach, A. K., Rines, A., Guthrie, C. and Sontheimer, E. J. (2006). Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p. RNA 12, 292-302. (PMID: 16428608)
Pham, J. W. and Sontheimer, E. J. (2005). Molecular requirements for RNA-induced silencing complex assembly in the Drosophila RNA interference pathway. Journal of Biological Chemistry 280, 39278-39283. (PMID: 16179342)
Preall, J. B., and Sontheimer, E. J. (2005). RNAi: RISC gets loaded. Cell 123, 543-545. (PMID: 16286001)
Sontheimer, E. J., and Carthew, R. W. (2005). Silence from within: Endogenous siRNAs and miRNAs. Cell 122, 9-12. (PMID: 16009127)
Pham, J. W., and Sontheimer, E. J. (2005). Separation of Drosophila RNA silencing complexes by native gel electrophoresis. In “Methods in Molecular Biology, vol. 309: RNA Silencing: Methods and Protocols” (ed. G. G. Carmichael), pp. 11-16. Humana Press, Totowa, New Jersey. (PMID: 15990394)
Sontheimer, E. J. (2005). Assembly and function of RNA silencing complexes. Nature Reviews Molecular Cell Biology 6, 127-138. (PMID: 15654322)
Pellino, J. L., Jaskiewicz, L., Filipowicz, W. and Sontheimer, E. J. (2005). ATP modulates siRNA interactions with an endogenous human Dicer complex. RNA 11, 1719-1724. (PMID: 16177131)
Pham, J. W., Radhakrishnan, I. and Sontheimer, E. J. (2004). Thermodynamic and structural characterization of 2’-nitrogen-modified RNA duplexes. Nucleic Acids Research 32, 3446-3455. (PMID: 15247335)
Sontheimer, E. J., and Carthew, R. W. (2004). Argonaute journeys into the heart of RISC. Science 305, 1409-1410. (PMID: 15353786)
Pham, J. W., and Sontheimer, E. J. (2004). The making of an siRNA. Molecular Cell 15, 163-164. (PMID: 15260964)
He, Z., and Sontheimer, E. J. (2004). “siRNAs and miRNAs”: A meeting review on RNA silencing. RNA 10, 1165-1173. (PMID: 15272116)
Pham, J. W., Pellino, J. L., Lee, Y. S., Carthew, R. W. and Sontheimer, E. J. (2004). A Dicer-2-dependent 80S complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117, 83-94. (PMID: 15066284)
Lee, Y. S., Nakahara, K., Pham, J. W., Kim, K., He, Z., Sontheimer, E. J. and Carthew, R. W. (2004). Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69-81. (PMID: 15066283)
Pellino, J. L. and Sontheimer, E. J. (2003). R2D2 leads the silencing trigger to mRNA's death star. Cell 115, 132-133. (PMID: 14567910)
Sontheimer, E. J. (2001). The spliceosome shows its metal. Nature Structural Biology 8, 11-13. (PMID: 11135658)
Gordon, P. M., Sontheimer, E. J. and Piccirilli, J. A. (2000). Kinetic characterization of the second step of group II intron splicing: Role of metal ions and the cleavage site 2’-OH in catalysis. Biochemistry 39, 12939-12952. (PMID: 11041859)
Gordon, P. M., Sontheimer, E. J. and Piccirilli, J. A. (2000). Metal ion catalysis during the exon ligation step of nuclear pre-mRNA splicing: Extending the parallels between the spliceosome and group II introns. RNA 6, 199-205. (PMID: 10688359)
Warnecke, J. M., Sontheimer, E. J., Piccirilli, J. A. and Hartmann, R. K. (2000). Active site constraints in the hydrolysis reaction catalyzed by bacterial RNase P: Analysis of precursor tRNAs with a single 3’-S-phosphorothiolate internucleotide linkage. Nucleic Acids Research 28, 720-727. (PMID: 10637323)
Sontheimer, E. J., Gordon, P. M. and Piccirilli, J. A. (1999). Metal ion catalysis during group II intron self-splicing: Parallels with the spliceosome. Genes and Development 13, 1729-1741. (PMID: 10398685)
Sontheimer, E. J. (1999). Bridging sulfur substitutions in the analysis of pre-mRNA splicing. Methods 18, 29-37. (PMID: 10208814)
Sontheimer, E. J., Sun, S. and Piccirilli, J. A. (1997). Metal ion catalysis during splicing of premessenger RNA. Nature 388, 801-805. (PMID: 9285595)
Sontheimer, E. J. (1994). Site-specific RNA crosslinking with 4-thiouridine. Molecular Biology Reports 20, 35-44. (PMID: 7531281)
Sontheimer, E. J. and Steitz, J. A. (1993). The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262, 1989-1996. (PMID: 8266094)
Cortes, J. J., Sontheimer, E. J., Seiwert, S. D. and Steitz, J. A. (1993). Mutations in the conserved loop of human U5 snRNA generate use of novel cryptic 5' splice sites in vivo. EMBO Journal 12, 5181-5189. (PMID: 8262061)
Wyatt, J. R., Sontheimer, E. J. and Steitz, J. A. (1992). Site-specific crosslinking of mammalian U5 snRNP to the 5' splice site prior to the first step of premessenger RNA splicing. Genes and Development 6, 2542-2553. (PMID: 1340469)
Gelpi, C., Sontheimer, E. J. and Rodriguez-Sanchez, J. L. (1992). Autoantibodies against a serine tRNA-protein complex implicated in cotranslational selenocysteine insertion. Proceedings of the National Academy of Sciences U.S.A. 89, 9739-9743. (PMID: 1409691)
Sontheimer, E. J. and Steitz, J. A. (1992). Three novel functional variants of human U5 small nuclear RNA. Molecular and Cell Biology12, 734-746. (PMID: 1310151)