Adiconis, X., Haber, A. L., Simmons, S. K., Levy Moonshine, A., Ji Z., Busby, M. A., et al. (2018). Comprehensive comparative analysis of 5'-end RNA-sequencing methods. Nature methods, 15, 505-511.
Akiva, P., Toporik, A., Edelheit, S., Peretz, Y., Diber, A., Shemesh, R., Novik, A., and Sorek, R. (2006). Transcription-mediated gene fusion in the human genome. Genome research 16, 30-36.
An, J.J., Gharami, K., Liao, G.Y., Woo, N.H., Lau, A.G., Vanevski, F., Torre, E.R., Jones, K.R., Feng, Y., Lu, B., et al. (2008). Distinct Role of Long 3' UTR BDNF mRNA in Spine Morphology and Synaptic Plasticity in Hippocampal Neurons. Cell 134, 175-187.
Araki, S., Dairiki, R., Nakayama, Y., Murai, A., Miyashita, R., Iwatani, M., Nomura, T., and Nakanishi, O. (2015). Inhibitors of CLK protein kinases suppress cell growth and induce apoptosis by modulating pre-mRNA splicing. PloS one 10, e0116929.
Beck, A.H., Weng, Z., Witten, D.M., Zhu, S., Foley, J.W., Lacroute, P., Smith, C.L., Tibshirani, R., van de Rijn, M., Sidow, A., et al. (2010). 3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PloS one 5, e8768.
Berg, M.G., Singh, L.N., Younis, I., Liu, Q., Pinto, A.M., Kaida, D., Zhang, Z., Cho, S., Sherrill-Mix, S., Wan, L., et al. (2012). U1 snRNP determines mRNA length and regulates isoform expression. Cell 150, 53-64.
Bergeron, D., Pal, G., Beaulieu, Y.B., Chabot, B., and Bachand, F. (2015). Regulated Intron Retention and Nuclear Pre-mRNA Decay Contribute to PABPN1 Autoregulation. Molecular and cellular biology 35, 2503-2517.
Bradner, J.E., Hnisz, D., and Young, R.A. (2017). Transcriptional Addiction in Cancer. Cell 168, 629-643.
Chan, S., Choi, E.A., and Shi, Y. (2011). Pre-mRNA 3'-end processing complex assembly and function. Wiley interdisciplinary reviews RNA 2, 321-335.
Chen, W., Jia, Q., Song, Y., Fu, H., Wei, G., and Ni, T. (2017). Alternative Polyadenylation: Methods, Findings, and Impacts. Genomics, proteomics & bioinformatics, 15(5), 287-300.
Chung, V., Heath, E., Schelman, W.R., Johnson, B.M., Kirby, L.C.,, et al. (2011). First-time- in-human study of GSK923295, a novel antimitotic inhibitor of centromere-associated protein E (CENP-E), in patients with refractory cancer. Cancer Chemotherapy and Pharmacology, 69(3), 733-741.
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., et al. (2016). A survey of best practices for RNA-seq data analysis. Genome biology 17, 13.
Crick, F.H.C. (1958). On protein synthesis. Symposia of Society Experimental Biology 12, 138-163.
Crick, F. (1970). Central dogma of molecular biology. Nature 227, 561-563.
Di Giammartino, D.C., Nishida, K., and Manley, J.L. (2011). Mechanisms and Consequences of Alternative Polyadenylation. Molecular cell 43, 853-866.
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T.R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England) 29, 15-21.
Dutertre, M., Chakrama, F.Z., Combe, E., Desmet, F.-O., Mortada, H., Polay Espinoza, M., Gratadou, L., and Auboeuf, D. (2014). A recently evolved class of alternative 3'-terminal exons involved in cell cycle regulation by topoisomerase inhibitors. Nature communications 5, 3395.
Elkon, R., Drost, J., van Haaften, G., Jenal, M., Schrier, M., Vrielink, J., and Agami, R. (2012).
E2F mediates enhanced alternative polyadenylation in proliferation. Genome biology 13, R59.
Elkon, R., Ugalde, A.P., and Agami, R. (2013). Alternative cleavage and polyadenylation: extent, regulation and function. Nature reviews Genetics 14, 496-506.
Fong, N., Brannan, K., Erickson, B., Kim, H., Cortazar, M.A., Sheridan, R.M., Nguyen, T., Karp, S., and Bentley, D.L. (2015). Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase I Termination Suggest Widespread Kinetic Competition. Molecular cell 60, 256-267.
Fares C.M., Van Allen E.M., Drake C.G., Allison J.P., Hu-Lieskovan S. (2019). Mechanisms of Resistance to Immune Checkpoint Blockade: Why Does Checkpoint Inhibitor Immunotherapy Not Work for All Patients? American Society of Clinical Oncology Educational Book 39, 147-164
Fong, N., Kim, H., Zhou, Y., Ji, X., Qiu, J., Saldi, T., Diener, K., Jones, K., Fu, X.D., and Bentley, D.L. (2014). Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes & development 28, 2663-2676.
Funnell, T., Tasaki, S., Oloumi, A., Araki, S., Kong, E., Yap, D., Nakayama, Y., Hughes, C.S., Cheng, S.G., Tozaki, H., et al. (2017). CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. Nature communications 8, 7.
Garraway, L.A., and Lander, E.S. (2013). Lessons from the cancer genome. Cell 153, 17-37.
Gomez-Benito, M., Loayza-Puch, F., Oude Vrielink, J.A., Odero, M.D., and Agami, R. (2011). 3'UTR-mediated gene silencing of the Mixed Lineage Leukemia (MLL) gene. PloS one 6, e25449.
Gonda, T. and Ramsay, R. (2015). Directly targeting transcriptional dysregulation in cancer. Nature Reviews Cancer 15, 686-694
Haslam A., Prasad V. (2019). Estimation of the Percentage of US Patients With Cancer Who Are Eligible for and Respond to Checkpoint Inhibitor Immunotherapy Drugs. JAMA network open 2, e192535.
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., and Glass, C.K. (2010). Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Molecular cell 38, 576-589.
Heitman, L.H., van Veldhoven, J.P., Zweemer, A.M., Ye, K., Brussee, J., and AP, I.J. (2008). False positives in a reporter gene assay: identification and synthesis of substituted N-pyridin- 2-ylbenzamides as competitive inhibitors of firefly luciferase. Journal of medicinal chemistry 51, 4724-4729.
Hira, Z.M., and Gillies, D.F. (2015). A Review of Feature Selection and Feature Extraction Methods Applied on Microarray Data. Advances in Bioinformatics 2015, 198363.
Ito, M., Tanaka, T., Toita, A., Uchiyama, N., Kokubo, H., Morishita, N., Klein, M. G., Zou, H., Murakami, M., Kondo, M., et al. (2018). Discovery of 3-Benzyl-1-( trans-4-(5- cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin- Dependent Kinase 12 (CDK12) Inhibitors. Journal of Medicinal Chemistry 13, 7710-7728.
Jenkins R. W., Barbie D. A., Flaherty K. T. (2018). Mechanisms of resistance to immune checkpoint inhibitors. British journal of cancer 118, 9-16.
Jenal, M., Elkon, R., Loayza-Puch, F., Van Haaften, G., Kühn, U., Menzies, F.M., Vrielink, J.a.F.O., Bos, A.J., Drost, J., Rooijers, K., et al. (2012). The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. Cell 149, 538-553.
Kaida, D., Berg, M.G., Younis, I., Kasim, M., Singh, L.N., Wan, L., and Dreyfuss, G. (2010). U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664-668.
Kanehisa, M. and Sato, Y. (2019), KEGG Mapper for inferring cellular functions from protein sequences. Protein Science, August 18 2019.
Katz, Y., Wang, E.T., Airoldi, E.M., and Burge, C.B. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature methods 7, 1009-1015.
Klerk, E.D., and Hoen, P.a.C. (2015). Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. Trends in Genetics, 1-12.
Klebanov, L., and Yakovlev, A. (2007). How high is the level of technical noise in microarray data? Biology Direct 2, 9.
Lackford, B., Yao, C., Charles, G.M., Weng, L., Zheng, X., Choi, E.a., Xie, X., Wan, J., Xing, Y., Freudenberg, J.M., et al. (2014). Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. EMBO Journal 33, 878-889.
Langfelder, P., and Horvath, S. (2008). WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics 9, 559.
Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods 9, 357-359.
Lawrence, M.S., Stojanov, P., Mermel, C.H., Robinson, J.T., Garraway, L.A., Golub, T.R., Meyerson, M., et al. (2014). Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495-501.
Lengauer, C., Kinzler, K. W. and Vogelstein, B. (1998). Genetic instabilities in human cancers. Nature 398, 643-649.
Li, H., Lovei, M. T., Kwon, Y. S., Rosenfeld, M. G., Fu, X. D., and Yeo, G. W. (2008). Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proceedings of the National Academy of Sciences of the United States of America, 105, 20179-20184.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009). The Sequence Alignment/ Map format and SAMtools. Bioinformatics (Oxford, England) 25, 2078-2079.
Li, W., You, B., Hoque, M., Zheng, D., Luo, W., Ji, Z., Park, J.Y., Gunderson, S.I., Kalsotra, A., Manley, J.L., et al. (2015). Systematic profiling of poly (A) + transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS genetics 11, e1005166.
Liu, X., Freitas, J., Zheng, D., Oliveira, M.S., Hoque, M., Martins, T., Henriques, T., Tian, B., and Moreira, A. (2017). Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster. RNA (New York, NY) 23, 1807-1816.
Luo, W., Ji, Z., Pan, Z., You, B., Hoque, M., Li, W., Gunderson, S.I., and Tian, B. (2013). The conserved intronic cleavage and polyadenylation site of CstF-77 gene imparts control of 3' end processing activity through feedback autoregulation and by U1 snRNP. PLoS genetics 9, e1003613.
Manning, K.S., and Cooper, T.A. (2017). The roles of RNA processing in translating genotype to phenotype. Nature reviews. Molecular cell biology 18, 102-114.
Maere, S., Heymans, K., and Kuiper, M. (2005). BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics (Oxford, England) 21, 3448-3449.
Marguerat, S., and Bähler, J. (2010). RNA-seq: from technology to biology. Cellular and molecular life sciences 67, 569-579.
Masamha, C. P., and Wagner E. J. (2018). The contribution of alternative polyadenylation to the cancer phenotype. Carcinogenesis 39, 2-10.
Mazloomian, A., Araki, S., Ohori, M., El-Naggar, A. M., Yap, D., Bashashati, A., and Aparicio, S. (2019). Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation. Communications biology 2, 165.
Merico, D., Isserlin, R., Stueker, O., Emili, A., and Bader, G.D. (2010). Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PloS one 5, e13984.
Miki, H., Okada, Y., and Hirokawa, N. (2005). Analysis of the kinesin superfamily: insights into structure and function. Trends Cell Biology 15, 467-476
Morgan P., Brown D., Lennard S., Anderton M., Barrett J., Eriksson U., Fidock M., Hamén B., Johnson A., et al. (2018). Impact of a five-dimensional framework on R&D productivity at AstraZeneca. Nature Reviews Drug Discovery 17, 167-181.
Ohashi, A., Zdzienicka, M.Z., Chen, J., and Couch, F.J. (2005). Fanconi anemia complementation group D2 (FANCD2) functions independently of BRCA2- and RAD51- associated homologous recombination in response to DNA damage. Journal of Biological Chemistry 280, 14877-14883
Ohashi, A., Ohori M., Iwai, K., Nakayama, Y., Nambu, T., et al. (2015). Aneuploidy generates proteotoxic stress and DNA damage concurrently with p53-mediated post-mitotic apoptosis in SAC-impaired cells. Nature Communications 6, 7668
Pal, S., Gupta, R., and Davuluri, R.V. (2012). Alternative transcription and alternative splicing in cancer. Pharmacology & Therapeutics 136, 283-294.
Paz, I., Kosti, I., Ares, M., Jr., Cline, M., and Mandel-Gutfreund, Y. (2014). RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic acids research 42, W361-367.
Peterson, M.L. (2007). Mechanisms controlling production of membrane and secreted immunoglobulin during B cell development. Immunologic research 37, 33-46.
Prakash, T., Sharma, V.K., Adati, N., Ozawa, R., Kumar, N., Nishida, Y., Fujikake, T., Takeda, T., and Taylor, T.D. (2010). Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. PloS one 5, e13284.
Rath, O., and Kozielski, F. (2012). Kinesins and cancer. Nature reviews. Cancer, 12(8), 527-539.
Ribas A., Wolchok J.D. (2018). Cancer immunotherapy using checkpoint blockade. Science 359, 1350-1355.
Rosario, S. R., Long, M. D., Affronti, H. C., Rowsam, A. M., Eng, K. H., and Smiraglia, D. J. (2018). Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas. Nature communications 9, 5330.
Salton, M., and Misteli, T. (2016). Small Molecule Modulators of Pre-mRNA Splicing in Cancer Therapy. Trends in molecular medicine 22, 28-37.
Schena, M., Shalon, D., Davis, RW. and Brown PO. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
Schmieder, R., and Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics (Oxford, England) 27, 863-864.
Shao, Z., Zhang, Y., Yuan, G.C., Orkin, S.H., and Waxman, D.J. (2012). MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome biology 13, R16.
Shi, Y. (2012). Alternative polyadenylation: new insights from global analyses. RNA (New York, NY) 18, 2105-2117.
Siu Tony, D.C., Kumarasinghe Sathyajith E, inventors (2011). Merck Sharp & Dohme Corp, assignee. Pyrazolo [3,4-b] pyridin-4-one kinase inhibitors. patent WO/2011/049722.
Stratton, M.R., Campbell, P.J., and Futreal, P.A. (2009). The cancer genome. Nature 458, 719-724.
Sur, I., and Taipale, J. (2016). The role of enhancers in cancer. Nature Reviews Cancer 16, 483-493.
Thompson L.L., Jeusset L.M., Lepage C.C, McManus K.J. (2017). Evolving Therapeutic Strategies to Exploit Chromosome Instability in Cancer. Cancers (Basel) 9, E151.
Tian, B., and Manley, J.L. (2013). Alternative cleavage and polyadenylation: The long and short of it. Trends in Biochemical Sciences 38, 312-320.
Tian, B., Pan, Z., and Lee, J.Y. (2007). Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome research 17, 156-165.
Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., and Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols 7, 562-578.
Uhlen M., Zhang C., Lee S., Sjöstedt E., Fagerberg L., Bidkhori G., Benfeitas R., et al. (2017). A pathology atlas of the human cancer transcriptome. Science 18, eaan2507.
Vicente-Dueñas, C., Romero-Camarero, I., Cobaleda, C., and Sánchez-García, I. (2013). Function of oncogenes in cancer development: a changing paradigm. The EMBO journal 32, 1502-1513.
Villicana, C., Cruz, G., and Zurita, M. (2014). The basal transcription machinery as a target for cancer therapy. Cancer cell international 14, 18.
Wang, J., Liu, Q., and Shyr, Y. (2015). Dysregulated transcription across diverse cancer types reveals the importance of RNA-binding protein in carcinogenesis. BMC genomics 16 Suppl 7, S5.
Wang, Z., Gerstein, M., and Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews Genetics 10, 57-63.
Wodicka, L, Dong, H., Mittmann, M., Ho, MH., and Lockhart, DJ. (1997). Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotechnology 15, 1359-1367.
Wood K.W., Lad L., Luo L., Qian X., Knight S.D., Nevins N., Brejc K., Sutton D., Gilmartin A.G., Chua P.R., Desai R., Schauer S.P., et al. (2010). Antitumor activity of an allosteric inhibitor of centromere-associated protein-E. Proceedings of the National Academy of Sciences of the United States of America 107, 5839-44.
Wu, T.D., and Nacu, S. (2010). Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics (Oxford, England) 26, 873-881.
Wu, Z. (2009)A review of statistical methods for preprocessing oligonucleotide microarrays. Statistical methods in medical research 18, 533-541.
Xia, Z., Donehower, L.A., Cooper, T.A.., Neilson, J.R., Wheeler, D.A., Wagner, E.J., and Li, W. (2014). Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nature communications 5, 5274.
Yao, C., Choi, E.-A., Weng, L., Xie, X., Wan, J., Xing, Y., Moresco, J.J., Tu, P.G., Yates, J.R., and Shi, Y. (2013). Overlapping and distinct functions of CstF64 and CstF64 + in mammalian mRNA 3' processing. RNA (New York, NY) 19, 1781-1790.
Yoshimoto, R., Kaida, D., Furuno, M., Burroughs, A.M., Noma, S., Suzuki, H., Kawamura, Y., Hayashizaki, Y., Mayeda, A., and Yoshida, M. (2017). Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. RNA (New York, NY) 23, 47-57.
Yu, G., Wang, L. G., Han, Y., and He, Q. Y. (2012). clusterProfiler: an R package for comparing biological themes among gene clusters. Omics: a journal of integrative biology 16, 284-287.
Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., et al. (2008). Model-based analysis of ChIP-Seq (MACS). Genome biology 9, R137.