Publications 2006

Author Title Publication
Aravin, A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., Morris, P., Brownstein, M.J., Kuramochi-Miyagawa, S., Nakano, T., Chien, M., Russo, J.J., Ju, J., Sheridan, R., Sander, C., Zavolan, M., Tuschl, T. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203-207.
Chern, T.M., van Nimwegen, E., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., Zavolan, M. A simple physical model predicts small exon length variations. PLoS Genetics 2, e45.
van Nimwegen, E., Paul, N., Sheridan, R., Zavolan, M. Spa: a probabilistic algorithm for spliced alignment. PLoS Genetics 2(4), e24.
Baralle, M., Skoko, N., Knezevich, A., de Conti, L., Motti, D., Baralle, D., Buratti, E., Baralle, F.E. NF1 mRNA biogenesis : Effect of the genomic milieu in splicing regulation of NF1 exon 37 region. FEBS Lett. 58018, 449-56.
Raponi, M., Upadhyaya, M. Baralle, D. Functional splicing assay show a pathogenic intronic mutation in Neurofibromatosis type 1 (NF1) due to intronic sequence exonization. Human Mutation 27(3), 294-295.
Izquierdo, J.M. and Valcárcel, J. A simple principle to explain the evolution of pre-mRNA splicing. Genes and Development. 23(2), 150-1.
Soares, L.M., Zanier K., Sattler M. and Valcárcel, J. Intron removal requires proofreading of U2AF / 3’ splice site recognition by DEK. Science 312(5782), 1961-5.
Mendes Soares, L.M., Valcárcel, J. The expanding transcriptome: the genome as the - Book of Sand. EMBO Journal 25, 923-931.
Soret, J., Gabut, M., and Tazi, J. SR proteins as potential targets for therapy. Progress in Molecular and Subcellular Biology (Invited review) 44, 65-87.
Kornblihtt, A.R. Chromatin transcript elongation and alternative splicing. Nature Structural and Molecular Biology 13, 5-7.
Srebrow, A.,  Kornblihtt, A. R. The splicing-cancer connection. Journal of Cell Science 119, 2635-2641.
Mühlemann, O., Akusjärvi, G. Preparation of soluble extracts from adenovirus-infected cells for studies of RNA splicing. Methods in Molecular Medicine 131, 33-46.
Törmänen, H., Backström, E. Carlsson, A., and Akusjärvi, G. L4-33K, an adenovirus encoded alternative RNA splicing factor. Journal of Biological Chemistry 281, 36510-36517.
de la Mata, M., Kornblihtt, A.R. RNA polymerase II C-terminal domain mediates regulation of alternative splicing by SRp20. Nature Structural and Molecular Biology 13, 973-980. (Commented as News and Views in Nature Structural and Molecular Biology 13, 952-953).
Ayala, Y.M., Pagani, F., and Baralle, F.E. TDP43 Depletion Rescues Aberrant CFTR Exon 9 Skipping. FEBS Letters, 580,  1339-1344.
Barbosa-Morais, N., Carmo-Fonseca, M., Aparicio, S. Systematic genome/wide annotation of spliceosomal proteins reveals differential gene family expansion. Genome Research 16, 66-77.
Gama-Carvalho, M., and Carmo-Fonseca, M. Heterokaryon assays.  In: Cell Biology – a Laboratory Manual, Ed. Julio Celis, Elsevier Science, USA.
Custodio, N., Carvalho, C., Carneiro, T., and Carmo-Fonseca, M. In situ hybridization for simultaneous detection of DNA, RNA and protein. In: Cell Biology – a Laboratory Manual, ed. Julio Celis, Elsevier Science, USA.
Kozlova, N., Braga, J., Lundgren, J., Rino, J., Young, P., Carmo-Fonseca, M. Studies on the role of NonA in mRNA biogenesis. Experimental Cell Research 312, 2619-30.
Custódio, N., Antoniou, M., Carmo-Fonseca, M. Abundance of the largest subunit of RNA polymerase II in the nucleus is regulated by nucleo-cytoplasmic shuttling. Experimental Cell Research 312,  2557-67.
Pacheco, T.R., Moita, L.F., Gomes, A.Q., Hacohen, N., Carmo-Fonseca, M. RNAi Knockdown of hU2AF35 Impairs Cell Cycle Progression and Modulates Alternative Splicing of Cdc25 Transcripts. Molecular Biology of the Cell 17(10), 4187-4199.
Pacheco, T.R., Coelho, M.B., Desterro, J.M.P., Mollet, I., and Carmo-Fonseca, M. In vivo requirement of the small subunit of U2AF for recognition of a weak 3’ splice site. Molecular Cellular Biology 26(21), 8183-90.
Mollet, I., Barbosa-Morais N.L., Andrade J, Carmo-Fonseca, M. Diversity of human U2AF splicing factors. FEBS Journal 273(21), 4807-16.
Gama-Carvalho, M., Barbosa-Morais, N.L., Brodsky, A.S., Silver, P.A., Carmo-Fonseca, M. Genome wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biology 7(11), R113.
Ben-Ari, S., Toiber, D., Sas, A.S., Soreq, H., and Ben-Shaul, Y. Modulated splicing-associated gene expression in P19 cells expressing distinct acetylcholinesterase splice variants. Journal of Neurochemistry 97 Suppl 1, 24-34.
PMID: 16635247.
Boon, K.L., Norman, C., Grainger, R.J., Newman, A.J., and Beggs, J.D. Prp8p dissection reveals domain structure and protein interaction sites. RNA 12, 198-205.
Buratti, E., Baralle, M., and Baralle, F.E. Defective splicing, disease, and therapy: searching for master checkpoints in exon definition. Nucleic Acids Research 34,  3494-3510.
Costessi, L., Devescovi, G., Baralle, F.E., and Muro, A.F. Brain-specific promoter and polyadenylation sites of the beta-adducin pre-mRNA generate an unusually long 30'-UTR. Nucleic Acids Research 34, 243-253.
Gabellini, D., D’Antona, G., Moggio, M., Prelle, A., Zecca, C., Adami, R., Angeletti, B., Ciscato, P., Pellegrino, M.A., Bottinelli, R., Green, M.R., Tupler, R. Facioscapulohumeral Muscular Dystrophy in Transgenic Mice by Over-Expression of FRG1. Nature 439, 973-977.
Gooding, C., Clark, F., Wollerton, M.C., Nagaraj-Grellscheid, S., Groom, H., and Smith, C.W.J. A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones. Genome Biology 7, R1.
Grisaru, D., Pick, M., Perry, C., Sklan, E.H., Almog, R., Goldberg, I., Naparstek, E., Lessing, J.B., Soreq H., and Deutsch, V. Hydrolytic and non-enzymatic functions of acetylcholinesterase co-modulate hematopoietic stress responses. Journal of  Immunology, 176, 27-35.
Guil, S., Long, J.C., and Caceres, J.F. hnRNP A1 relocalization to the stress granules reflects a role in the stress response. Molecular and Cellular Biology 26, 5744-5758. PMID: 16847328.
Karaduman, R., Fabrizio, P., Hartmuth, K., Urlaub, H., Luhrmann, R. RNA Structure and RNA-Protein Interactions in Purified Yeast U6 snRNPs. Journal of Molecular Biology 356, 1248-62.
Klingauf, M., Stanek, D., and Neugebauer, K.M. Enhancement of U4/U6 snRNP association in Cajal bodies predicted by mathematical modeling. Molcular Biology of the Cell  17, 4972.
PMID: 16987958.
Kishore, S., and Stamm, S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311, 230-232.
Listerman, I., Sapra, A.K., and Neugebauer, K.M. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nature Structural and Molecular Biology 13, 815 - 822.
PMID: 16921380.
Kalyna, M., Lopato, S., Voronin, V., Barta, A. Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins. Nucleic Acids Research 34(16), 4395-405.
Manival X., Charron C., Fourmann J.B., Godard, F., Charpentier B., and Branlant C. Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity. Nucleic Acids Research 34, 826-839.
Meshorer, E., and Soreq, H. Virtues and woes of AChE alternative splicing in stress-related neuropathologies. Trends in Neurosciences 29, 216-224. PMID: 16516310.
Neugebauer, K.M. Keeping tabs on the women: life scientists in Europe. PLoS Biology 4, e97.
PMID: 16602822.
Neugebauer, K.M. Please hold--the next available exon will be right with you. Nature Structural and Molecular Biology 13, 385-386.
PMID: 16738604.
Öhrmalm, C., and Akusjärvi, G. The cellular splicing/transcription regulatory protein p32 represses adenovirus major late transcription unit and causes RNA polymerase II hyperphosphorylation. Journal of Virology 80, 5010-5020.
Sklan, E.H., Berson, A., Birikh, K. R., Gutnick, A., Shahar, O., Shoham, S., and Soreq, H. Acetylcholinesterase Modulates Stress-Induced Motor Responses Through Catalytic and Noncatalytic Properties. Biological Psychiatry 60(7), 741-751.
PMID: 16904653.
Stamm, S., Riethoven, J.J., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Tang, Y., Barbosa-Morais, N.L., and Thanaraj, T.A. ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Research 34, D46-55.
Stanek, D., and Neugebauer, K.M. The Cajal body: a meeting place for spliceosomal snRNPs in the nuclear maze. Chromosoma 115, 343-354. PMID: 16575476.
Wu, C.H., Apweiler, R., Bairoch, A., Natale, D.A, Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Mazumder, R., O'Donovan, C., Redaschi, N., and Suzek, B. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Research 34, D187-D91.