Items where Subject is "RNA splicing"

A

Allemand, E., Myers, M. P., Garcia-Bernardo, J., Harel-Bellan, A., Krainer, A. R., Muchardt, C. (September 2016) A Broad Set of Chromatin Factors Influences Splicing. PLoS Genet, 12 (9). e1006318. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

Anczukow, O., Krainer, A. R. (September 2016) Splicing-factor alterations in cancers. RNA, 22 (9). pp. 1285-301. ISSN 1469-9001 (Electronic)1355-8382 (Linking)

Andersen, L., Ballester, R., Marchuk, D., Saulino, A., Wigler, M. H., Collins, F. (October 1991) Alternative Splicing in the Proposed Catalytic Domain of the Type-1 Neurofibromatosis Gene. American Journal of Human Genetics, 49 (4). p. 21. ISSN 0002-9297

Ando, S., Sarlis, N. J., Krishnan, J., Feng, X., Refetoff, S., Zhang, M. Q., Oldfield, E. H., Yen, P. M. (September 2001) Aberrant alternative splicing of thyroid hormone receptor in a TSH-secreting pituitary tumor is a mechanism for hormone resistance. Molecular Endocrinology, 15 (9). pp. 1529-1538. ISSN 0888-8809

Andresen, B. S., Krainer, A. R. (2009) When the genetic code is not enough: How sequence variations can affect pre-mRNA splicing and cause (complex) disease. In: Genetics of Complex Human Diseases: A Laboratory Manual. Cold Spring Harbor Laboratory Press, pp. 165-182. ISBN 9780879698836

Arun, G., Aggarwal, D., Spector, D. L. (June 2020) MALAT1 Long Non-Coding RNA: Functional Implications. Noncoding RNA, 6 (2). E22.

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

Barnhart, Michael D, Yang, Yi, Nakagaki-Silva, Erick E, Hammond, Thomas H, Pizzinga, Mariavittoria, Gooding, Clare, Stott, Katherine, Smith, Christopher WJ (November 2022) Phosphorylation of the smooth muscle master splicing regulator RBPMS regulates its splicing activity. Nucleic Acids Research, 50 (20). pp. 11895-11915. ISSN 0305-1048

Bilodeau, P. S., Domsic, J. K., Mayeda, A., Krainer, A. R., Stoltzfus, C. M. (September 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. ISSN 0022-538X

Boudrez, A., Beullens, M., Groenen, P., Van Eynde, A., Vulsteke, V., Jagiello, I., Murray, M., Krainer, A. R., Stalmans, W., Bollen, M. (August 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. 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.

Broner, S, Doktor, T, Hua, Y, Larsen, M, Krainer, A, Andresen, B (October 2018) SRSF10 effects splicing of SMN2 exon 7. In: 50th European-Society-of-Human-Genetics (ESHG) Conference.

Burns, C. G., Ohi, R., Krainer, A. R., Gould, K. L. (November 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. ISSN 0027-8424

C

Caceres, J. F., Krainer, A. R. (December 1993) Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains. EMBO Journal, 12 (12). pp. 4715-4726. ISSN 0261-4189

Caceres, J. F., Krainer, A. R. (1997) Mammalian pre-mRNA splicing factors. In: Eukaryotic mRNA processing. IRL Press at Oxford University Press. ISBN 9780199634187

Caceres, J. F., Screaton, G. R., Krainer, A. R. (January 1998) A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. Genes & Development, 12 (1). pp. 55-66. ISSN 0890-9369

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

Chandler, S. D., Mayeda, A., Yeakley, J. M., Krainer, A. R., Fu, X. D. (April 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. ISSN 0027-8424

Chang, An-Yun, Castel, Stephane E., Ernst, Evan, Kim, Hyun Soo, Martienssen, Robert A. (June 2017) The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly. Cell Reports, 19 (12). pp. 2477-2489. ISSN 2211-1247

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, 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)

Chew, S. L., Liu, H. X., Mayeda, A., Krainer, A. R. (September 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. ISSN 0027-8424

Chow, L. T., Broker, T. R., Lewis, J. B. (October 1979) Complex splicing patterns of RNAs from the early regions of adenovirus-2. J Mol Biol, 134 (2). pp. 265-303. ISSN 0022-2836 (Print)0022-2836 (Linking)

Chow, L. T., Kilpatrick, B. A., Lewis, J. B., Grodzicker, T., Sambrook, J., Gelinas, R. E., Broker, T. R. (1979) Splicing Patterns and Pathways of Adenoviral Rna Transcripts. Journal of Supramolecular Structure, 8 (SUPPL.). p. 45.

Chow, L. T., Lewis, J. B., Broker, T. R. (1980) RNA transcription and splicing at early and intermediate times after adenovirus-2 infection. Cold Spring Harb Symp Quant Biol, 44 (1). pp. 401-414.

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)

Conway, G. C., Krainer, A. R., Spector, D. L., Roberts, R. J. (December 1989) Multiple splicing factors are released from endogenous complexes during in vitro pre-mRNA splicing. Molecular & Cellular Biology, 9 (12). pp. 5273-80. ISSN 0270-7306

Coté, Allison, O'Farrell, Aoife, Dardani, Ian, Dunagin, Margaret, Coté, Chris, Wan, Yihan, Bayatpour, Sareh, Drexler, Heather L, Alexander, Katherine A, Chen, Fei, Wassie, Asmamaw T, Patel, Rohan, Pham, Kenneth, Boyden, Edward S, Berger, Shelly, Phillips-Cremins, Jennifer, Churchman, L Stirling, Raj, Arjun (April 2024) Post-transcriptional splicing can occur in a slow-moving zone around the gene. eLife, 12. ISSN 2050-084X (Public Dataset)

D

Dance, G. S. C., Sowden, M. P., Cartegni, L., Cooper, E., Krainer, A. R., Smith, H. C. (April 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. ISSN 0021-9258

E

Engström, P. G., Steijger, T., Sipos, B., Grant, G. R., Kahles, A., Rätsch, G., Goldman, N., Hubbard, T. J., Harrow, J., Guigó, R., Bertone, P., Alioto, T., Behr, J., Bohnert, R., Campagna, D., Davis, C. A., Dobin, A., Gingeras, T. R., Jean, G., Kosarev, P., Li, S., Liu, J., Mason, C. E., Molodtsov, V., Ning, Z., Ponstingl, H., Prins, J. F., Ribeca, P., Seledtsov, I., Solovyev, V., Valle, G., Vitulo, N., Wang, K., Wu, T. D., Zeller, G. (December 2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods, 10 (12). pp. 1185-1191. ISSN 15487091 (ISSN)

Eperon, I. C., Krainer, A. R. (1994) Splicing of mRNA precursors in mammalian cells. In: RNA Processing, a practical approach. IRL, Oxford, pp. 57-101. ISBN 9780199633432

F

Fu, X. D., Mayeda, A., Maniatis, T., Krainer, A. R. (December 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. ISSN 0027-8424 (Print)0027-8424

G

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., 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

Hanamura, A., Caceres, J. F., Mayeda, A., Franza, B. R., Krainer, A. R. (April 1998) Regulated tissue-specific expression of antagonistic pre-mRNA splicing factors. RNA, 4 (4). pp. 430-444. ISSN 1355-8382

Hannon, G. J., Maroney, P. A., Ayers, D. G., Shambaugh, J. D., Nilsen, T. W. (1990) Transcription of a nematode trans-spliced leader RNA require internal elements for both initiation and 3' end-formation. EMBO Journal, 9 (6). pp. 1915-1921. ISSN 02614189 (ISSN)

Hannon, G. J., Maroney, P. A., Denker, J. A., Nilsen, T. W. (1990) Trans splicing of nematode pre-messenger RNA in vitro. Cell, 61 (7). pp. 1247-1255. ISSN 00928674 (ISSN)

Hannon, G. J., Maroney, P. A., Nilsen, T. W. (1991) U small nuclear ribonucleoprotein requirements for nematode cis- and trans-splicing in vitro. Journal of Biological Chemistry, 266 (34). pp. 22792-22695. ISSN 00219258 (ISSN)

Hannon, G. J., Maroney, P. A., Yu, Y. T., Hannon, G. E., Nilsen, T. W. (1992) Interaction of U6 snRNA with a sequence required for function of the nematode SL RNA in trans-splicing. Science, 258 (5089). pp. 1775-1780. ISSN 00368075 (ISSN)

Hao, L. N., Tiganis, T., Tonks, N. K., Charbonneau, H. (November 1997) The noncatalytic C-terminal segment of the T cell protein tyrosine phosphatase regulates activity via an intramolecular mechanism. Journal of Biological Chemistry, 272 (46). pp. 29322-29329. ISSN 0021-9258

Hastings, M. L., Krainer, A. R. (March 2001) Functions of SR proteins in the U12-dependent AT-AC pre-mRNA splicing pathway. RNA, 7 (3). pp. 471-482. ISSN 1355-8382

Hastings, M. L., Krainer, A. R. (June 2001) Pre-mRNA splicing in the new millennium. Current Opinion in Cell Biology, 13 (3). pp. 302-309. ISSN 0955-0674

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., 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.

Horowitz, D. S., Kobayashi, R., Krainer, A. R. (December 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. ISSN 1355-8382

Horowitz, D. S., Krainer, A. R. (January 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. ISSN 0890-9369

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. (November 2002) Decrease in hnRNP A/B expression during erythropoiesis mediates a pre-mRNA splicing switch. Embo Journal, 21 (22). pp. 6195-6204. ISSN 0261-4189

Hua, Y., Krainer, A. R. (2016) Antisense-Oligonucleotide Modulation of SMN2 Pre-mRNA Splicing. In: Spinal Muscular Atrophy: Disease Mechanisms and Therapy. Elsevier, pp. 301-311. ISBN 978-012803686-0978-012803685-3

Hua, Yimin, Sahashi, Kentaro, Rigo, Frank, Hung, Gene, Bennett, C. Frank, Krainer, AdrianR (2013) Correction of RNA Splicing with Antisense Oligonucleotides as a Therapeutic Strategy for a Neurodegenerative Disease. In: Chembiomolecular Science. Springer Japan, pp. 301-313. ISBN 978-4-431-54037-3

Huang, S., Spector, D. L. (1997) Pre-mRNA splicing: Nuclear organization of factors and substrates. In: Eukaryotic mRNA processing. Frontiers in Molecular Biology . IRL Press at Oxford University Press, pp. 37-67. ISBN 9780199634187

J

Jimenez-Garcia, L. F., Spector, D. L. (September 1992) Reorganization of the Pre-Messenger-Rna Splicing Apparatus Upon Adenovirus Infection. Molecular Biology of the Cell, 3. A322-A322. ISSN 1059-1524

K

Khoo, B., Krainer, A. R. (April 2009) Splicing therapeutics in SMN2 and APOB. Current Opinion in Molecular Therapeutics, 11 (2). pp. 108-115. ISSN 1464-8431

Kilpatrick, B. A., Gelinas, R. E., Broker, T. R., Chow, L. T. (1979) Comparison of late mRNA splicing among class B and class C adenoviruses. Journal of Virology, 30 (3). pp. 899-912. ISSN 0022-538X

Kim, Young Jin, Krainer, Adrian R (January 2023) Antisense Oligonucleotide Therapeutics for Cystic Fibrosis: Recent Developments and Perspectives. Molecules and Cells, 46 (1). pp. 10-20. ISSN 1016-8478

Krainer, A. (November 2012) Pre-mRNA Splicing Mechanisms, Misregulation in Disease, and Therapeutic Strategies. Blood, 120 (21). ISSN 0006-4971

Krainer, A. R. (June 2011) Oligonucleotide therapeutics for correcting defective RNA splicing. FEBS Journal, 278 (Issue ). p. 11. ISSN 1742-464X

Krainer, A. R. (April 2015) Splicing: still so much to learn. RNA, 21 (4). pp. 500-1. ISSN 1355-8382

Krainer, A. R. (November 2011) Talk from Adrian Krainer at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Krainer, A. R., Maniatis, T. (October 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. ISSN 0092-8674 (Print)0092-8674

Krainer, A. R., Maniatis, T. (1988) RNA splicing. In: Frontiers in Molecular Biology: Transcription and splicing. IRL Press, Oxford, pp. 131-206. ISBN 9781852210809

Krainer, A. R., Maniatis, T., Ruskin, B., Green, M. R. (April 1984) Normal and mutant human beta-globin pre-mRNAs are faithfully and efficiently spliced in vitro. Cell, 36 (4). pp. 993-1005. ISSN 0092-8674 (Print)0092-8674

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 ). p. 45.

Krainer, A. R., Reed, R., Maniatis, T. (1985) Mechanisms of human β-globin pre-mRNA splicing. In: Proceedings of the Robert A. Welch Foundation Conferences on Chemical Research. Robert A. Welch Foundation, pp. 353-378. ISBN 0557-1588

Krainer, A. R., Reed, R., Maniatis, T. (1985) Sequences and factors involved in pre-mRNA splicing in vitro. In: Sequence specificity in transcription and translation: proceedings of a conference from a UCLA symposium held in Steamboat Springs, Colorado, April, 1985. A.R. Liss, New York, pp. 461-473. ISBN 9780845126295

L

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)

Lees-Miller, J. P., Yan, A., Helfman, D. M. (June 1990) Structure and complete nucleotide sequence of the gene encoding rat fibroblast tropomyosin 4. J Mol Biol, 213 (3). pp. 399-405. ISSN 0022-2836 (Print)0022-2836 (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

Lin, K. T., Ma, W. K., Scharner, J., Liu, Y. R., Krainer, A. R. (February 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. ISSN 1088-9051

Liu, H. X., Cartegni, L., Zhang, M. Q., Krainer, A. R. (January 2001) A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nature Genetics, 27 (1). pp. 55-58. ISSN 1061-4036

Liu, H. X., Chew, S. L., Cartegni, L., Zhang, M. Q., Krainer, A. R. (February 2000) Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. Molecular and Cellular Biology, 20 (3). pp. 1063-1071. ISSN 0270-7306

Lopato, S., Kalyna, M., Dorner, S., Kobayashi, R., Krainer, A. R., Barta, A. (April 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. ISSN 0890-9369

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. (November 2018) Therapeutic Targeting of an RNA Splicing Factor Network for the Treatment of Myeloid Neoplasms. Blood, 132 (Supple). Meeting Abstract 427. ISSN 0006-4971

M

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 (December 2021) ASO-based PKM splice-switching therapy inhibits hepatocellular carcinoma growth. Cancer Research. canres.0948.2020-canres.0948.2020. ISSN 0008-5472

Majerciak, V., Yamanegi, K., Allemand, E., Kruhlak, M., Krainer, A. R., Zheng, Z. M. (March 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.

Maroney, P. A., Hannon, G. J., Denker, J. A., Nilsen, T. W. (1990) The nematode spliced leader RNA participates in trans-splicing as an Sm snRNP. Embo Journal, 9 (11). pp. 3667-3673. ISSN 0261-4189

Maroney, P. A., Hannon, G. J., Shambaugh, J. D., Nilsen, T. W. (1991) Intramolecular base pairing between the nematode spliced leader and its 5' splice site is not essential for trans-splicing in vitro. EMBO Journal, 10 (12). pp. 3869-3875. ISSN 02614189 (ISSN)

Mayeda, A., Badolato, J., Kobayashi, R., Zhang, M. Q., Gardiner, E. M., Krainer, A. R. (August 1999) Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. EMBO Journal, 18 (16). pp. 4560-4570. ISSN 0261-4189

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. (1999) Mammalian in vitro splicing assays. Methods in Molecular Biology, 118. pp. 315-21. ISSN 1064-3745 (Print)1064-3745

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. ISSN 1064-3745 (Print)1064-3745

Mayeda, A., Munroe, S. H., Xu, R. M., Krainer, A. R. (September 1998) Distinct functions of the closely related tandem RNA-recognition motifs of hnRNP A1. RNA, 4 (9). pp. 1111-1123. ISSN 1355-8382

Mayeda, A., Screaton, G. R., Chandler, S. D., Fu, X. D., Krainer, A. R. (March 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. ISSN 0270-7306

Mayeda, A., Zahler, A. M., Krainer, A. R., Roth, M. B. (February 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. ISSN 0027-8424

Monroe, S. H., Mayeda, A., Krainer, A. R. (February 1994) Role of hnRNP A1 structural domains in messenger-RNA splicing and RNA-RNA annealing. Journal of Cellular Biochemistry. p. 116. ISSN 0730-2312

Munroe, S. H. (August 1988) Antisense RNA inhibits splicing of pre-mRNA in vitro. Embo J, 7 (8). pp. 2523-32. ISSN 0261-4189

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

N

Nilsson, C. E., Petersen-Mahrt, S., Durot, C., Shtrichman, R., Krainer, A. R., Kleinberger, T., Akusjarvi, G. (February 2001) The adenovirus E4-ORF4 splicing enhancer protein interacts with a subset of phosphorylated SR proteins. EMBO Journal, 20 (4). pp. 864-871. ISSN 0261-4189

Nomakuchi, T. T., Rigo, F., Aznarez, I., Krainer, A. R. (February 2016) Antisense oligonucleotide-directed inhibition of nonsense-mediated mRNA decay. Nat Biotechnol, 34 (2). pp. 164-166. ISSN 1546-1696 (Electronic)1087-0156 (Linking)

Nussaume, L., Harrison, K., Klimyuk, V., Martienssen, R., Sundaresan, V., Jones, J. D. G. (November 1995) Analysis of splice donor and acceptor site function in a transposable gene trap derived from the maize element Activator. Molecular & General Genetics, 249 (1). pp. 91-101. ISSN 0026-8925

O

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

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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. (November 2019) Differential Functions of Splicing Factors in Mammary Transformation and Breast Cancer Metastasis. Cell Rep, 29 (9). 2672-2688.e7. ISSN 2211-1247 (Public Dataset)

Potashkin, J., Frendewey, D. (October 1989) Splicing of the U6 RNA precursor is impaired in fission yeast pre-mRNA splicing mutants. Nucleic Acids Res, 17 (19). pp. 7821-31. ISSN 0305-1048

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., Lin, K. T., Bradley, R. K., Abdel-Wahab, O., Krainer, A. R. (March 2020) Recurrent SRSF2 mutations in MDS affect both splicing and NMD. Genes Dev, 34 (5-6). pp. 413-427. ISSN 0890-9369

Rigo, F., Hua, Y. M., Chun, S. J., Prakash, T. P., Krainer, A. R., Bennett, C. F. (June 2012) Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing. Nature Chemical Biology, 8 (6). pp. 555-561. ISSN 1552-4450

Roca, X., Krainer, A. R. (2013) RNA Splicing. In: Brenner's Encyclopedia of Genetics. Elsevier Science. ISBN 9780080961569

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

Roca, X., Krainer, A. R. (March 2009) A splicing component adapted to gene silencing. Nat Biotechnol, 27 (3). pp. 250-1. ISSN 1546-1696 (Electronic)1087-0156 (Linking)

Ruskin, B., Krainer, A. R., Maniatis, T., Green, M. R. (August 1984) Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell, 38 (1). pp. 317-31. ISSN 0092-8674 (Print)0092-8674

S

Sacco-Bubulya, P. A., Spector, D. L. (November 2001) Interchromatin granule clusters are essential for coordinating transcription and pre-mRNA splicing. Molecular Biology of the Cell, 12. 103A-103A. ISSN 1059-1524

Scharner, J., Ma, W. K., Zhang, Q., Lin, K. T., Rigo, F., Bennett, C. F., Krainer, A. R. (December 2019) Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides. Nucleic Acids Res, 48 (2). ISSN 0305-1048 (Public Dataset)

Segovia, Danilo, Adams, Dexter W, Hoffman, Nickolas, Safaric Tepes, Polona, Wee, Tse-Luen, Cifani, Paolo, Joshua-Tor, Leemor, Krainer, Adrian R (May 2024) SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proceedings of the National Academy of Sciences of the United States of America, 121 (21). e2322974121. ISSN 0027-8424 (Public Dataset)

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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)

Shi, H., Xu, R. M. (April 2003) Crystal structure of the Drosophila Mago nashi-Y14 complex. Genes & Development, 17 (8). pp. 971-976. ISSN 0890-9369

Sinha, R., Kim, Y. J., Nomakuchi, T., Sahashi, K., Hua, Y., Rigo, F., Bennett, C. F., Krainer, A. R. (June 2018) Antisense oligonucleotides correct the familial dysautonomia splicing defect in IKBKAP transgenic mice. Nucleic Acids Res, 46 (10). pp. 4833-4844. ISSN 0305-1048

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. (November 2017) Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers. Nat Commun, 8 (1). p. 1476. ISSN 2041-1723

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Sun, Q., Mayeda, A., Hampson, R. K., Krainer, A. R., Rottman, F. M. (December 1993) General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes & Development, 7 (12b). pp. 2598-608. ISSN 0890-9369 (Print)0890-9369

T

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. (January 2011) Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Molecular and Cellular Proteomics, 10 (1).

Tilgner, H., Knowles, D. G., Johnson, R., Davis, C. A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T. R., Guigo, R. (September 2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for IncRNAs. Genome Research, 22 (9). pp. 1616-1625. ISSN 1088-9051

V

van Oordt, W. V., Diaz-Meco, M. T., Lozano, J., Krainer, A. R., Moscat, J., Caceres, J. F. (April 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. ISSN 0021-9525

W

Wanner, L. A., Li, G., Ware, D., Somssich, I. E., Davis, K. R. (January 1995) The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana. Plant Mol Biol, 27 (2). pp. 327-38. ISSN 0167-4412 (Print)

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

Wu, J., Akerman, M., Sun, S., McCombie, W. R., Krainer, A. R., Zhang, M. Q. (November 2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27 (21). 3010-3016 . ISSN 1367-4803

Wu, Q., Krainer, A. R. (May 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. ISSN 0270-7306

Wu, Q., Krainer, A. R. (December 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. ISSN 1355-8382

Wu, X., Wang, S. H., Sun, J., Krainer, A. R., Hua, Y., Prior, T. W. (April 2017) A-44G transition in SMN2 intron 6 protects patients with spinal muscular atrophy. Hum Mol Genet. ISSN 0964-6906

X

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. (December 2014) RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science, 347 (6218). ISSN 0036-8075

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

Yoshimi, Akihide, Lin, Kuan-Ting, Wiseman, Daniel, Intlekofer, Andrew M, Wang, Bo, Pastore, Alessandro, Rahman, Mohammad, Lee, Stanley Chun-Wei, Liu, Bo, Micol, Jean-Baptiste, De Botton, Stephane, Penard-Lacronique, Virginie, Shih, Alan H, Stein, Eytan M, Durham, Benjamin H, Inoue, Daichi, Zhang, Xiao Jing, Albrecht, Todd, Chung, Young Rock, Peng, Shouyong, Buonamici, Silvia, Palacino, James, Smith, Peter, Thompson, Craig B, Levine, Ross L, Wagner, Eric, Krainer, Adrian R, Abdel-Wahab, Omar (December 2017) Spliceosomal Dysfunction Is a Critical Mediator of IDH2 Mutant Leukemogenesis. In: 59th Annual Meeting of the American Society of Hematology.

Z

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

Zhang, M. Q., Marr, T. G. (October 1993) A weight array method for splicing signal analysis. Comput Appl Biosci, 9 (5). pp. 499-509. ISSN 0266-7061 (Print)

Zhou, Juannan, Wong, Mandy S, Chen, Wei-Chia, Krainer, Adrian R, Kinney, Justin B, McCandlish, David M (September 2022) Higher-order epistasis and phenotypic prediction. Proceedings of the National Academy of Sciences of USA, 119 (39). e2204233119. ISSN 0027-8424

Zhu, J., Krainer, A. R. (December 2000) Pre-mRNA splicing in the absence of an SR protein RS domain. Genes & Development, 14 (24). pp. 3166-3178. ISSN 0890-9369

Š

Šušnjar, Urša, Škrabar, Neva, Brown, Anna-Leigh, Abbassi, Yasmine, Phatnani, Hemali, NYGC ALS Consortium, Cortese, Andrea, Cereda, Cristina, Bugiardini, Enrico, Cardani, Rosanna, Meola, Giovanni, Ripolone, Michela, Moggio, Maurizio, Romano, Maurizio, Secrier, Maria, Fratta, Pietro, Buratti, Emanuele (April 2022) Cell environment shapes TDP-43 function with implications in neuronal and muscle disease. Communications Biology, 5 (1). p. 314. ISSN 2399-3642