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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 Cas9Nature Communications 14, 6175. (PMID: 37794046)

Kraus, C., and Sontheimer, E. J. (2023) Viruses use RNA decoys to thwart CRISPR defencesNature, in press (ePub ahead of print: https://doi.org/10.1038/d41586-023-03133-z).

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 templatesNature 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. Manuscript submitted (preprint available at https://ecoevorxiv.org/repository/view/5811/). 

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. Manuscript submitted. (preprint available at https://www.biorxiv.org/content/10.1101/2023.04.14.536905v2). (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. Manuscript submitted (preprint available at https://biorxiv.org/cgi/content/short/2023.03.20.533459v2). (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, in press (ePub ahead of print: https://www.nature.com/articles/s41592-023-01859-2). (PMID: 37156841)

Kraus, C., and Sontheimer, E. J. (2023) Applications of anti-CRISPR proteins in genome editing and biotechnologyJournal 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 vitroNature 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 donorsThe 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 Biology17, 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 Biotechnology9, 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)