Items where Subject is "Alternative Splicing"

A

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 (July 2021) Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia. Nature Communications, 12 (1). p. 4507. ISSN 2041-1723

Allemand, E., Hastings, M. L., Murray, M. V., Myers, M. P., Krainer, A. R. (July 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. ISSN 1545-9993 (Print)

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. (October 2015) SRSF1-Regulated Alternative Splicing in Breast Cancer. Mol Cell, 60 (1). pp. 105-17. ISSN 1097-4164 (Electronic)1097-2765 (Linking)

Aznarez, Isabel, Nomakuchi, Tomoki T., Tetenbaum-Novatt, Jaclyn, Rahman, Mohammad Alinoor, Fregoso, Oliver, Rees, Holly, Krainer, Adrian R. (May 2018) Mechanism of Nonsense-Mediated mRNA Decay Stimulation by Splicing Factor SRSF1. Cell Reports, 23 (7). pp. 2186-2198. ISSN 2211-1247

B

Balvay, L., Pret, A. M., Libri, D., Helfman, D. M., Fiszman, M. Y. (August 1994) Splicing of the Alternative Exons of the Chicken, Rat, and Xenopus Beta-Tropomyosin Transcripts Requires Class-Specific Elements. Journal of Biological Chemistry, 269 (31). pp. 19675-19678. ISSN 0021-9258

Broker, T. R., Chow, L. T. (1979) Alternative Rna Splicing Patterns and the Clustered Transcription and Splicing Signals of Human Adenovirus 2. In: Eucaryotic gene regulation. ICN-UCLA symposia on molecular and cellular biology, 14 (ED.). Academic Press, New York, pp. 611-636.

Bruun, G. H., Doktor, T. K., Borch-Jensen, J., Masuda, A., Krainer, A. R., Ohno, K., Andresen, B. S. (July 2016) Global identification of hnRNP A1 binding sites for SSO-based splicing modulation. BMC Biol, 14 (1). p. 54. ISSN 1741-7007 (Electronic)1741-7007 (Linking)

C

Caceres, J. F., Stamm, S., Helfman, D. M., Krainer, A. R. (September 1994) Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science, 265 (5179). pp. 1706-9. ISSN 0036-8075 (Print)0036-8075

Chen, C. D., Helfman, D. M. (February 1999) Donor site competition is involved in the regulation of alternative splicing of the rat beta-tropomyosin pre-mRNA. Rna, 5 (2). pp. 290-301. ISSN 1355-8382 (Print)

Chen, C. D., Kobayashi, R., Helfman, D. M. (March 1999) Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta-tropomyosin gene. Genes and Development, 13 (5). pp. 593-606. ISSN 0890-9369 (Print)

Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason, Kinney, Justin, McCandlish, David (December 2020) Non-parametric Bayesian density estimation for biological sequence space with applications to pre-mRNA splicing and the karyotypic diversity of human cancer. BioRxiv. (Unpublished)

Conlon, E. G., Fagegaltier, D., Agius, P., Davis-Porada, J., Gregory, J., Hubbard, I., Kang, K., Kim, D., Phatnani, H., Shneider, N. A., Manley, J. L., Kwan, J., Sareen, D., Broach, J. R., Simmons, Z., Arcila-Londono, X., Lee, E. B., Van Deerlin, V. M., Fraenkel, E., Ostrow, L. W., Baas, F., Zaitlen, N., Berry, J. D., Malaspina, A., Fratta, P., Cox, G. A., Thompson, L. M., Finkbeiner, S., Dardiotis, E., Miller, T. M., Chandran, S., Pal, S., Hornstein, E., Macgowan, D. J., Heiman-Patterson, T., Hammell, M. G., Patsopoulos, N. A., Dubnau, J., Nath, A., Phatnani, H., Shneider, N. A., Manley, J. L. (July 2018) Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism. eLife, 7. ISSN 2050084X (ISSN)

D

Das, G., Herr, W. (November 1993) Enhanced activation of the human histone H2B promoter by an Oct-1 variant generated by alternative splicing. J Biol Chem, 268 (33). pp. 25026-32. ISSN 0021-9258 (Print)

E

Einson, Jonah, Glinos, Dafni, Boerwinkle, Eric, Castaldi, Peter, Darbar, Dawood, de Andrade, Mariza, Ellinor, Patrick, Fornage, Myriam, Gabriel, Stacey, Germer, Soren, Gibbs, Richard, Hersh, Craig P, Johnsen, Jill, Kaplan, Robert, Konkle, Barbara A, Kooperberg, Charles, Nassir, Rami, Loos, Ruth JF, Meyers, Deborah A, Mitchell, Braxton D, Psaty, Bruce, Vasan, Ramachandran S, Rich, Stephen S, Rienstra, Michael, Rotter, Jerome I, Saferali, Aabida, Shoemaker, Moore Benjamin, Silverman, Edwin, Smith, Albert Vernon, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mohammadi, Pejman, Castel, Stephane E, Iossifov, Ivan, Lappalainen, Tuuli (August 2023) Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. Genetics, 224 (4). iyad115. ISSN 0016-6731

F

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. (June 2019) Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites. Mol Cell, 74 (6). 1189-1204.e6. ISSN 1097-2765

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 (March 2021) Identification of SRSF10 as a regulator of SMN2 ISS-N1. Human Mutation, 42 (3). pp. 246-260. ISSN 1059-7794

G

Gann, A. A., Gates, P. B., Stark, D., Brockes, J. P. (June 1996) Receptor isoform specificity in a cellular response to retinoic acid. Proceedings of the Royal Society B: Biological Sciences, 263 (1371). pp. 729-34. ISSN 0962-8452 (Print)0962-8452

Gimona, M., Watakabe, A., Helfman, D. M. (October 1995) Specificity of dimer formation in tropomyosins: influence of alternatively spliced exons on homodimer and heterodimer assembly. Proc Natl Acad Sci U S A, 92 (21). pp. 9776-80. ISSN 0027-8424 (Print)

Goodwin, L. O., Lees-Miller, J. P., Leonard, M. A., Cheley, S. B., Helfman, D. M. (May 1991) Four fibroblast tropomyosin isoforms are expressed from the rat alpha-tropomyosin gene via alternative RNA splicing and the use of two promoters. J Biol Chem, 266 (13). pp. 8408-15. ISSN 0021-9258 (Print)0021-9258 (Linking)

Grossman, J. S., Meyer, M. I., Wang, Y. C., Mulligan, G. J., Kobayashi, R., Helfman, D. M. (June 1998) The use of antibodies to the polypyrimidine tract binding protein (PTB) to analyze the protein components that assemble on alternatively spliced pre-mRNAs that use distant branch points. Rna, 4 (6). pp. 613-25. ISSN 1355-8382 (Print)

Grotewold, E., Athma, P., Peterson, T. (June 1991) Alternatively spliced products of the maize P gene encode proteins with homology to the DNA-binding domain of myb-like transcription factors. Proc Natl Acad Sci U S A, 88 (11). pp. 4587-91. ISSN 0027-8424 (Print)0027-8424 (Linking)

Guo, W., Helfman, D. M. (1991) Alternative Rna Splicing of Beta Tropomyosin Pre-Messenger Rna Identification of Exon and Intron Elements That Inhibit the Use of the Skeletal Muscle-Specific Exon in Nonmuscle Cells. Journal of Cellular Biochemistry, 47 (Suppl ). p. 73.

Guo, W., Helfman, D. M. (October 1993) Cis-Elements Involved in Alternative Splicing in the Rat Beta-Tropomyosin Gene - the 3'-Splice Site of the Skeletal-Muscle Exon-7 Is the Major Site of Blockage in Nonmuscle Cells. Nucleic Acids Res, 21 (20). pp. 4762-4768. ISSN 0305-1048

Guo, W., Mulligan, G. J., Wormsley, S., Helfman, D. M. (November 1991) Alternative splicing of beta-tropomyosin pre-mRNA: cis-acting elements and cellular factors that block the use of a skeletal muscle exon in nonmuscle cells. Genes Dev, 5 (11). pp. 2096-107. ISSN 0890-9369 (Print)0890-9369 (Linking)

H

Harper, J. E., Manley, J. L. (December 1991) A novel protein factor is required for use of distal alternative 5' splice sites in vitro. Mol Cell Biol, 11 (12). pp. 5945-53. ISSN 0270-7306 (Print)0270-7306 (Linking)

Helfman, D. M. (December 1993) Generation of Protein Isoform Diversity by Alternative Rna Splicing. Journal of General Physiology, 102 (6). A5-A5. ISSN 0022-1295

Helfman, D. M. (1994) The generation of protein isoform diversity by alternative RNA splicing. Soc Gen Physiol Ser, 49. pp. 105-15. ISSN 0094-7733 (Print)

Helfman, D. M., Guo, W., Lees-Miller, J. P., Mulligan, G. J., Tsukahara, T., Wormsley, S. (October 1991) Alternative Rna Splicing in the Control of Cytoskeletal Protein Gene-Expression. Journal of Muscle Research and Cell Motility, 12 (5). p. 487. ISSN 0142-4319

Helfman, D. M., Guo, W., Mulligan, G. J., Tsukahara, T., Wormsley, S. (1991) Alternative Rna Splicing in the Control of Gene Expression. Journal of Cellular Biochemistry, 47 (Suppl ). p. 15.

Helfman, D. M., Ricci, W. M. (July 1989) Branch point selection in alternative splicing of tropomyosin pre-mRNAs. Nucleic Acids Res, 17 (14). pp. 5633-50. ISSN 0305-1048

Helfman, D. M., Roscigno, R. F., Mulligan, G. J., Finn, L. A., Weber, K. S. (January 1990) Identification of two distinct intron elements involved in alternative splicing of beta-tropomyosin pre-mRNA. Genes Dev, 4 (1). pp. 98-110. ISSN 0890-9369 (Print)0890-9369 (Linking)

Hwang, I., Cao, D., Na, Y., Kim, D. Y., Zhang, T., Yao, J., Oh, H., Hu, J., Zheng, H., Yao, Y., Paik, J. (March 2018) Far Upstream Element-Binding Protein 1 Regulates LSD1 Alternative Splicing to Promote Terminal Differentiation of Neural Progenitors. Stem Cell Reports, 10 (4). pp. 1208-1221. ISSN 2213-6711 (Electronic)2213-6711 (Linking)

J

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 (May 2023) RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer. Nature, 617 (7959). pp. 147-153. ISSN 0028-0836 (Public Dataset)

L

Lazarev, D., Miller, R. L., Dimango, E., Fu, X. D., Li, H. R., Logan, C. J., Manley, J. L. (May 2014) CFLIP expression is altered in severe corticosteroid-resistant asthma. Genomics Data, 2. pp. 99-104. ISSN 22135960

Lees-Miller, J. P., Goodwin, L. O., Helfman, D. M. (April 1990) Three novel brain tropomyosin isoforms are expressed from the rat alpha-tropomyosin gene through the use of alternative promoters and alternative RNA processing. Mol Cell Biol, 10 (4). pp. 1729-42. ISSN 0270-7306 (Print)0270-7306 (Linking)

Lin, K. T., Krainer, A. R. (May 2019) PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis. Bioinformatics, 35 (23). pp. 5048-5054. ISSN 1367-4803

Ludlow, A. T., Wong, M. S., Robin, J. D., Batten, K., Yuan, L., Lai, T. P., Dahlson, N., Zhang, L., Mender, I., Tedone, E., Sayed, M. E., Wright, W. E., Shay, J. W. (August 2018) NOVA1 regulates hTERT splicing and cell growth in non-small cell lung cancer. Nat Commun, 9 (1). p. 3112. ISSN 2041-1723

M

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

Mayeda, A., Krainer, A. R. (2012) In vitro splicing assays. In: Alternative pre-mRNA Splicing: Theory and Protocols. Wiley, pp. 321-330. ISBN 9783527636785

Mayeda, A., Krainer, A. R. (January 1992) Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell, 68 (2). pp. 365-75. ISSN 0092-8674 (Print)0092-8674

Miller, M., Shirole, N., Tian, R., Pal, D., Sordella, R. (December 2016) The Evolution of TP53 Mutations: From Loss-of-Function to Separation-of-Function Mutants. J Cancer Biol Res, 4 (4). ISSN 2373-9436

Mulligan, G. J., Guo, W., Wormsley, S., Helfman, D. M. (December 1992) Polypyrimidine Tract Binding-Protein Interacts with Sequences Involved in Alternative Splicing of Beta-Tropomyosin Premessenger Rna. Journal of Biological Chemistry, 267 (35). pp. 25480-25487. ISSN 0021-9258

Murray, M. V. (1999) Role of phosphorylation in pre-mRNA splicing. Frontiers of Hormone Research, 25. pp. 83-100. ISSN 0301-3073 (Print)

P

Pollard, A. J., Krainer, A. R., Robson, S. C., Europe-Finner, G. N. (May 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. ISSN 0021-9258 (Print)0021-9258

R

Rahman, M. A., Krainer, A. R., Abdel-Wahab, O. (January 2020) SnapShot: Splicing Alterations in Cancer. Cell, 180 (1). 208-208.e1. ISSN 0092-8674

Rahman, M.A., Nasrin, F., Bhattacharjee, S., Nandi, S. (May 2020) Hallmarks of Splicing Defects in Cancer: Clinical Applications in the Era of Personalized Medicine. Cancers (Basel), 12 (6). E1381. ISSN 2072-6694

S

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. (July 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). E3287-E3296. ISSN 0027-8424

Sheng, L., Rigo, F., Bennett, C. F., Krainer, A. R., Hua, Y. (April 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. ISSN 0305-1048 (Public Dataset)

Stamm, S., Casper, D., Dinsmore, J., Kaufmann, C. A., Brosius, J., Helfman, D. M. (October 1992) Clathrin light chain B: gene structure and neuron-specific splicing. Nucleic Acids Res, 20 (19). pp. 5097-103. ISSN 0305-1048 (Print)0305-1048 (Linking)

Stamm, S., Zhang, M. Q., Marr, T. G., Helfman, D. M. (May 1994) A sequence compilation and comparison of exons that are alternatively spliced in neurons. Nucleic Acids Res, 22 (9). pp. 1515-26. ISSN 0305-1048 (Print)

W

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 (July 2023) Splicing Factor SRSF1 Promotes Pancreatitis and KRASG12D-Mediated Pancreatic Cancer. Cancer Discovery, 13 (7). pp. 1678-1695. ISSN 2159-8274 (Public Dataset)

Wan, Ledong, Lin, Kuan-Ting, Rahman, Mohammad A, Wang, Zhikai, Park, Youngkyu, Tuveson, David A, Krainer, Adrian R (November 2021) Loss of compensatory feedback mechanism involving splicing factor SRSF1 accelerates Kras(G12D)-mediated pancreatic cancer initiation. In: AACR Virtual Special Conference on Pancreatic Cancer.

Wang, B., Kumar, V., Olson, A., Ware, D. (April 2019) Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing. Front Genet, 10. Article no.384. ISSN 1664-8021 (Print)1664-8021

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. (February 2019) Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Cancer Cell, 35 (3). 359-384.e7. ISSN 1535-6108

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. (March 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. ISSN 22111247 (ISSN)

Wong, M. S., Kinney, J. B., Krainer, A. R. (August 2018) Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites. Mol Cell, 71 (6). 1012-1026.e3. ISSN 1097-2765

Y

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. (October 2019) Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis. Nature, 574 (7777). pp. 273-277. ISSN 0028-0836

Z

Zhang, Z., Krainer, A. R. (2006) Nonsense-Mediated Alternative Splicing. In: Nonsense-mediated mRNA decay. Landes Bioscience, Georgetown, TX, pp. 250-359. ISBN 9781587062964