Publications
2024
Duan, C., Mooney, T., Buerer, L., Bowers, C., Rong, S., Kim, S.W., Fredericks, A.M., Monaghan, S.F., and Fairbrother, W.G. (2024). The unusual gene architecture of polyubiquitin is created by dual-specific splice sites. Genome Biol 25, 33. 10.1186/s13059-023-03157-8. Download PDF
2023
Clark, N.E., Katolik, A., Gallant, P., Welch, A., Murphy, E., Buerer, L., Schorl, C., Naik, N., Naik, M.T., Holloway, S.P., et al. (2023). Activation of human RNA lariat debranching enzyme Dbr1 by binding protein TTDN1 occurs though an intrinsically disordered C-terminal domain. J Biol Chem 299, 105100. 10.1016/j.jbc.2023.105100. Download PDF
Townley, B.A., Buerer, L., Tsao, N., Bacolla, A., Mansoori, F., Rusanov, T., Clark, N., Goodarzi, N., Schmidt, N., Srivatsan, S.N., et al. (2023). A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy. Mol Cell 83, 2258-2275.e11. 10.1016/j.molcel.2023.06.011. Download PDF
Rong, S., Neil, C.R., Welch, A., Duan, C., Maguire, S., Meremikwu, I.C., Meyerson, M., Evans, B.J., and Fairbrother, W.G. (2023). Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans. Proc Natl Acad Sci U S A 120, e2218308120. 10.1073/pnas.2218308120. Download PDF
2022
Clark, N.E., Katolik, A., Welch, A., Schorl, C., Holloway, S.P., Schuermann, J.P., Hart, P.J., Taylor, A.B., Damha, M.J., and Fairbrother, W.G. (2022). Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product. Biochemistry 61, 2933–2939. 10.1021/acs.biochem.2c00590. Download PDF
Fredericks, A.M., East, K.W., Shi, Y., Liu, J., Maschietto, F., Ayala, A., Cioffi, W.G., Cohen, M., Fairbrother, W.G., Lefort, C.T., et al. (2022). Identification and mechanistic basis of non-ACE2 blocking neutralizing antibodies from COVID-19 patients with deep RNA sequencing and molecular dynamics simulations. Front Mol Biosci 9, 1080964. 10.3389/fmolb.2022.1080964. Download PDF
Fredericks, A.M., Jentzsch, M.S., Cioffi, W.G., Cohen, M., Fairbrother, W.G., Gandhi, S.J., Harrington, E.O., Nau, G.J., Reichner, J.S., Ventetuolo, C.E., et al. (2022). Deep RNA sequencing of intensive care unit patients with COVID-19. Sci Rep 12, 15755. 10.1038/s41598-022-20139-1. Download PDF
Clark, N.E., Katolik, A., Taggart, A.J., Buerer, L., Holloway, S.P., Miller, N., Phillips, J.D., Farrell, C.P., Damha, M.J., and Fairbrother, W.G. (2022). Metal content and kinetic properties of yeast RNA lariat debranching enzyme Dbr1. RNA 28, 927–936. 10.1261/rna.079159.122. Download PDF
Rhine, C.L., Neil, C., Wang, J., Maguire, S., Buerer, L., Salomon, M., Meremikwu, I.C., Kim, J., Strande, N.T., and Fairbrother, W.G. (2022). Massively parallel reporter assays discover de novo exonic splicing mutants in paralogs of Autism genes. PLoS Genet 18, e1009884. 10.1371/journal.pgen.1009884. Download PDF
2021
Duan, C., Buerer, L., Wang, J., Kaplan, S., Sabalewski, G., Jay, G.D., Monaghan, S.F., Arena, A.E., and Fairbrother, W.G. (2021). Efficient Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Exhaled Breath. J Mol Diagn 23, 1661–1670. 10.1016/j.jmoldx.2021.09.005. Download PDF
Wang, Z., Fan, X., Shen, Y., Pagadala, M.S., Signer, R., Cygan, K.J., Fairbrother, W.G., Carter, H., Chung, W.K., and Huang, K.-L. (2021). Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes. Genome Med 13, 147. 10.1186/s13073-021-00964-1. Download PDF
Glidden, D.T., Buerer, J.L., Saueressig, C.F., and Fairbrother, W.G. (2021). Hotspot exons are common targets of splicing perturbations. Nat Commun 12, 2756. 10.1038/s41467-021-22780-2. Download PDF
2020
Rong, S., Buerer, L., Rhine, C.L., Wang, J., Cygan, K.J., and Fairbrother, W.G. (2020). Mutational bias and the protein code shape the evolution of splicing enhancers. Nat Commun 11, 2845. 10.1038/s41467-020-16673-z. Download PDF
Fredericks, A.M., Wang, L.J., Fairbrother, W.G., Ayala, A., and Monaghan, S.F. (2020). Alternative RNA splicing and alternative transcription start/end in acute respiratory distress syndrome. Intensive Care Med 46, 813–815. 10.1007/s00134-020-05953-3. Download PDF
2019
Neil, C.R., and Fairbrother, W.G. (2019). Intronic RNA: Ad’junk’ mediator of post-transcriptional gene regulation. Biochim Biophys Acta Gene Regul Mech 1862, 194439. 10.1016/j.bbagrm.2019.194439. Download PDF
Mount, S.M., Avsec, Ž., Carmel, L., Casadio, R., Çelik, M.H., Chen, K., Cheng, J., Cohen, N.E., Fairbrother, W.G., Fenesh, T., et al. (2019). Assessing predictions of the impact of variants on splicing in CAGI5. Hum Mutat 40, 1215–1224. 10.1002/humu.23869. Download PDF
Rhine, C.L., Neil, C., Glidden, D.T., Cygan, K.J., Fredericks, A.M., Wang, J., Walton, N.A., and Fairbrother, W.G. (2019). Future directions for high-throughput splicing assays in precision medicine. Hum Mutat 40, 1225–1234. 10.1002/humu.23866. Download PDF
Cheng, J., Nguyen, T.Y.D., Cygan, K.J., Çelik, M.H., Fairbrother, W.G., Avsec, Ž., and Gagneur, J. (2019). MMSplice: modular modeling improves the predictions of genetic variant effects on splicing. Genome Biol 20, 48. 10.1186/s13059-019-1653-z. Download PDF
2018
Taggart, A.J., and Fairbrother, W.G. (2018). ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data. Quant Biol 6, 267–274. 10.1007/s40484-018-0141-x. Download PDF
Monaghan, S.F., Banerjee, D., Chung, C.-S., Lomas-Neira, J., Cygan, K.J., Rhine, C.L., Fairbrother, W.G., Heffernan, D.S., Levy, M.M., Cioffi, W.G., et al. (2018). Changes in the process of alternative RNA splicing results in soluble B and T lymphocyte attenuator with biological and clinical implications in critical illness. Mol Med 24, 32. 10.1186/s10020-018-0036-3. Download PDF
Rhine, C.L., Cygan, K.J., Soemedi, R., Maguire, S., Murray, M.F., Monaghan, S.F., and Fairbrother, W.G. (2018). Hereditary cancer genes are highly susceptible to splicing mutations. PLoS Genet 14, e1007231. 10.1371/journal.pgen.1007231. Download PDF
Zhang, S.-Y., Clark, N.E., Freije, C.A., Pauwels, E., Taggart, A.J., Okada, S., Mandel, H., Garcia, P., Ciancanelli, M.J., Biran, A., et al. (2018). Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection. Cell 172, 952-965.e18. 10.1016/j.cell.2018.02.019. Download PDF
2017
Kim, S.W., Taggart, A.J., Heintzelman, C., Cygan, K.J., Hull, C.G., Wang, J., Shrestha, B., and Fairbrother, W.G. (2017). Widespread intra-dependencies in the removal of introns from human transcripts. Nucleic Acids Res 45, 9503–9513. 10.1093/nar/gkx661. Download PDF
Cygan, K.J., Sanford, C.H., and Fairbrother, W.G. (2017). Spliceman2: a computational web server that predicts defects in pre-mRNA splicing. Bioinformatics 33, 2943–2945. 10.1093/bioinformatics/btx343. Download PDF
Cygan, K.J., Soemedi, R., Rhine, C.L., Profeta, A., Murphy, E.L., Murray, M.F., and Fairbrother, W.G. (2017). Defective splicing of the RB1 transcript is the dominant cause of retinoblastomas. Hum Genet 136, 1303–1312. 10.1007/s00439-017-1833-4. Download PDF
Soemedi, R., Cygan, K.J., Rhine, C.L., Glidden, D.T., Taggart, A.J., Lin, C.-L., Fredericks, A.M., and Fairbrother, W.G. (2017). The effects of structure on pre-mRNA processing and stability. Methods 125, 36–44. 10.1016/j.ymeth.2017.06.001. Download PDF
Soemedi, R., Cygan, K.J., Rhine, C.L., Wang, J., Bulacan, C., Yang, J., Bayrak-Toydemir, P., McDonald, J., and Fairbrother, W.G. (2017). Pathogenic variants that alter protein code often disrupt splicing. Nat Genet 49, 848–855. 10.1038/ng.3837. Download PDF
Taggart, A.J., Lin, C.-L., Shrestha, B., Heintzelman, C., Kim, S., and Fairbrother, W.G. (2017). Large-scale analysis of branchpoint usage across species and cell lines. Genome Res 27, 639–649. 10.1101/gr.202820.115. Download PDF
2016
Monaghan, S.F., Chung, C.-S., Chen, Y., Lomas-Neira, J., Fairbrother, W.G., Heffernan, D.S., Cioffi, W.G., and Ayala, A. (2016). Soluble programmed cell death receptor-1 (sPD-1): a potential biomarker with anti-inflammatory properties in human and experimental acute respiratory distress syndrome (ARDS). J Transl Med 14, 312. 10.1186/s12967-016-1071-x. Download PDF
Lin, C.-L., Taggart, A.J., and Fairbrother, W.G. (2016). RNA structure in splicing: An evolutionary perspective. RNA Biol 13, 766–771. 10.1080/15476286.2016.1208893. Download PDF
Stracquadanio, G., Wang, X., Wallace, M.D., Grawenda, A.M., Zhang, P., Hewitt, J., Zeron-Medina, J., Castro-Giner, F., Tomlinson, I.P., Goding, C.R., et al. (2016). The importance of p53 pathway genetics in inherited and somatic cancer genomes. Nat Rev Cancer 16, 251–265. 10.1038/nrc.2016.15. Download PDF
Lin, C.-L., Taggart, A.J., Lim, K.H., Cygan, K.J., Ferraris, L., Creton, R., Huang, Y.-T., and Fairbrother, W.G. (2016). RNA structure replaces the need for U2AF2 in splicing. Genome Res 26, 12–23. 10.1101/gr.181008.114. Download PDF
2015
Fredericks, A.M., Cygan, K.J., Brown, B.A., and Fairbrother, W.G. (2015). RNA-Binding Proteins: Splicing Factors and Disease. Biomolecules 5, 893–909. 10.3390/biom5020893. Download PDF
2014
Soemedi, R., Vega, H., Belmont, J.M., Ramachandran, S., and Fairbrother, W.G. (2014). Genetic variation and RNA binding proteins: tools and techniques to detect functional polymorphisms. Adv Exp Med Biol 825, 227–266. 10.1007/978-1-4939-1221-6_7
2013
Ceyhan-Birsoy, O., Agrawal, P.B., Hidalgo, C., Schmitz-Abe, K., DeChene, E.T., Swanson, L.C., Soemedi, R., Vasli, N., Iannaccone, S.T., Shieh, P.B., et al. (2013). Recessive truncating titin gene, TTN, mutations presenting as centronuclear myopathy. Neurology 81, 1205–1214. 10.1212/WNL.0b013e3182a6ca62.
2012
Yajima, M., Fairbrother, W.G., and Wessel, G.M. (2012). ISWI contributes to ArsI insulator function in development of the sea urchin. Development 139, 3613–3622. 10.1242/dev.081828. Download PDF
Taggart, A.J., DeSimone, A.M., Shih, J.S., Filloux, M.E., and Fairbrother, W.G. (2012). Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo. Nat Struct Mol Biol 19, 719–721. 10.1038/nsmb.2327. Download PDF
Lim, K.H., and Fairbrother, W.G. (2012). Spliceman--a computational web server that predicts sequence variations in pre-mRNA splicing. Bioinformatics 28, 1031–1032. 10.1093/bioinformatics/bts074. Download PDF
2011
Lim, K.H., Ferraris, L., Filloux, M.E., Raphael, B.J., and Fairbrother, W.G. (2011). Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc Natl Acad Sci U S A 108, 11093–11098. 10.1073/pnas.1101135108. Download PDF
Ferraris, L., Stewart, A.P., Kang, J., DeSimone, A.M., Gemberling, M., Tantin, D., and Fairbrother, W.G. (2011). Combinatorial binding of transcription factors in the pluripotency control regions of the genome. Genome Res 21, 1055–1064. 10.1101/gr.115824.110. Download PDF
Ferraris, L., Stewart, A.P., Gemberling, M.P., Reid, D.C., Lapadula, M.J., Thompson, W.A., and Fairbrother, W.G. (2011). High-throughput mapping of protein occupancy identifies functional elements without the restriction of a candidate factor approach. Nucleic Acids Res 39, e33. 10.1093/nar/gkq1213. Download PDF
Waugh, J.L., Celver, J., Sharma, M., Dufresne, R.L., Terzi, D., Risch, S.C., Fairbrother, W.G., Neve, R.L., Kane, J.P., Malloy, M.J., et al. (2011). Association between regulator of G protein signaling 9-2 and body weight. PLoS One 6, e27984. 10.1371/journal.pone.0027984. Download PDF
2010
Chang, B., Levin, J., Thompson, W.A., and Fairbrother, W.G. (2010). High-throughput binding analysis determines the binding specificity of ASF/SF2 on alternatively spliced human pre-mRNAs. Comb Chem High Throughput Screen 13, 242–252. 10.2174/138620710790980522. Download PDF
2009
Reid, D.C., Chang, B.L., Gunderson, S.I., Alpert, L., Thompson, W.A., and Fairbrother, W.G. (2009). Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence. RNA 15, 2385–2397. 10.1261/rna.1821809. Download PDF
Kang, J., Gemberling, M., Nakamura, M., Whitby, F.G., Handa, H., Fairbrother, W.G., and Tantin, D. (2009). A general mechanism for transcription regulation by Oct1 and Oct4 in response to genotoxic and oxidative stress. Genes Dev 23, 208–222. 10.1101/gad.1750709. Download PDF
2008
Tantin, D., Gemberling, M., Callister, C., and Fairbrother, W.G. (2008). High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes. Genome Res 18, 631–639. 10.1101/gr.072942.107. Download PDF
Fairbrother, W.G., and Lipscombe, D. (2008). Repressing the neuron within. Bioessays 30, 1–4. 10.1002/bies.20696. Download PDF
2005
Pfarr, N., Prawitt, D., Kirschfink, M., Schroff, C., Knuf, M., Habermehl, P., Mannhardt, W., Zepp, F., Fairbrother, W.G., Loos, M., et al. (2005). Linking C5 deficiency to an exonic splicing enhancer mutation. J Immunol 174, 4172–4177. 10.4049/jimmunol.174.7.4172. Download PDF
2004
Fairbrother, W.G., Holste, D., Burge, C.B., and Sharp, P.A. (2004). Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol 2, E268. 10.1371/journal.pbio.0020268. Download PDF
Fairbrother, W.G., Yeo, G.W., Yeh, R., Goldstein, P., Mawson, M., Sharp, P.A., and Burge, C.B. (2004). RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res 32, W187-190. 10.1093/nar/gkh393. Download PDF
2002
Fairbrother, W.G., Yeh, R.-F., Sharp, P.A., and Burge, C.B. (2002). Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007–1013. 10.1126/science.1073774. Download PDF
2000
Fairbrother, W.G., and Chasin, L.A. (2000). Human genomic sequences that inhibit splicing. Mol Cell Biol 20, 6816–6825. 10.1128/MCB.20.18.6816-6825.2000. Download PDF