Additional materials of the author at
CSHL Institutional Repository

Ishigami, Yuma, Wong, Mandy S, Martí-Gómez, Carlos, Ayaz, Andalus, Kooshkbaghi, Mahdi, Hanson, Sonya M, McCandlish, David M, Krainer, Adrian R , Kinney, Justin B (2024) Specificity, synergy, and mechanisms of splice-modifying drugs. Nature Communications, 15(1) pp. 1880.

Ecker, DJ, Aiello, CD, Arron, JR, Bennett, CF, Bernard, A, Breakefield, XO, Broderick, TJ, Callier, SL, Canton, B, Chen, JS, Fishburn, CS, Garrett, B, Hecht, SM, Janowitz, T, Kliegman, M, Krainer, A, Louis, CU, Lowe, C, Sehgal, A, Tozan, Y, Tracey, KJ, Urnov, F, Wattendorf, D, Williams, TW, Zhao, X , Hayden, MR (2024) Opportunities and challenges for innovative and equitable healthcare. Nature Reviews Drug Discovery,

Xiang, Xiyan, Bhowmick, Krishanu, Shetty, Kirti, Ohshiro, Kazufumi, Yang, Xiaochun, Wong, Linda L, Yu, Herbert, Latham, Patricia S, Satapathy, Sanjaya K, Brennan, Christina, Dima, Richard J, Chambwe, Nyasha, Sharifova, Gulru, Cacaj, Fellanza, John, Sahara, Crawford, James M, Huang, Hai, Dasarathy, Srinivasan, Krainer, Adrian R, He, Aiwu R, Amdur, Richard L , Mishra, Lopa (2024) Mechanistically based blood proteomic markers in the TGF-β pathway stratify risk of hepatocellular cancer in patients with cirrhosis. Genes and Cancer, 15 pp. 1-14.

Wan, Ledong, Lin, Kuan-Ting, Rahman, Mohammad Alinoor, Ishigami, Yuma, Wang, Zhikai, Jensen, Mads A, Wilkinson, John E, Park, Youngkyu, Tuveson, David A , Krainer, Adrian R (2023) Splicing Factor SRSF1 Promotes Pancreatitis and KRASG12D-Mediated Pancreatic Cancer. Cancer Discovery, 13(7) pp. 1678-1695.

Jbara, Amina, Lin, Kuan-Ting, Stossel, Chani, Siegfried, Zahava, Shqerat, Haya, Amar-Schwartz, Adi, Elyada, Ela, Mogilevsky, Maxim, Raitses-Gurevich, Maria, Johnson, Jared L, Yaron, Tomer M, Ovadia, Ofek, Jang, Gun Ho, Danan-Gotthold, Miri, Cantley, Lewis C, Levanon, Erez Y, Gallinger, Steven, Krainer, Adrian R, Golan, Talia , Karni, Rotem (2023) RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer. Nature, 617(7959) pp. 147-153.

Zhang, Qian, Yang, Lucia, Liu, Ying Hsiu, Wilkinson, John E , Krainer, Adrian R (2023) Antisense oligonucleotide therapy for H3.3K27M diffuse midline glioma. Science Translational Medicine, 15(691) pp. eadd8280.

Hastings, Michelle L , Krainer, Adrian R (2023) RNA therapeutics. RNA, 29(4) pp. 393-395.

Kim, Young Jin , Krainer, Adrian R (2023) Antisense Oligonucleotide Therapeutics for Cystic Fibrosis: Recent Developments and Perspectives. Molecules and Cells, 46(1) pp. 10-20.

Ishigami, Yuma, Wong, Mandy S, Martí-Gómez, Carlos, Ayaz, Andalus, Kooshkbaghi, Mahdi, Hanson, Sonya, McCandlish, David M, Krainer, Adrian R , Kinney, Justin B (2022) Specificity, synergy, and mechanisms of splice-modifying drugs.

Zhou, Juannan, Wong, Mandy S, Chen, Wei-Chia, Krainer, Adrian R, Kinney, Justin B , McCandlish, David M (2022) Higher-order epistasis and phenotypic prediction. Proceedings of the National Academy of Sciences of USA, 119(39) pp. e2204233119.

Marasco, Luciano E, Dujardin, Gwendal, Sousa-Luís, Rui, Liu, Ying Hsiu, Stigliano, Jose N, Nomakuchi, Tomoki, Proudfoot, Nick J, Krainer, Adrian R , Kornblihtt, Alberto R (2022) Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy. Cell, 185(12) pp. 2057-2070.e15.

Kim, Young Jin, Nomakuchi, Tomoki, Papaleonidopoulou, Foteini, Yang, Lucia, Zhang, Qian , Krainer, Adrian R (2022) Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy. Nature Communications, 13(1) pp. 2978.

Kim, Young Jin, Sivetz, Nicole, Layne, Jessica, Voss, Dillon M, Yang, Lucia, Zhang, Qian , Krainer, Adrian R (2022) Exon-skipping antisense oligonucleotides for cystic fibrosis therapy. Proceedings of the National Academy of Sciences of USA, 119(3) pp. e2114858118-e2114858118.

Gao, Yuan, Lin, Kuan-Ting, Jiang, Tao, Yang, Yang, Rahman, Mohammad A, Gong, Shuaishuai, Bai, Jialin, Wang, Li, Sun, Junjie, Sheng, Lei, Krainer, Adrian R , Hua, Yimin (2022) Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA.. Nucleic Acids Research,

Ma, Wai Kit, Voss, Dillon M, Scharner, Juergen, Costa, Ana SH, Lin, Kuang-Ting, Jeon, Hyun Yong, Wilkinson, John E, Jackson, Michaela, Rigo, Frank, Bennett, C Frank , Krainer, Adrian R (2021) ASO-based PKM splice-switching therapy inhibits hepatocellular carcinoma growth.. Cancer Research, pp. canres.0948.2020-canres.0948.2020.

Abou-el-Enein, M, Angelis, A, Appelbaum, FR, Andrews, NC, Bates, SE, Bierman, AS, Brenner, MK, Cavazzana, M, Caligiuri, MA, Clevers, H, Cooke, E, Daley, GQ, Dzau, VJ, Ellis, LM, Fineberg, HV, Goldstein, LSB, Gottschalk, S, Hamburg, MA, Ingber, DE, Kohn, DB, Krainer, AR, Maus, MV, Marks, P, Mummery, CL, Pettigrew, RI, Rutter, JL, Teichmann, SA, Terzic, A, Urnov, FD, Williams, DA, Wolchok, JD, Lawler, M, Turtle, CJ, Bauer, G , Ioannidis, JPA (2021) Evidence generation and reproducibility in cell and gene therapy research: A call to action. Molecular Therapy - Methods and Clinical Development, 22 pp. 11-14.

Kim, Young Jin, Sivetz, Nicole, Layne, Jessica, Voss, Dillon, Yang, Lucia, Zhang, Qian , Krainer, Adrian (2021) Exon-Skipping Antisense Oligonucleotides for Cystic Fibrosis Therapy. BioRxiv,

Ajiro, Masahiko, Awaya, Tomonari, Kim, Young Jin, Iida, Kei, Denawa, Masatsugu, Tanaka, Nobuo, Kurosawa, Ryo, Matsushima, Shingo, Shibata, Saiko, Sakamoto, Tetsunori, Studer, Rolenz, Krainer, Adrian R , Hagiwara, Masatoshi (2021) Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia.. Nature Communications, 12(1) pp. 4507.

Kim, Young Jin, Nomakuchi, Tomoki, Papaleonidopoulou, Foteini , Krainer, Adrian (2021) Gene-Specific Nonsense-Mediated mRNA Decay Targeting for Cystic Fibrosis Therapy. BioRxiv,

Frederiksen, Sabrina B, Holm, Lise L, Larsen, Martin R, Doktor, Thomas K, Andersen, Henriette S, Hastings, Michelle L, Hua, Yimin, Krainer, Adrian R , Andresen, Brage S (2021) Identification of SRSF10 as a regulator of SMN2 ISS-N1. Human Mutation, 42(3) pp. 246-260.

Marasco, Luciano, Dujardin, Gwendal, Sousa-Luís, Rui, Liu, Ying Hsiu, Stigliano, José, Nomakuchi, Tomoki, Proudfoot, Nick, Krainer, Adrian , Kornblihtt, Alberto (2021) Towards a combined therapy for spinal muscular atrophy based on opposing effects of an antisense oligonucleotide on chromatin and splicing. Cell,

Wan, Ledong, Lin, Kuan-Ting, Rahman, Mohammad Alinoor, Wang, Zhikai, Jensen, Mads, Park, Youngkyu, Tuveson, David , Krainer, Adrian (2021) Loss of KRAS G12D feedback regulation involving splicing factor SRSF1 accelerates pancreatic cancer. bioRxiv,

Zhou, Juannan, Wong, Mandy, Chen, Wei-Chia, Krainer, Adrian, Kinney, Justin , McCandlish, David (2020) Empirical variance component regression for sequence-function relationships. BioRxiv,

Ma, Wai Kit, Scharner, Juergen, Costa, Ana SH, Jeong, Hyun Yun, Jackson, Michaela, Rigo, Frank, Bennett, C Frank , Krainer, Adrian R (2020) ASO-basedPKMSplice-switching Therapy Inhibits Hepatocellular Carcinoma Cell Growth. BioRxiv,

Sheng, L., Rigo, F., Bennett, C. F., Krainer, A. R. , Hua, Y. (2020) Comparison of the Efficacy of MOE and PMO Modifications of Systemic Antisense Oligonucleotides in a Severe SMA Mouse Model. Nucleic Acids Research, 6(48) pp. 2853-2865.

Rahman, M. A., Lin, K. T., Bradley, R. K., Abdel-Wahab, O. , Krainer, A. R. (2020) Recurrent SRSF2 mutations in MDS affect both splicing and NMD. Genes Dev, 34(5-6) pp. 413-427.

Sinnakannu, J. R., Lee, K. L., Cheng, S., Li, J., Yu, M., Tan, S. P., Ong, C. C. H., Li, H., Than, H., Anczukow-Camarda, O., Krainer, A. R., Roca, X., Rozen, S. G., Iqbal, J., Yang, H., Chuah, C. , Ong, S. T. (2020) SRSF1 mediates cytokine-induced impaired imatinib sensitivity in chronic myeloid leukemia. Leukemia, 34(7) pp. 1787-1798.

Rahman, M. A., Krainer, A. R. , Abdel-Wahab, O. (2020) SnapShot: Splicing Alterations in Cancer. Cell, 180(1) pp. 208-208.e1.

Li, Jin-Jing, Lin, Xiang, Tang, Cheng, Lu, Ying-Qian, Hu, Xinde, Zuo, Erwei, Li, He, Ying, Wenqin, Sun, Yidi, Lai, Lu-Lu, Chen, Hai-Zhu, Guo, Xin-Xin, Zhang, Qi-Jie, Wu, Shuang, Zhou, Changyang, Shen, Xiaowen, Wang, Qifang, Lin, Min-Ting, Ma, Li-Xiang, Wang, Ning, Krainer, Adrian R, Shi, Linyu, Yang, Hui , Chen, Wan-Jin (2020) Disruption of splicing-regulatory elements using CRISPR/Cas9 to rescue spinal muscular atrophy in human iPSCs and mice. National Science Review, 7(1) pp. 92-101.

Scharner, J., Ma, W. K., Zhang, Q., Lin, K. T., Rigo, F., Bennett, C. F. , Krainer, A. R. (2019) Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides. Nucleic Acids Res, 48(2)

Park, S., Brugiolo, M., Akerman, M., Das, S., Urbanski, L., Geier, A., Kesarwani, A. K., Fan, M., Leclair, N., Lin, K. T., Hu, L., Hua, I., George, J., Muthuswamy, S. K., Krainer, A. R. , Anczukow, O. (2019) Differential Functions of Splicing Factors in Mammary Transformation and Breast Cancer Metastasis. Cell Rep, 29(9) pp. 2672-2688.e7.

Yoshimi, A., Lin, K. T., Wiseman, D. H., Rahman, M. A., Pastore, A., Wang, B., Lee, S. C., Micol, J. B., Zhang, X. J., de Botton, S., Penard-Lacronique, V., Stein, E. M., Cho, H., Miles, R. E., Inoue, D., Albrecht, T. R., Somervaille, T. C. P., Batta, K., Amaral, F., Simeoni, F., Wilks, D. P., Cargo, C., Intlekofer, A. M., Levine, R. L., Dvinge, H., Bradley, R. K., Wagner, E. J., Krainer, A. R. , Abdel-Wahab, O. (2019) Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis. Nature, 574(7777) pp. 273-277.

Bennett, C. F., Krainer, A. R. , Cleveland, D. W. (2019) Antisense Oligonucleotide Therapies for Neurodegenerative Diseases. Annu Rev Neurosci, 42 pp. 385-406.

Feng, H., Bao, S., Rahman, M. A., Weyn-Vanhentenryck, S. M., Khan, A., Wong, J., Shah, A., Flynn, E. D., Krainer, A. R. , Zhang, C. (2019) Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites. Mol Cell, 74(6) pp. 1189-1204.e6.

Lin, K. T. , Krainer, A. R. (2019) PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis. Bioinformatics, 35(23) pp. 5048-5054.

Scharner, J., Qi, S., Rigo, F., Bennett, C. F. , Krainer, A. R. (2019) Delivery of GalNAc-Conjugated Splice-Switching ASOs to Non-hepatic Cells through Ectopic Expression of Asialoglycoprotein Receptor. Mol Ther Nucleic Acids, 16 pp. 313-325.

Wang, E., Lu, S. X., Pastore, A., Chen, X., Imig, J., Chun-Wei Lee, S., Hockemeyer, K., Ghebrechristos, Y. E., Yoshimi, A., Inoue, D., Ki, M., Cho, H., Bitner, L., Kloetgen, A., Lin, K. T., Uehara, T., Owa, T., Tibes, R., Krainer, A. R., Abdel-Wahab, O. , Aifantis, I. (2019) Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Cancer Cell, 35(3) pp. 359-384.e7.

Lu, S. X., Wang, E., Pastore, A., Chen, X. F., Imig, J., Lee, S. C., Ghebrechristos, Y., Yoshimi, A., Bitner, L. E., Ki, M., Kloetgen, A., Lin, K. T., Tibes, R., Krainer, A. R., Uehara, T., Owa, T., Aifantis, I. , Abdel-Wahab, O. I. (2018) Therapeutic Targeting of an RNA Splicing Factor Network for the Treatment of Myeloid Neoplasms. Blood, 132(Supple) pp. Meeting Abstract 427.

Wong, M. S., Kinney, J. B. , Krainer, A. R. (2018) Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites. Mol Cell, 71(6) pp. 1012-1026.e3.

Sinha, R., Kim, Y. J., Nomakuchi, T., Sahashi, K., Hua, Y., Rigo, F., Bennett, C. F. , Krainer, A. R. (2018) Antisense oligonucleotides correct the familial dysautonomia splicing defect in IKBKAP transgenic mice. Nucleic Acids Res, 46(10) pp. 4833-4844.

Aznarez, Isabel, Nomakuchi, Tomoki T., Tetenbaum-Novatt, Jaclyn, Rahman, Mohammad Alinoor, Fregoso, Oliver, Rees, Holly , Krainer, Adrian R. (2018) Mechanism of Nonsense-Mediated mRNA Decay Stimulation by Splicing Factor SRSF1. Cell Reports, 23(7) pp. 2186-2198.

Lin, K. T., Ma, W. K., Scharner, J., Liu, Y. R. , Krainer, A. R. (2018) A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma. Genome Res, 28(3) pp. 275-284.

Sheng, L., Wan, B., Feng, P., Sun, J., Rigo, F., Bennett, C. F., Akerman, M., Krainer, A. R. , Hua, Y. (2018) Downregulation of Survivin contributes to cell-cycle arrest during postnatal cardiac development in a severe spinal muscular atrophy mouse model. Hum Mol Genet, 27(3) pp. 486-498.

Sivaramakrishnan, M., McCarthy, K. D., Campagne, S., Huber, S., Meier, S., Augustin, A., Heckel, T., Meistermann, H., Hug, M. N., Birrer, P., Moursy, A., Khawaja, S., Schmucki, R., Berntenis, N., Giroud, N., Golling, S., Tzouros, M., Banfai, B., Duran-Pacheco, G., Lamerz, J., Hsiu Liu, Y., Luebbers, T., Ratni, H., Ebeling, M., Clery, A., Paushkin, S., Krainer, A. R., Allain, F. H. , Metzger, F. (2017) Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers. Nat Commun, 8(1) pp. 1476.

Munoz, Adriana, Yamrom, Boris, Lee, Yoon-ha, Andrews, Peter, Marks, Steven, Lin, Kuan-Ting, Wang, Zihua, Krainer, Adrian R., Darnell, Robert B., Wigler, Michael , Iossifov, Ivan (2017) De novo indels within introns contribute to ASD incidence. bioRxiv, pp. 137471.

Wu, X., Wang, S. H., Sun, J., Krainer, A. R., Hua, Y. , Prior, T. W. (2017) A-44G transition in SMN2 intron 6 protects patients with spinal muscular atrophy. Hum Mol Genet,

Jangi, M., Fleet, C., Cullen, P., Gupta, S. V., Mekhoubad, S., Chiao, E., Allaire, N., Bennett, C. F., Rigo, F., Krainer, A. R., Hurt, J. A., Carulli, J. P. , Staropoli, J. F. (2017) SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage. Proc Natl Acad Sci U S A, 114(12) pp. E2347-2356.

Doktor, T. K., Hua, Y., Andersen, H. S., Broner, S., Liu, Y. H., Wieckowska, A., Dembic, M., Bruun, G. H., Krainer, A. R. , Andresen, B. S. (2017) RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns. Nucleic Acids Res, 45(1) pp. 395-416.

Allemand, E., Myers, M. P., Garcia-Bernardo, J., Harel-Bellan, A., Krainer, A. R. , Muchardt, C. (2016) A Broad Set of Chromatin Factors Influences Splicing. PLoS Genet, 12(9) pp. e1006318.

Anczukow, O. , Krainer, A. R. (2016) Splicing-factor alterations in cancers. RNA, 22(9) pp. 1285-301.

Bruun, G. H., Doktor, T. K., Borch-Jensen, J., Masuda, A., Krainer, A. R., Ohno, K. , Andresen, B. S. (2016) Global identification of hnRNP A1 binding sites for SSO-based splicing modulation. BMC Biol, 14(1) pp. 54.

Arun, G., Diermeier, S., Akerman, M., Chang, K. C., Wilkinson, J. E., Hearn, S., Kim, Y., MacLeod, A. R., Krainer, A. R., Norton, L., Brogi, E., Egeblad, M. , Spector, D. L. (2016) Differentiation of mammary tumors and reduction in metastasis upon Malat1 LncRNA loss. Cancer Research, 76(Supple)

Nomakuchi, T. T., Rigo, F., Aznarez, I. , Krainer, A. R. (2016) Antisense oligonucleotide-directed inhibition of nonsense-mediated mRNA decay. Nat Biotechnol, 34(2) pp. 164-166.

Anczukow, O. , Krainer, A. R. (2015) The spliceosome, a potential Achilles heel of MYC-driven tumors. Genome Med, 7(1) pp. 107.

Anczukow, O., Akerman, M., Clery, A., Wu, J., Shen, C., Shirole, N. H., Raimer, A., Sun, S., Jensen, M. A., Hua, Y., Allain, F. H. , Krainer, A. R. (2015) SRSF1-Regulated Alternative Splicing in Breast Cancer. Mol Cell, 60(1) pp. 105-17.

Akerman, M., Fregoso, O. I., Das, S., Ruse, C., Jensen, M. A., Pappin, D. J., Zhang, M. Q. , Krainer, A. R. (2015) Differential connectivity of splicing activators and repressors to the human spliceosome. Genome Biol, 16(1) pp. 119.

Krainer, A. R. (2015) Splicing: still so much to learn. RNA, 21(4) pp. 500-1.

Staropoli, John F., Li, Huo, Chun, Seung J., Allaire, Norm, Cullen, Patrick, Thai, Alice, Fleet, Christina M., Hua, Yimin, Bennett, C. Frank, Krainer, Adrian R., Kerr, Doug, McCampbell, Alexander, Rigo, Frank , Carulli, John P. (2015) Rescue of gene-expression changes in an induced mouse model of spinal muscular atrophy by an antisense oligonucleotide that promotes inclusion of SMN2 exon 7. Genomics, 105(4) pp. 220-228.

Hua, Y., Liu, Y. H., Sahashi, K., Rigo, F., Bennett, C. F. , Krainer, A. R. (2015) Motor neuron cell-nonautonomous rescue of spinal muscular atrophy phenotypes in mild and severe transgenic mouse models. Genes Dev, 29(3) pp. 288-297.

Guo, Ya, Xu, Quan, Canzio, Daniele, Shou, Jia, Li, Jinhuan, Gorkin, David U, Jung, Inkyung, Wu, Haiyang, Zhai, Yanan, Tang, Yuanxiao, Lu, Yichao, Wu, Yonghu, Jia, Zhilian, Li, Wei, Zhang, Michael Q, Ren, Bing, Krainer, Adrian R, Maniatis, Tom , Wu, Qiang (2015) CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell, 162(4) pp. 900-910.

Xiong, H. Y., Alipanahi, B., Lee, L. J., Bretschneider, H., Merico, D., Yuen, R. K., Hua, Y., Gueroussov, S., Najafabadi, H. S., Hughes, T. R., Morris, Q., Barash, Y., Krainer, A. R., Jojic, N., Scherer, S. W., Blencowe, B. J. , Frey, B. J. (2014) RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science, 347(6218)

Paz, S., Krainer, A. R. , Caputi, M. (2014) HIV-1 transcription is regulated by splicing factor SRSF1. Nucleic Acids Research, 42(22) pp. 13812-13823.

Chen, Hsu-Hsin, Welling, Maaike, Bloch, Donald B, Muñoz, Javier, Mientjes, Edwin, Chen, Xinjie, Tramp, Cody, Wu, Jie, Yabuuchi, Akiko, Chou, Yu-Fen, Buecker, Christa, Krainer, Adrian, Willemsen, Rob, Heck, Albert J , Geijsen, Niels (2014) DAZL Limits Pluripotency, Differentiation, and Apoptosis in Developing Primordial Germ Cells. Stem Cell Reports, 3(5) pp. 892-904.

Senturk, S., Yao, Z., Camiolo, M., Stiles, B., Rathod, T., Walsh, A. M., Nemajerova, A., Lazzara, M. J., Altorki, N. K., Krainer, A., Moll, U. M., Lowe, S. W., Cartegni, L. , Sordella, R. (2014) p53Psi is a transcriptionally inactive p53 isoform able to reprogram cells toward a metastatic-like state. Proceedings of the National Academy of Sciences of the United States of America, 111(32) pp. E3287-E3296.

Rigo, F., Chun, S. J., Norris, D. A., Hung, G., Lee, S., Matson, J., Fey, R. A., Gaus, H., Hua, Y., Grundy, J. S., Krainer, A. R., Henry, S. P. , Bennett, C. F. (2014) Pharmacology of a central nervous system delivered 2′-O-methoxyethyl- modified survival of motor neuron splicing oligonucleotide in mice and nonhuman primates. Journal of Pharmacology and Experimental Therapeutics, 350(1) pp. 46-55.

Das, S. , Krainer, A. R. (2014) Emerging functions of SRSF1, splicing factor and oncoprotein, in RNA metabolism and cancer. Molecular Cancer Research, 12(9) pp. 1195-1204.

Weyn-Vanhentenryck, Sebastien M., Mele, A., Yan, Q., Sun, S., Farny, N., Zhang, Z., Xue, C., Herre, M., Silver, Pamela A., Zhang, Michael Q., Krainer, Adrian R., Darnell, Robert B. , Zhang, C. (2014) HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism. Cell Reports, 6(6) pp. 1139-1152.

Jensen, M. A., Wilkinson, J. E. , Krainer, A. R. (2014) Splicing factor SRSF6 promotes hyperplasia of sensitized skin. Nature Structural and Molecular Biology, 21 pp. 189-197.

Sahashi, K., Ling, K. K., Hua, Y., Wilkinson, J. E., Nomakuchi, T., Rigo, F., Hung, G., Xu, D., Jiang, Y. P., Lin, R. Z., Ko, C. P., Bennett, C. F. , Krainer, A. R. (2013) Pathological impact of SMN2 mis-splicing in adult SMA mice. EMBO Molecular Medicine, 5(10) pp. 1586-1601.

Cléry, A., Sinha, R., Anczuków, O., Corrionero, A., Moursy, A., Daubner, G. M., Valcárcel, J., Krainer, A. R. , Allain, F. H. T. (2013) Isolated pseudo-RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition. Proceedings of the National Academy of Sciences of the United States of America, 110(30) pp. E2802-E2811.

Fregoso, O. I., Das, S., Akerman, M. , Krainer, A. R. (2013) Splicing-Factor Oncoprotein SRSF1 Stabilizes p53 via RPL5 and Induces Cellular Senescence. Molecular Cell, 50(1) pp. 56-66.

Ben-Hur, V., Denichenko, P., Siegfried, Z., Maimon, A., Krainer, A., Davidson, B. , Karni, R. (2013) S6K1 Alternative Splicing Modulates Its Oncogenic Activity and Regulates mTORC1. Cell Reports, 3(1) pp. 103-115.

Roca, X., Krainer, A. R. , Eperon, I. C. (2013) Pick one, but be quick: 5′ splice sites and the problems of too many choices. Genes and Development, 27(2) pp. 129-144.

Das, S., Fregoso, O. I. , Krainer, A. R. (2013) A new path to oncogene-induced senescence: At the cross-roads of splicing and translation. Cell Cycle, 12(10)

Wu, J., Anczukow, O., Krainer, A. R., Zhang, M. Q. , Zhang, C. (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Research, 41(10) pp. 5149-5163.

Krainer, A. (2012) Pre-mRNA Splicing Mechanisms, Misregulation in Disease, and Therapeutic Strategies. Blood, 120(21)

Rigo, F., Hua, Y. M., Krainer, A. R. , Bennett, C. F. (2012) Antisense-based therapy for the treatment of spinal muscular atrophy. Journal of Cell Biology, 199(1) pp. 21-25.

Wang, Z., Jeon, H. Y., Rigo, F., Bennett, C. F. , Krainer, A. R. (2012) Manipulation of PK-M mutually exclusive alternative splicing by antisense oligonucleotides. Open Biol, 2(10) pp. 120133.

Sahashi, K., Hua, Y., Ling, K. K., Hung, G., Rigo, F., Horev, G., Katsuno, M., Sobue, G., Ko, C. P., Bennett, C. F. , Krainer, A. R. (2012) TSUNAMI: an antisense method to phenocopy splicing-associated diseases in animals. Genes Dev, 26(16) pp. 1874-84.

Beaulieu, C. L., Samuels, M. E., Ekins, S., McMaster, C. R., Edwards, A. M., Krainer, A. R., Hicks, G. G., Frey, B. J., Boycott, K. M. , Mackenzie, A. E. (2012) A generalizable pre-clinical research approach for orphan disease therapy. Orphanet J Rare Dis, 7 pp. 1750-1172.

Rigo, F., Hua, Y. M., Chun, S. J., Prakash, T. P., Krainer, A. R. , Bennett, C. F. (2012) Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing. Nature Chemical Biology, 8(6) pp. 555-561.

Roca, X., Akerman, M., Gaus, H., Berdeja, A., Bennett, C. F. , Krainer, A. R. (2012) Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides. Genes & Development, 26(10) pp. 1098-109.

Kole, R., Krainer, A. R. , Altman, S. (2012) RNA therapeutics: Beyond RNA interference and antisense oligonucleotides. Nature Reviews Drug Discovery, 11(2) pp. 125-140.

Sun, S. Y., Zhang, Z., Fregoso, O. , Krainer, A. R. (2012) Mechanisms of activation and repression by the alternative splicing factors RBFOX1/2. RNA, 18(2) pp. 274-283.

Anczukow, O., Rosenberg, A. Z., Akerman, M., Das, S., Zhan, L., Karni, R., Muthuswamy, S. K. , Krainer, A. R. (2012) The splicing factor SRSF1 regulates apoptosis and proliferation to promote mammary epithelial cell transformation. Nature Structural Molecular Biology, 19(2) pp. 220-228.

Das, S., Anczuków, O., Akerman, M. , Krainer, A. R (2012) Oncogenic Splicing Factor SRSF1 Is a Critical Transcriptional Target of MYC. Cell Reports, 1(2) pp. 110-117.

Hua, Y. , Krainer, A. R. (2012) Antisense-mediated exon inclusion. Methods Mol Biol, 867 pp. 307-323.

Wang, Z. X., Chatterjee, D., Jeon, H. Y., Akerman, M., Vander Heiden, M. G., Cantley, L. C. , Krainer, A. R. (2012) Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons. Journal of Molecular Cell Biology, 4(2) pp. 79-87.

Wu, J., Akerman, M., Sun, S., McCombie, W. R., Krainer, A. R. , Zhang, M. Q. (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27(21) pp. 3010-3016 .

Hua, Y., Sahashi, K., Rigo, F., Hung, G., Horev, G., Bennett, C. F. , Krainer, A. R. (2011) Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model. Nature, 478(7367) pp. 123-6.

Krainer, A. R., Hua, Y. M., Sahashi, K., Rigo, F., Hung, G. N., Horev, G. , Bennett, C. F. (2011) Systemic Versus CNS Delivery Of MOE Antisense Oligonucleotide to Correct Defective Splicing in a Severe Mouse Model of Spinal Muscular Atrophy. Nucleic Acid Therapeutics, 21(5) pp. A57-A57.

Rigo, F., Hua, Y. M., Chun, S. J., Krainer, A. R. , Bennett, C. F. (2011) Modulation of Gene Expression By Oligonucleotide Chemistry-Dependent Recruitment of Proteins to RNA Transcripts. Nucleic Acid Therapeutics, 21(5) pp. A53-A54.

Kubota, T., Roca, X., Kimura, T., Kokunai, Y., Nishino, I., Sakoda, S., Krainer, A. R. , Takahashi, M. P. (2011) A mutation in a rare type of intron in a sodium-channel gene results in aberrant splicing and causes myotonia. Human Mutation, 32(7) pp. 773-782.

Krainer, A. R. (2011) Oligonucleotide therapeutics for correcting defective RNA splicing. FEBS Journal, 278(Issue ) pp. 11-11.

Cho, S. Y., Hoang, A., Sinha, R., Zhong, X. Y., Fu, X. D., Krainer, A. R. , Ghosh, G. (2011) Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assembly. Proceedings of the National Academy of Sciences of the United States of America, 108(20) pp. 8233-8238.

Passini, M. A., Bu, J., Richards, A. M., Kinnecom, C., Sardi, S. P., Stanek, L. M., Hua,  Y., Rigo, F., Matson, J., Hung, G., Kaye, E. M., Shihabuddin, L. S., Krainer, A. R., Bennett, C. F. , Cheng, S. H. (2011) Antisense oligonucleotides delivered to the mouse CNS ameliorate symptoms of severe spinal muscular atrophy. Science Translational Medicine, 3(72)

Thorsen, K., Mansilla, F., Schepeler, T., Oster, B., Rasmussen, M. H., Dyrskjot, L., Karni, R., Akerman, M., Krainer, A. R., Laurberg, S., Andersen, C. L. , Orntoft, T. F. (2011) Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Molecular and Cellular Proteomics, 10(1)

Hua, Y., Sahashi, K., Hung, G., Rigo, F., Passini, M. A., Bennett, C. F. , Krainer, A. R. (2010) Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model. Genes and Development, 24(15) pp. 1634-44.

Wu, H., Sun, S., Tu, K., Gao, Y., Xie, B., Krainer, A. R. , Zhu, J. (2010) A Splicing-Independent Function of SF2/ASF in MicroRNA Processing. Molecular Cell, 38(1) pp. 67-77.

Sinha, R., Allemand, E., Zhang, Z., Karni, R., Myers, M. P. , Krainer, A. R. (2010) Arginine Methylation Controls the Subcellular Localization and Functions of the Oncoprotein Splicing Factor SF2/ASF. Molecular and Cellular Biology, 30(11) pp. 2762-2774.

Sun, S., Zhang, Z., Sinha, R., Karni, R. , Krainer, A. R. (2010) SF2/ASF autoregulation involves multiple layers of post-transcriptional and translational control. Nat Struct Mol Biol, 17(3) pp. 306-12.

Clower, C. V., Chatterjee, D., Wang, Z. X., Cantley, L. C., Heiden, M. G. V. , Krainer, A. R. (2010) The alternative splicing repressors hnRNP A1/A2 and PTB influence pyruvate kinase isoform expression and cell metabolism. Proceedings of the National Academy of Sciences of the United States of America, 107(5) pp. 1894-1899.

Manley, J. L. , Krainer, A. R. (2010) A rational nomenclature for serine/arginine-rich protein splicing factors (SR proteins). Genes and Development, 24(11) pp. 1073-1074.

Hastings, M. L., Berniac, J., Liu, Y. H., Abato, P., Jodelka, F. M., Barthel, L., Kumar, S., Dudley, C., Nelson, M., Larson, K., Edmonds, J., Bowser, T., Draper, M., Higgins, P. , Krainer, A. R. (2009) Tetracyclines That Promote SMN2 Exon 7 Splicing as Therapeutics for Spinal Muscular Atrophy. Science Translational Medicine, 1(5)

Okunola, H. L. , Krainer, A. R. (2009) Cooperative-binding and splicing-repressive properties of hnRNP A1. Mol Cell Biol, 29(20) pp. 5620-5631.

Prior, T. W., Krainer, A. R., Hua, Y., Swoboda, K. J., Snyder, P. C., Bridgeman, S. J., Burghes, A. H. M. , Kissel, J. T. (2009) A Positive Modifier of Spinal Muscular Atrophy in the SMN2 Gene. The American Journal of Human Genetics, 85(3) pp. 408-413.

De Araújo, M. M., Bonnal, S., Hastings, M. L., Krainer, A. R. , Valcárcel, J. (2009) Differential 3′ splice site recognition of SMN1 and SMN2 transcripts by U2AF and U2 snRNP. RNA, 15(4) pp. 515-523.

Khoo, B. , Krainer, A. R. (2009) Splicing therapeutics in SMN2 and APOB. Current Opinion in Molecular Therapeutics, 11(2) pp. 108-115.

Roca, X. , Krainer, A. R. (2009) A splicing component adapted to gene silencing. Nat Biotechnol, 27(3) pp. 250-1.

Roca, X. , Krainer, A. R. (2009) Recognition of atypical 5' splice sites by shifted base-pairing to U1 snRNA. Nat Struct Mol Biol, 16(2) pp. 176-182.

Karni, R., Hippo, Y., Lowe, S. W. , Krainer, A. R. (2008) The splicing-factor oncoprotein SF2/ASF activates mTORC1. Proc Natl Acad Sci U S A, 105(40) pp. 15323-7.

Zhang, C., Zhang, Z., Castle, J., Sun, S., Johnson, J., Krainer, A. R. , Zhang, M. Q. (2008) Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev, 22(18) pp. 2550-63.

Thorsen, K., Sorensen, K. D., Brems-Eskildsen, A. S., Modin, C., Gaustadnes, M., Hein, A. M. K., Kruhoffer, M., Laurberg, S., Borre, M., Wang, K., Brunak, S., Krainer, A. R., Torring, N., Dyrskjot, L., Andersen, C. L. , Orntoft, T. F. (2008) Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Molecular & Cellular Proteomics, 7(7) pp. 1214-1224.

Steitz, J. A., Dreyfuss, G., Krainer, A. R., Lamond, A. I., Matera, A. G. , Padgett, R. A. (2008) Where in the cell is the minor spliceosome?. Proc Natl Acad Sci U S A, 105(25) pp. 8485-6.

Zhang, C., Li, W. H., Krainer, A. R. , Zhang, M. Q. (2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A, 105(15) pp. 5797-5802 .

Hua, Y., Vickers, T. A., Okunola, H. L., Bennett, C. F. , Krainer, A. R. (2008) Antisense Masking of an hnRNP A1/A2 Intronic Splicing Silencer Corrects SMN2 Splicing in Transgenic Mice. Am J Hum Genet, 82(4) pp. 834-48.

Majerciak, V., Yamanegi, K., Allemand, E., Kruhlak, M., Krainer, A. R. , Zheng, Z. M. (2008) Kaposi sarcoma-associated herpesvirus ORF57 functions as a viral splicing factor and promotes the expression of intron-containing viral lytic genes in spliceosome-mediated RNA splicing. J Virol, 82(6) pp. 2792-2801.

Chen, G., Li, W., Zhang, Q. S., Regulski, M. R., Sinha, N., Barditch, J., Tully, T., Krainer, A. R., Zhang, M. Q. , Dubnau, J. T. (2008) Identification of Synaptic Targets of Drosophila Pumilio. PLoS Computational Biology, 4(2) pp. e1000026.

Roca, X., Olson, A. J., Rao, A. R., Enerly, E., Kristensen, V. N., Borresen-Dale, A. L., Andresen, B. S., Krainer, A. R. , Sachidanandam, R. (2008) Features of 5'-splice-site efficiency derived from disease-causing mutations and comparative genomics. Genome Res, 18(1) pp. 77-87.

Zhang, C., Krainer, A. R. , Zhang, M. Q. (2007) Evolutionary impact of limited splicing fidelity in mammalian genes. Trends Genet, 23(10) pp. 484-488.

Zhang, C. L., Hastings, M. L., Krainer, A. R. , Zhang, M. Q. (2007) Dual-specificity splice sites function alternatively as 5 ' and 3 ' splice sites. Proceedings of the National Academy of Sciences of the United States of America, 104(38) pp. 15028-15033.

Caceres, J. F., Krainer, A. R. , Kornblihtt, A. R. (2007) The pathology of pre-mRNA splicing: a meeting in the Italian Alps - Workshop on pre-mRNA processing and disease. Embo Reports, 8(8) pp. 730-734.

Zhang, Z. , Krainer, A. R. (2007) Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components. Proc Natl Acad Sci U S A, 104(28) pp. 11574-9.

Allemand, E., Hastings, M. L., Murray, M. V., Myers, M. P. , Krainer, A. R. (2007) Alternative splicing regulation by interaction of phosphatase PP2Cgamma with nucleic acid-binding protein YB-1. Nat Struct Mol Biol, 14(7) pp. 630-638.

Hastings, M. L., Allemand, E., Duelli, D. M., Myers, M. P. , Krainer, A. R. (2007) Control of Pre-mRNA Splicing by the General Splicing Factors PUF60 and U2AF65. PLoS ONE, 2(6) pp. e538.

Buratti, E., Chivers, M., Královičová, J., Romano, M., Baralle, M., Krainer, Adrian R. , Vořechovský, I. (2007) Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res, 35(13) pp. 4250-4263.

Das, R., Yu, J., Zhang, Z., Gygi, M. P., Krainer, A. R., Gygi, S. P. , Reed, R. (2007) SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Molecular Cell, 26(6) pp. 867-881.

Wimmer, K., Roca, X., Beiglbock, H., Callens, T., Etzler, J., Rao, A. R., Krainer, A. R., Fonatsch, C. , Messiaen, L. (2007) Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5 ' splice-site disruption. Human Mutation, 28(6) pp. 599-612.

Hua, Y. M., Vickers, T. A., Baker, B. F., Bennett, C. F. , Krainer, A. R. (2007) Enhancement of SMN2 Exon 7 inclusion by antisense oligonucleotides targeting the exon. PLoS Biology, 5(4) pp. e73.

Karni, R., de Stanchina, E., Lowe, S. W., Sinha, R., Mu, D. , Krainer, A. R. (2007) The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nat Struct Mol Biol, 14(3) pp. 185-93.

Nielsen, K. B., Sorensen, S., Cartegni, L., Corydon, T. J., Doktor, T. K., Schroeder, L. D., Reinert, L. S., Elpeleg, O., Krainer, A. R., Gregersen, N., Kjems, J. , Andresen, B. S. (2007) Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: A synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. American Journal of Human Genetics, 80(3) pp. 416-432.

Khoo, B., Roca, X., Chew, S. L. , Krainer, A. R. (2007) Antisense oligonucleotide-induced alternative splicing of the APOB mRNA generates a novel isoform of APOB. BMC Molecular Biology, 8

Shaw, S. D., Chakrabarti, S., Ghosh, G. , Krainer, A. R. (2007) Deletion of the N-terminus of SF2/ASF permits RS-domain-independent pre-mRNA splicing. PLoS ONE, 2(9) pp. e854.

Smith, P. J., Zhang, C., Wang, J., Chew, S. L., Zhang, M. Q. , Krainer, A. R. (2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet, 15(16) pp. 2490-508.

Zhang, Q. S., Manche, L., Xu, R. M. , Krainer, A. R. (2006) hnRNP A1 associates with telomere ends and stimulates telomerase activity. RNA, 12(6) pp. 1116-28.

Krainer, A. R. , Karni, R. (2006) Oncogenic activity of alternative splicing factors. Faseb Journal, 20(4) pp. A456-A456.

Cartegni, L., Hastings, M. L., Calarco, J. A., de Stanchina, E. , Krainer, A. R. (2006) Determinants of exon 7 splicing in the spinal muscular atrophy genes, SMN1 and SMN2. Am J Hum Genet, 78(1) pp. 63-77.

Kimura, H., Takizawa, N., Allemand, E., Hori, T., Iborra, F. J., Nozaki, N., Muraki, M., Hagiwara, M., Krainer, A. R., Fukagawa, T. , Okawa, K. (2006) A novel histone exchange factor, protein phosphatase 2Cgamma, mediates the exchange and dephosphorylation of H2A-H2B.. Journal of Cell Biology, 175(3) pp. 389-400.

Madsen, P. P., Kibæk, M., Roca, X., Sachidanandam, R., Krainer, A. R., Christensen, E., Steiner, R. D., Gibson, K. M., Corydon, T. J., Knudsen, I., Wanders, R. J. A., Ruiter, J. P. N., Gregersen, N. , Andresen, B. S. (2006) Short/branched-chain acyl-CoA dehydrogenase deficiency due to an IVS3+3A>G mutation that causes exon skipping. Human Genetics, 118(6) pp. 680-690.

Sheth, N., Roca, X., Hastings, M. L., Roeder, T., Krainer, A. R. , Sachidanandam, R. (2006) Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res, 34(14) pp. 3955-3967.

Tyson-Capper, A. J., Bailey, J., Krainer, A. R., Robson, S. C. , Europe-Finner, G. N. (2005) The switch in alternative splicing of cyclic AMP-response element modulator protein CREM tau(2)alpha (activator) to CREM alpha (repressor) in human myometrial cells is mediated by SRp40. Journal of Biological Chemistry, 280(41) pp. 34521-34529.

Roca, Xavier, Sachidanandam, Ravi , Krainer, Adrian R. (2005) Determinants of the inherent strength of human 5' splice sites. Rna, 11(5) pp. 683-98.

Allemand, E., Guil, S., Myers, M., Moscat, J., Caceres, J. F. , Krainer, A. R. (2005) Regulation of heterogenous nuclear ribonucleoprotein A1 transport by phosphorylation in cells stressed by osmotic shock. Proc Natl Acad Sci U S A, 102(10) pp. 3605-10.

Hastings, M. L., Resta, N., Traum, D., Stella, A., Guanti, G. , Krainer, A. R. (2005) An LKB1 AT-AC intron mutation causes Peutz-Jeghers syndrome via splicing at noncanonical cryptic splice sites. Nat Struct Mol Biol, 12(1) pp. 54-9.

Coutinho, G., Xie, J. Y., Du, L. T., Brusco, A., Krainer, A. R. , Gatti, R. A. (2005) Functional significance of deep intronic mutation in the ATM gene and evidence for an alternative Exon 28a. Human Mutation, 25(2) pp. 118-124.

Wang, J., Smith, P. J., Krainer, A. R. , Zhang, M. Q. (2005) Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res, 33(16) pp. 5053-62.

Zhang, Z. , Krainer, A. R. (2004) Involvement of SR proteins in mRNA surveillance. Molecular Cell, 16(4) pp. 597-607.

Muraki, M., Ohkawara, B., Hosoya, T., Onogi, H., Koizumi, J., Koizumi, T., Sumi, K., Jun-ichiro, Y., Murray, M. V., Kimura, H., Furuichi, K., Shibuya, H., Krainer, A. R., Suzuki, M. , Hagiwara, M. (2004) Manipulation of alternative splicing by a newly developed inhibitor of Clks. Journal of Biological Chemistry, 279(23) pp. 24246-24254.

Muraki, M., Ohkawara, B., Hosoya, T., Onogi, H., Koizumi, J., Koizumi, T., Sumi, K., Yomoda, J., Murray, M. V., Kimura, H., Furuichi, K., Shibuya, H., Krainer, A. R., Suzuki, M. , Hagiwara, M. (2004) Manipulation of alternative splicing by a novel inhibitor of Clks. Journal of Pharmacological Sciences, 94(S(1)) pp. 244P-244P.

Zatkova, A., Messiaen, L., Vandenbroucke, I., Wieser, R., Fonatsch, C., Krainer, A. R. , Wimmer, K. (2004) Disruption of exonic splicing enhancer elements is the principal cause of exon skipping associated with seven nonsense or missense alleles of NF1. Human Mutation, 24(6) pp. 491-501.

Domsic, J. K., Wang, Y. B., Mayeda, A., Krainer, A. R. , Stoltzfus, C. M. (2003) Human immunodeficiency virus type 1 hnRNP A/B-Dep endent exonic splicing silencer ESSV antagonizes binding of U2AF65 to viral polypyrimidine tracts. Molecular and Cellular Biology, 23(23) pp. 8762-8772.

Roca, X., Sachidanandam, R. , Krainer, A. R. (2003) Intrinsic differences between authentic and cryptic 5 ' splice sites. Nucleic Acids Research, 31(21) pp. 6321-6333.

Cartegni, L., Wang, J. H., Zhu, Z. W., Zhang, M. Q. , Krainer, A. R. (2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Research, 31(13) pp. 3568-3571.

Cartegni, L. , Krainer, A. R. (2003) Correction of disease-associated exon skipping by synthetic exon-specific activators. Nature Structural Biology, 10(2) pp. 120-125.

Hou, V. C., Lersch, R., Gee, S. L., Ponthier, J. L., Lo, A. J., Wu, M., Turck, C. W., Koury, M., Krainer, A. R., Mayeda, A. , Conboy, J. G. (2002) Decrease in hnRNP A/B expression during erythropoiesis mediates a pre-mRNA splicing switch. Embo Journal, 21(22) pp. 6195-6204.

Andresen, B. S., Nielsen, K. B., Madsen, P. P., Corydon, T. J., Kjems, J., Krainer, A. R., Elpeleg, O. N., Schroeder, L. D. , Gregersen, N. (2002) Simple mutations in the coding region of three acyl-CoA dehydrogenase genes may lead to skipping of the constitutive exon due to disruption of potential splice enhancer sequences or mRNA secondary structures. American Journal of Human Genetics, 71(4) pp. 196-196.

Cazalla, D., Zhu, J., Manche, L., Huber, E., Krainer, A. R. , Caceres, J. F. (2002) Nuclear export and retention signals in the RS domain of SR proteins. Molecular and Cellular Biology, 22(19) pp. 6871-6882.

Fackenthal, J. D., Cartegni, L., Krainer, A. R. , Olopade, O. I. (2002) BRCA2 T2722R is a deleterious allele that causes exon skipping. American Journal of Human Genetics, 71(3) pp. 625-631.

Pollard, A. J., Krainer, A. R., Robson, S. C. , Europe-Finner, G. N. (2002) Alternative splicing of the adenylyl cyclase stimulatory G-protein G alpha(s) is regulated by SF2/ASF and heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) and involves the use of an unusual TG 3'-splice Site. Journal of Biological Chemistry, 277(18) pp. 15241-51.

Cartegni, L., Chew, S. L. , Krainer, A. R. (2002) Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nature Reviews Genetics, 3(4) pp. 285-298.

Cartegni, L. , Krainer, A. R. (2002) Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nature Genetics, 30(4) pp. 377-384.

Dance, G. S. C., Sowden, M. P., Cartegni, L., Cooper, E., Krainer, A. R. , Smith, H. C. (2002) Two proteins essential for apolipoprotein B mRNA editing are expressed from a single gene through alternative splicing. Journal of Biological Chemistry, 277(15) pp. 12703-12709.

Vitali, J., Ding, J. Z., Jiang, J. Z., Zhang, Y., Krainer, A. R. , Xu, R. M. (2002) Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1. Nucleic Acids Research, 30(7) pp. 1531-1538.

Smith, P. J., Spurrell, E. L., Coakley, J., Hinds, C. J., Ross, R. J. M., Krainer, A. R. , Chew, S. L. (2002) An exonic splicing enhancer in human IGF-I pre-mRNA mediates recognition of alternative exon 5 by the serine-arginine protein splicing factor-2/alternative splicing factor. Endocrinology, 143(1) pp. 146-154.

Zhu, J., Mayeda, A. , Krainer, A. R. (2001) Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. Molecular Cell, 8(6) pp. 1351-1361.

Hou, V. C., Gee, S. L., Wu, M., Turck, C. W., Koury, M., Krainer, A. R., Mayeda, A. , Conboy, J. G. (2001) Characterization of a second hnRNP A/B-dependent exonic splicing silencer in protein 4.1R exon 16. Blood, 98(11) pp. 436A-436A.

Bilodeau, P. S., Domsic, J. K., Mayeda, A., Krainer, A. R. , Stoltzfus, C. M. (2001) RNA splicing at human immunodeficiency virus type 1 3 ' splice site A2 is regulated by binding of hnRNP A/B proteins to an exonic splicing silencer element. Journal of Virology, 75(18) pp. 8487-8497.

Hastings, M. L. , Krainer, A. R. (2001) Pre-mRNA splicing in the new millennium. Current Opinion in Cell Biology, 13(3) pp. 302-309.

Hastings, M. L. , Krainer, A. R. (2001) Functions of SR proteins in the U12-dependent AT-AC pre-mRNA splicing pathway. RNA, 7(3) pp. 471-482.

Nilsson, C. E., Petersen-Mahrt, S., Durot, C., Shtrichman, R., Krainer, A. R., Kleinberger, T. , Akusjarvi, G. (2001) The adenovirus E4-ORF4 splicing enhancer protein interacts with a subset of phosphorylated SR proteins. EMBO Journal, 20(4) pp. 864-871.

Liu, H. X., Cartegni, L., Zhang, M. Q. , Krainer, A. R. (2001) A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nature Genetics, 27(1) pp. 55-58.

Zhu, J. , Krainer, A. R. (2000) Pre-mRNA splicing in the absence of an SR protein RS domain. Genes & Development, 14(24) pp. 3166-3178.

Eperon, I. C., Makarova, O. V., Mayeda, A., Munroe, S. H., Caceres, J. F., Hayward, D. G. , Krainer, A. R. (2000) Selection of alternative 5 ' splice sites: Role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1. Molecular and Cellular Biology, 20(22) pp. 8303-8318.

Dirksen, W. P., Li, X. L., Mayeda, A., Krainer, A. R. , Rottman, F. M. (2000) Mapping the SF2/ASF binding sites in the bovine growth hormone exonic splicing enhancer. Journal of Biological Chemistry, 275(37) pp. 29170-29177.

Van Scoy, S., Watakabe, I., Krainer, A. R. , Hearing, J. (2000) Human p32: A coactivator for Epstein-Barr virus nuclear antigen-1-mediated transcriptional activation and possible role in viral latent cycle DNA replication. Virology, 275(1) pp. 145-157.

Boudrez, A., Beullens, M., Groenen, P., Van Eynde, A., Vulsteke, V., Jagiello, I., Murray, M., Krainer, A. R., Stalmans, W. , Bollen, M. (2000) NIPP1-mediated interaction of protein phosphatase-1 with CDC5L, a regulator of pre-mRNA splicing and mitotic entry. Journal of Biological Chemistry, 275(33) pp. 25411-25417.

Pollard, A. J., Sparey, C., Robson, S. C., Krainer, A. R. , Europe-Finner, G. N. (2000) Spatio-temporal expression of the trans-acting splicing factors SF2/ASF and heterogeneous ribonuclear proteins A1/A1(B) in the myometrium of the pregnant human uterus: A molecular mechanism for regulating regional protein isoform expression in vivo. Journal of Clinical Endocrinology & Metabolism, 85(5) pp. 1928-1936.

van Oordt, W. V., Diaz-Meco, M. T., Lozano, J., Krainer, A. R., Moscat, J. , Caceres, J. F. (2000) The MKK3/6-p38-signaling cascade alters the subcellular distribution of hnRNP A1 and modulates alternative splicing regulation. Journal of Cell Biology, 149(2) pp. 307-316.

Liu, H. X., Chew, S. L., Cartegni, L., Zhang, M. Q. , Krainer, A. R. (2000) Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. Molecular and Cellular Biology, 20(3) pp. 1063-1071.

Burns, C. G., Ohi, R., Krainer, A. R. , Gould, K. L. (1999) Evidence that Myb-related CDC5 proteins are required for pre-mRNA splicing. Proceedings of the National Academy of Sciences of the United States of America, 96(24) pp. 13789-13794.

Chew, S. L., Liu, H. X., Mayeda, A. , Krainer, A. R. (1999) Evidence for the function of an exonic splicing enhancer after the first catalytic step of pre-mRNA splicing. Proceedings of the National Academy of Sciences of the United States of America, 96(19) pp. 10655-10660.

Mayeda, A., Badolato, J., Kobayashi, R., Zhang, M. Q., Gardiner, E. M. , Krainer, A. R. (1999) Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. EMBO Journal, 18(16) pp. 4560-4570.

Caputi, M., Mayeda, A., Krainer, A. R. , Zahler, A. M. (1999) hnRNP A/B proteins are required for inhibition of HIV-1 pre-mRNA splicing. EMBO Journal, 18(14) pp. 4060-4067.

Ismaili, N., Perez-Morga, D., Walsh, P., Mayeda, A., Pays, A., Tebabi, P., Krainer, A. R. , Pays, E. (1999) Characterization of a SR protein from Trypanosoma brucei with homology to RNA-binding cis-splicing proteins. Molecular and Biochemical Parasitology, 102(1) pp. 103-115.

Ding, J. Z., Hayashi, M. K., Zhang, Y., Manche, L., Krainer, A. R. , Xu, R. M. (1999) Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes & Development, 13(9) pp. 1102-1115.

Wu, Q. , Krainer, A. R. (1999) AT-AC Pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes. Molecular and Cellular Biology, 19(5) pp. 3225-3236.

Koizumi, J., Okamoto, Y., Onogi, H., Mayeda, A., Krainer, A. R. , Hagiwara, M. (1999) The subcellular localization of SF2/ASF is regulated by direct interaction with SR protein kinases (SRPKs). Journal of Biological Chemistry, 274(16) pp. 11125-11131.

Lopato, S., Kalyna, M., Dorner, S., Kobayashi, R., Krainer, A. R. , Barta, A. (1999) atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes. Genes & Development, 13(8) pp. 987-1001.

Jiang, J., Zhang, Y., Krainer, A. R. , Xu, R. M. (1999) Crystal structure of human p32, a doughnut-shaped acidic mitochondrial matrix protein. Proceedings of the National Academy of Sciences of the United States of America, 96(7) pp. 3572-7.

Mayeda, A., Screaton, G. R., Chandler, S. D., Fu, X. D. , Krainer, A. R. (1999) Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements. Molecular and Cellular Biology, 19(3) pp. 1853-1863.

Murray, M. V., Kobayashi, R. , Krainer, A. R. (1999) The type 2C Ser/Thr phosphatase PP2C gamma is a pre-mRNA splicing factor. Genes & Development, 13(1) pp. 87-97.

Mayeda, A. , Krainer, A. R. (1999) Mammalian in vitro splicing assays. Methods in Molecular Biology, 118 pp. 315-21.

Mayeda, A. , Krainer, A. R. (1999) Preparation of HeLa cell nuclear and cytosolic S100 extracts for in vitro splicing. Methods in Molecular Biology, 118 pp. 309-14.

Wu, Q. , Krainer, A. R. (1998) Purine-rich enhancers function in the AT-AC pre-mRNA splicing pathway and do so independently of intact U1 snRNP. RNA, 4(12) pp. 1664-1673.

Mayeda, A., Munroe, S. H., Xu, R. M. , Krainer, A. R. (1998) Distinct functions of the closely related tandem RNA-recognition motifs of hnRNP A1. RNA, 4(9) pp. 1111-1123.

Liu, H. X., Zhang, M. , Krainer, A. R. (1998) Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes & Development, 12(13) pp. 1998-2012.

Hanamura, A., Caceres, J. F., Mayeda, A., Franza, B. R. , Krainer, A. R. (1998) Regulated tissue-specific expression of antagonistic pre-mRNA splicing factors. RNA, 4(4) pp. 430-444.

Caceres, J. F., Screaton, G. R. , Krainer, A. R. (1998) A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. Genes & Development, 12(1) pp. 55-66.

Misteli, T., Cáceres, J. F., Clement, J. Q., Krainer, A. R., Wilkinson, M. F. , Spector, D. L. (1998) Serine phosphorylation of SR proteins is required for their recruitment to sites of transcription in vivo. Journal of Cell Biology, 143(2) pp. 297-307.

Horowitz, D. S., Kobayashi, R. , Krainer, A. R. (1997) A new cyclophilin and the human homologues of yeast Prp3 and Prp4 form a complex associated with U4/U6 snRNPs. Rna-a Publication of the Rna Society, 3(12) pp. 1374-1387.

Misteli, T., Cáceres, J. F., Krainer, A. R. , Spector, D. L. (1997) The control of splicing factor recruitment to sites of transcription in-vivo. Molecular Biology of the Cell, 8 pp. 597-597.

Jokhan, L., Dong, A. P., Mayeda, A., Krainer, A. R. , Xu, R. M. (1997) Crystallization and preliminary X-ray diffraction studies of UP1, the two-RRM domain of hnRNP A1. Acta Crystallographica Section D-Biological Crystallography, 53 pp. 615-618.

Cáceres, J. F., Misteli, T., Screaton, G. R., Spector, D. L. , Krainer, A. R. (1997) Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity. Journal of Cell Biology, 138(2) pp. 225-38.

Wu, Q. , Krainer, A. R. (1997) Splicing of a divergent subclass of AT-AC introns requires the major spliceosomal snRNAs. RNA, 3(6) pp. 586-601.

Xu, R. M., Jokhan, L., Cheng, X., Mayeda, A. , Krainer, A. R. (1997) Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs. Structure, 5(4) pp. 559-70.

Chandler, S. D., Mayeda, A., Yeakley, J. M., Krainer, A. R. , Fu, X. D. (1997) RNA splicing specificity determined by the coordinated action of RNA recognition motifs in SR proteins. Proceedings of the National Academy of Sciences of the United States of America, 94(8) pp. 3596-3601.

Basu, A., Dong, B., Krainer, A. R. , Howe, C. C. (1997) The intracisternal A-particle proximal enhancer-binding protein activates transcription and is identical to the RNA- and DNA-binding protein p54nrb/NonO. Molecular and Cellular Biology, 17(2) pp. 677-86.

Horowitz, D. S. , Krainer, A. R. (1997) A human protein required for the second step of pre-mRNA splicing is functionally related to a yeast splicing factor. Genes & Development, 11(1) pp. 139-151.

Huang, S., Mayeda, A., Krainer, A. R. , Spector, D. L. (1997) RCC1 and nuclear organization. Molecular Biology of the Cell, 8(6) pp. 1143-1157.

Tseng, T. I. , Krainer, A. R. (1996) Defining and characterizing the functions of RS domains in yeast. Molecular Biology of the Cell, 7 pp. 3661-3661.

Wu, Q. , Krainer, A. R. (1996) U1-mediated exon definition interactions between AT-AC and GT-AG introns. Science, 274(5289) pp. 1005-1008.

Lopato, S., Mayeda, A., Krainer, A. R. , Barta, A. (1996) Pre-mRNA splicing in plants: Characterization of Ser Arg splicing factors. Proceedings of the National Academy of Sciences of the United States of America, 93(7) pp. 3074-3079.

Screaton, G. R., Caceres, J. F., Mayeda, A., Bell, M. V., Plebanski, M., Jackson, D. G., Bell, J. I. , Krainer, A. R. (1995) Identification and characterization of three members of the human SR family of pre-mRNA splicing factors.. EMBO Journal, 14(17) pp. 4336-4349.

Mayeda, A., Munroe, S. H., Caceres, J. F. , Krainer, A. R. (1994) Function of conserved domains of hnRNP A1 and other hnRNP A/B proteins.. EMBO Journal, 13(22) pp. 5483-5495.

Caceres, J. F., Stamm, S., Helfman, D. M. , Krainer, A. R. (1994) Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science, 265(5179) pp. 1706-9.

Horowitz, D. S. , Krainer, A. R. (1994) Mechanisms for selecting 5' splice sites in mammalian pre-mRNA splicing. Trends in Genetics, 10(3) pp. 100-106.

Monroe, S. H., Mayeda, A. , Krainer, A. R. (1994) Role of hnRNP A1 structural domains in messenger-RNA splicing and RNA-RNA annealing. Journal of Cellular Biochemistry, pp. 116-116.

Huang, M., Rech, J. E., Northington, S. J., Flicker, P. F., Mayeda, A., Krainer, A. R. , Lestourgeon, W. M. (1994) The C-protein tetramer binds 230 to 240 nucleotides of pre-mRNA and nucleates the assembly of 40S heterogeneous nuclear ribonucleoprotein particles.. Molecular and Cellular Biology, 14(1) pp. 518-533.

Stamm, S., Mulligan, G. J., Krainer, A. R. , Helfman, D. M. (1994) Non-radioactive detection of m3G capped RNAs by immunoblotting. Nucleic Acids Research, 22(2) pp. 252-253.

O'Keefe, R. T., Mayeda, A., Sadowski, C. L., Krainer, A. R. , Spector, D. L. (1994) Disruption of pre-mRNA splicing in vivo results in reorganization of splicing factors. Journal of Cell Biology, 124(3) pp. 249-260.

Birney, E., Kumar, S. , Krainer, A. R. (1993) Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Research, 21(25) pp. 5803-5816.

Caceres, J. F. , Krainer, A. R. (1993) Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains. EMBO Journal, 12(12) pp. 4715-4726.

Sun, Q., Mayeda, A., Hampson, R. K., Krainer, A. R. , Rottman, F. M. (1993) General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes & Development, 7(12b) pp. 2598-608.

Eperon, I. C., Ireland, D. C., Smith, R. A., Mayeda, A. , Krainer, A. R. (1993) Pathways for selection of 5' splice sites by U1 snRNPs and SF2/ASF. EMBO Journal, 12(9) pp. 3607-3617.

Dong, B. H., Horowitz, D. S., Kobayashi, R. , Krainer, A. R. (1993) Purification and cDNA cloning of HeLa cell p54nrb, a nuclear protein with two RNA recognition motifs and extensive homology to human splicing factor PSF and Drosophila NONA/BJ6. Nucleic Acids Research, 21(17) pp. 4085-4092.

Mayeda, A., Helfman, D. M. , Krainer, A. R. (1993) Modulation of exon skipping and inclusion by heterogeneous nuclear ribonucleoprotein A1 and pre-mRNA splicing factor SF2/ASF. Molecular and Cellular Biology, 13(5) pp. 2993-3001.

Fu, X. D., Mayeda, A., Maniatis, T. , Krainer, A. R. (1992) General splicing factors SF2 and SC35 have equivalent activities in vitro, and both affect alternative 5' and 3' splice site selection. Proceedings of the National Academy of Sciences of the United States of America, 89(23) pp. 11224-8.

Amero, S. A., Raychaudhuri, G., Cass, C. L., Vanvenrooij, W. J., Habets, W. J., Krainer, A. R. , Beyer, A. L. (1992) Independent deposition of heterogeneous nuclear ribonucleoproteins and small nuclear ribonucleoprotein particles at sites of transcription. Proceedings of the National Academy of Sciences of the United States of America, 89(18) pp. 8409-8413.

Birney, E., Kumar, S. , Krainer, A. R. (1992) A putative homolog of U2AF65 in S. cerevisiae. Nucleic Acids Research, 20(17) pp. 4663-4663.

Mayeda, A., Zahler, A. M., Krainer, A. R. , Roth, M. B. (1992) Two members of a conserved family of nuclear phosphoproteins are involved in pre-mRNA splicing. Proceedings of the National Academy of Sciences of the United States of America, 89(4) pp. 1301-1304.

Mayeda, A. , Krainer, A. R. (1992) Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell, 68(2) pp. 365-75.

Krainer, A. R., Mayeda, A., Kozak, D. , Binns, G. (1991) Functional expression of cloned human splicing factor SF2: homology to RNA-binding proteins, U1 70K, and Drosophila splicing regulators. Cell, 66(2) pp. 383-394.

Mayeda, A. , Krainer, A. R. (1991) Long-term storage of concentrated tris-borate-EDTA electrophoresis buffers without precipitation. Biotechniques, 10(2) pp. 182-182.

Krainer, A. R., Mayeda, A., Helfman, D., Conway, G. C. , Kozak, D. (1991) Biochemistry of Mammalian Nuclear Pre-Messenger Rna Splicing and Splice Site Selection. Journal of Cellular Biochemistry, 47(Suppl ) pp. 45.

Krainer, A. R., Conway, G. C. , Kozak, D. (1990) Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes & Development, 4(7) pp. 1158-1171.

Krainer, A. R., Conway, G. C. , Kozak, D. (1990) The essential pre-mRNA splicing factor SF2 influences 5' splice site selection by activating proximal sites. Cell, 62(1) pp. 35-42.

Conway, G. C., Krainer, A. R., Spector, D. L. , Roberts, R. J. (1989) Multiple splicing factors are released from endogenous complexes during in vitro pre-mRNA splicing. Molecular & Cellular Biology, 9(12) pp. 5273-80.

Tschudi, C., Krainer, A. R. , Ullu, E. (1988) The U6 small nuclear RNA from Trypanosoma brucei. Nucleic Acids Research, 16(23) pp. 11375-11375.

Krainer, A. R. (1988) Pre-mRNA splicing by complementation with purified human U1, U2, U4/U6 and U5 snRNPs. Nucleic Acids Research, 16(20) pp. 9415-9429.

Krainer, A. R. , Maniatis, T. (1985) Multiple factors including the small nuclear ribonucleoproteins U1 and U2 are necessary for pre-mRNA splicing in vitro. Cell, 42(3) pp. 725-36.

Ruskin, B., Krainer, A. R., Maniatis, T. , Green, M. R. (1984) Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell, 38(1) pp. 317-31.

Krainer, A. R., Maniatis, T., Ruskin, B. , Green, M. R. (1984) Normal and mutant human beta-globin pre-mRNAs are faithfully and efficiently spliced in vitro. Cell, 36(4) pp. 993-1005.

Squires, C., Krainer, A., Barry, G., Shen, W. F. , Squires, C. L. (1981) Nucleotide sequence at the end of the gene for the RNA polymerase beta' subunit (rpoC). Nucleic Acids Research, 9(24) pp. 6827-40.