Afanasyeva A, Bockwoldt M, Cooney CR, Heiland I, Gossmann TI (2018) Human long intrinsically disordered protein regions are frequent targets of positive selection. Genome Res 28: 975-982.
Allen, B.L., and Taatjes, D.J. (2015). The Mediator complex: a central integrator of transcription. Nat Rev Mol Cell Biol 16: 155-166.
Auyeung, V.C., Ulitsky, I., McGeary, S.E., and Bartel, D.P. (2013). Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell 152: 844-858.
Banani, S.F., Lee, H.O., Hyman, A.A., and Rosen, M.K. (2017). Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 18: 285-298.
Banerjee, S., and Chakraborty, S. (2017). Protein intrinsic disorder negatively associates with gene age in different eukaryotic lineages. Mol Biosyst 13: 2044-2055.
Bao, W., Kojima, K.K., and Kohany, O. (2015). Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA 6: 11.
Barbosa-Morais, N.L., Irimia, M., Pan, Q., Xiong, H.Y., Gueroussov, S., Lee, L.J., Slobodeniuc, V., Kutter, C., Watt, S., Colak, R., et al. (2012). The evolutionary landscape of alternative splicing in vertebrate species. Science 338: 1587-1593.
Boija, A., Klein, I.A., Sabari, B.R., Dall'Agnese, A., Coffey, E.L., Zamudio, A.V., Li, C.H., Shrinivas, K., Manteiga, J.C., Hannett, N.M., et al. (2018). Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains. Cell 175: 1842-1855 e1816.
Bolisetty, M.T., and Beemon, K.L. (2012). Splicing of internal large exons is defined by novel cis- acting sequence elements. Nucleic Acids Res 40: 9244-9254.
Brown, C.J., Takayama, S., Campen, A.M., Vise, P., Marshall, T.W., Oldfield, C.J., Williams, C.J., and Dunker, A.K. (2002). Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 55: 104-110.
Bruce, S.R., and Peterson, M.L. (2001). Multiple features contribute to efficient constitutive splicing of an unusually large exon. Nucleic Acids Res 29: 2292-2302.
Buljan, M., Chalancon, G., Eustermann, S., Wagner, G.P., Fuxreiter, M., Bateman, A., and Babu, M.M. (2012). Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Molecular cell 46: 871-883.
Busch, A., and Hertel, K.J. (2012). Evolution of SR protein and hnRNP splicing regulatory factors. Wiley Interdiscip Rev RNA 3: 1-12.
Chong, S., Dugast-Darzacq, C., Liu, Z., Dong, P., Dailey, G.M., Cattoglio, C., Heckert, A., Banala, S., Lavis, L., Darzacq, X., et al. (2018). Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 361: eaar2555.
Consortium, E.P. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
Consortium, G. (2015). The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 348: 648-660.
Corbo, C., Orru, S., and Salvatore, F. (2013). SRp20: an overview of its role in human diseases. Biochem Biophys Res Commun 436: 1-5.
Crooks, G.E., Hon, G., Chandonia, J.-M., and Brenner, S.E. (2004). WebLogo: a sequence logo generator. Genome research 14: 1188-1190.
Damianov, A., Ying, Y., Lin, C.H., Lee, J.A., Tran, D., Vashisht, A.A., Bahrami-Samani, E., Xing, Y., Martin, K.C., Wohlschlegel, J.A., et al. (2016). Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR. Cell 165: 606-619.
Davis, C.A., Hitz, B.C., Sloan, C.A., Chan, E.T., Davidson, J.M., Gabdank, I., Hilton, J.A., Jain, K., Baymuradov, U.K., Narayanan, A.K., et al. (2018). The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res 46: D794-D801.
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 29: 15-21.
Ellis, J.D., Barrios-Rodiles, M., Çolak, R., Irimia, M., Kim, T., Calarco, J.A., Wang, X., Pan, Q., O'Hanlon, D., and Kim, P.M. (2012). Tissue-specific alternative splicing remodels protein-protein interaction networks. Molecular cell 46: 884-892.
Feng, H., Bao, S., Rahman, M.A., Weyn-Vanhentenryck, S.M., Khan, A., Wong, J., Shah, A., Flynn, E.D., Krainer, A.R., and Zhang, C. (2019). Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites. Mol Cell 74: 1189-1204 e1186.
Fontrodona, N., Aube, F., Claude, J.B., Polveche, H., Lemaire, S., Tranchevent, L.C., Modolo, L., Mortreux, F., Bourgeois, C.F., and Auboeuf, D. (2019). Interplay between coding and exonic splicing regulatory sequences. Genome Res 29: 711-722.
Fu, X.D., and Ares, M., Jr. (2014). Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 15: 689-701.
Gonatopoulos-Pournatzis, T., Wu, M., Braunschweig, U., Roth, J., Han, H., Best, A.J., Raj, B., Aregger, M., O'Hanlon, D., Ellis, J.D., et al. (2018). Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons. Mol Cell 72: 510-524 e512.
Gueroussov, S., Weatheritt, R.J., O'Hanlon, D., Lin, Z.Y., Narula, A., Gingras, A.C., and Blencowe, B.J. (2017). Regulatory Expansion in Mammals of Multivalent hnRNP Assemblies that Globally Control Alternative Splicing. Cell 170: 324-339 e23.
Haeussler, M., Zweig, A.S., Tyner, C., Speir, M.L., Rosenbloom, K.R., Raney, B.J., Lee, C.M., Lee, B.T., Hinrichs, A.S., and Gonzalez, J.N. (2019). The UCSC genome browser database: 2019 update. Nucleic acids research 47: D853-D858.
Harlen, K.M., and Churchman, L.S. (2017). The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat Rev Mol Cell Biol 18: 263-273.
Hu, H., Miao, Y.-R., Jia, L.-H., Yu, Q.-Y., Zhang, Q., and Guo, A.-Y. (2019). AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. Nucleic acids research 47: D33-D38.
Irimia, M., Weatheritt, R.J., Ellis, J.D., Parikshak, N.N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallieres, M., Tapial, J., Raj, B., O'Hanlon, D., et al. (2014). A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 159: 1511-1523.
Katz, Y., Wang, E.T., Airoldi, E.M., and Burge, C.B. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7: 1009-1015.
Kim, S., and Shendure, J. (2019). Mechanisms of interplay between transcription factors and the 3D genome. Molecular cell 76: 306-319.
Kumar, S., Stecher, G., Suleski, M., and Hedges, S.B. (2017). TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. Mol Biol Evol 34: 1812-1819.
Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921.
Lee, F.C.Y., and Ule, J. (2018). Advances in CLIP Technologies for Studies of Protein-RNA Interactions. Mol Cell 69: 354-369.
Linding, R., Jensen, L.J., Diella, F., Bork, P., Gibson, T.J., and Russell, R.B. (2003). Protein disorder prediction: implications for structural proteomics. Structure 11: 1453-1459.
Lubelsky, Y., and Ulitsky, I. (2018). Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Nature 555: 107-111.
Mészáros, B., Erdős, G., and Dosztányi, Z. (2018). IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic acids research 46: W329-W337.
Machanick, P., and Bailey, T.L. (2011). MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27: 1696-1697.
Martin, M. (2011). Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads. EMBnet. journal 17: 10-12.
Masamha, C.P., Xia, Z., Yang, J., Albrecht, T.R., Li, M., Shyu, A.-B., Li, W., and Wagner, E.J. (2014). CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature 510: 412-416.
Masuda A, Kawachi T, Ohno K (2021) Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein-RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing. Int J Mol Sci 22: 5312.
Masuda, A., Kawachi, T., Takeda, J.I., Ohkawara, B., Ito, M., and Ohno, K. (2020). tRIP-seq reveals repression of premature polyadenylation by co-transcriptional FUS-U1 snRNP assembly. EMBO Rep 21: e49890.
Masuda, A., Takeda, J., Okuno, T., Okamoto, T., Ohkawara, B., Ito, M., Ishigaki, S., Sobue, G., and Ohno, K. (2015). Position-specific binding of FUS to nascent RNA regulates mRNA length. Genes Dev 29: 1045-1057.
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.
Mittal, P., and Roberts, C.W.M. (2020). The SWI/SNF complex in cancer - biology, biomarkers and therapy. Nat Rev Clin Oncol 17: 435-448.
Mizushima S, Nagata S (1990) pEF-BOS, a powerful mammalian expression vector. Nucleic Acids Res 18: 5322.
Muller-McNicoll, M., Botti, V., de Jesus Domingues, A.M., Brandl, H., Schwich, O.D., Steiner, M.C., Curk, T., Poser, I., Zarnack, K., and Neugebauer, K.M. (2016). SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export. Genes Dev 30: 553-566.
Nojima, T., Gomes, T., Carmo-Fonseca, M., and Proudfoot, N.J. (2016). Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide. Nat Protoc 11: 413-428.
Oldfield, C.J., and Dunker, A.K. (2014). Intrinsically disordered proteins and intrinsically disordered protein regions. Annual review of biochemistry 83: 553-584.
Patel, A., Lee, H.O., Jawerth, L., Maharana, S., Jahnel, M., Hein, M.Y., Stoynov, S., Mahamid, J., Saha, S., Franzmann, T.M., et al. (2015). A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation. Cell 162: 1066-1077.
Piva, F., Giulietti, M., Burini, A.B., and Principato, G. (2012). SpliceAid 2: a database of human splicing factors expression data and RNA target motifs. Hum Mutat 33: 81-85.
Raudvere, U., Kolberg, L., Kuzmin, I., Arak, T., Adler, P., Peterson, H., and Vilo, J. (2019). g: Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic acids research 47: W191-W198.
Robberson, B.L., Cote, G.J., and Berget, S.M. (1990). Exon definition may facilitate splice site selection in RNAs with multiple exons. Molecular and cellular biology 10: 84-94.
Romero, P., Obradovic, Z., Li, X., Garner, E.C., Brown, C.J., and Dunker, A.K. (2001). Sequence complexity of disordered protein. Proteins: Structure, Function, and Bioinformatics 42: 38-48.
Romero, P.R., Zaidi, S., Fang, Y.Y., Uversky, V.N., Radivojac, P., Oldfield, C.J., Cortese, M.S., Sickmeier, M., LeGall, T., and Obradovic, Z. (2006). Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proceedings of the National Academy of Sciences 103: 8390-8395.
Sabari, B.R., Dall'Agnese, A., Boija, A., Klein, I.A., Coffey, E.L., Shrinivas, K., Abraham, B.J., Hannett, N.M., Zamudio, A.V., Manteiga, J.C., et al. (2018). Coactivator condensation at super- enhancers links phase separation and gene control. Science 361: eaar3958.
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012). Fiji: an open-source platform for biological-image analysis. Nat Methods 9: 676-682.
Schneider, C.A., Rasband, W.S., and Eliceiri, K.W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature methods 9: 671-675.
Schwich OD, Blumel N, Keller M, Wegener M, Setty ST, Brunstein ME, Poser I, Mozos IRL, Suess B, Munch C, McNicoll F, Zarnack K, Muller-McNicoll M (2021) SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biol 22: 82.
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research 13: 2498-2504.
Silveira, M.A.D., and Bilodeau, S. (2018). Defining the Transcriptional Ecosystem. Mol Cell 72: 920- 924.
Smithers, B., Oates, M.E., and Gough, J. (2015). Splice junctions are constrained by protein disorder. Nucleic acids research 43: 4814-4822.
So BR, Di C, Cai Z, Venters CC, Guo J, Oh JM, Arai C, Dreyfuss G (2019) A Complex of U1 snRNP with Cleavage and Polyadenylation Factors Controls Telescripting, Regulating mRNA Transcription in Human Cells. Mol Cell 76: 590-599.
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., et al. (2005). Gene set enrichment analysis: a knowledge- based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
Szklarczyk, D., Gable, A.L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N.T., Morris, J.H., Bork, P., et al. (2019). STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 47: D607-D613.
Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., Van Baren, M.J., Salzberg, S.L., Wold, B.J., and Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology 28: 511-515.
Ule, J., and Blencowe, B.J. (2019). Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. Mol Cell 76: 329-345.
Van Nostrand, E.L., Freese, P., Pratt, G.A., Wang, X., Wei, X., Xiao, R., Blue, S.M., Chen, J.Y., Cody, N.A.L., Dominguez, D., et al. (2020). A large-scale binding and functional map of human RNA- binding proteins. Nature 583: 711-719.
Wang, Z., Qiu, H., He, J., Liu, L., Xue, W., Fox, A., Tickner, J., and Xu, J. (2020). The emerging roles of hnRNPK. J Cell Physiol 235: 1995-2008.
Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F., and Jones, D.T. (2004). Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337: 635-645.
Yamamoto, K., Furukawa, M.T., Fukumura, K., Kawamura, A., Yamada, T., Suzuki, H., Hirose, T., Sakamoto, H., and Inoue, K. (2016). Control of the heat stress-induced alternative splicing of a subset of genes by hnRNP K. Genes Cells 21: 1006-1014.
Yandell, M., Mungall, C.J., Smith, C., Prochnik, S., Kaminker, J., Hartzell, G., Lewis, S., and Rubin, G.M. (2006). Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput Biol 2: e15.
Yeo, G., and Burge, C.B. (2004). Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11: 377-394.
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 Biol 9: R137.
Zhu, Y., Wang, X., Forouzmand, E., Jeong, J., Qiao, F., Sowd, G.A., Engelman, A.N., Xie, X., Hertel, K.J., and Shi, Y. (2018). Molecular mechanisms for CFIm-mediated regulation of mRNA alternative polyadenylation. Molecular cell 69: 62-74. e64.
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