Preprint
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2021
Yeom KH, Pan Z, Lin CH, Lim HY, Xiao W, Xing Y, Black DL. Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring. Genome Res. 2021 Jun;31(6):1106-1119. doi: 10.1101/gr.273904.120. Epub 2021 Apr 8. PMID: 33832989.
2020
A protein assembly mediates Xist localization and gene silencing. Nature. 2020 Sep 9;. doi: 10.1038/s41586-020-2703-0. [Epub ahead of print] PubMed PMID: 32908311; NIHMSID:NIHMS1605140.
Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers. Proc Natl Acad Sci U S A. 2020 Mar 10;117(10):5269-5279. doi: 10.1073/pnas.1915975117. Epub 2020 Feb 21. PubMed PMID: 32086391; PubMed Central PMCID: PMC7071906.
2019
Deep-learning augmented RNA-seq analysis of transcript splicing. Nat Methods. 2019 Apr;16(4):307-310. doi: 10.1038/s41592-019-0351-9. Epub 2019 Mar 25. PubMed PMID: 30923373.
2018
Author Correction: Inhibiting amyloid-β cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design. Nat Chem. 2018 Dec;10(12):1267. doi: 10.1038/s41557-018-0182-9. PubMed PMID: 30420778; PubMed Central PMCID: PMC7124629.
Inhibiting amyloid-β cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design. Nat Chem. 2018 Dec;10(12):1213-1221. doi: 10.1038/s41557-018-0147-z. Epub 2018 Oct 8. PubMed PMID: 30297750; PubMed Central PMCID: PMC6250578.
Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):E11061-E11070. doi: 10.1073/pnas.1809609115. Epub 2018 Nov 6. PubMed PMID: 30401736; PubMed Central PMCID: PMC6255174.
Rbfox1 Regulates Synaptic Transmission through the Inhibitory Neuron-Specific vSNARE Vamp1. Neuron. 2018 Apr 4;98(1):127-141.e7. doi: 10.1016/j.neuron.2018.03.008. PubMed PMID: 29621484; PubMed Central PMCID: PMC5890944.
2017
Correction: The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. Elife. 2017 Oct 9;6. doi: 10.7554/eLife.31550. PubMed PMID: 28990924; PubMed Central PMCID: PMC5633341.
Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain. Cell. 2017 Jul 13;170(2):312-323.e10. doi: 10.1016/j.cell.2017.06.022. PubMed PMID: 28708999; PubMed Central PMCID: PMC5553710.
m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev. 2017 May 15;31(10):990-1006. doi: 10.1101/gad.301036.117. PubMed PMID: 28637692; PubMed Central PMCID: PMC5495127.
RNA-binding protein PSPC1 promotes the differentiation-dependent nuclear export of adipocyte RNAs. J Clin Invest. 2017 Mar 1;127(3):987-1004. doi: 10.1172/JCI89484. Epub 2017 Feb 13. PubMed PMID: 28192372; PubMed Central PMCID: PMC5330726.
2016
PTBP1 and PTBP2 Serve Both Specific and Redundant Functions in Neuronal Pre-mRNA Splicing. Cell Rep. 2016 Dec 6;17(10):2766-2775. doi: 10.1016/j.celrep.2016.11.034. PubMed PMID: 27926877; PubMed Central PMCID: PMC5179036.
Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing. Elife. 2016 Nov 24;5. doi: 10.7554/eLife.19743. PubMed PMID: 27882870; PubMed Central PMCID: PMC5122456.
Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex. Cell. 2016 Aug 25;166(5):1147-1162.e15. doi: 10.1016/j.cell.2016.07.025. PubMed PMID: 27565344; PubMed Central PMCID: PMC5248659.
Multiple determinants of splicing repression activity in the polypyrimidine tract binding proteins, PTBP1 and PTBP2. RNA. 2016 Aug;22(8):1172-80. doi: 10.1261/rna.057505.116. Epub 2016 Jun 10. PubMed PMID: 27288314; PubMed Central PMCID: PMC4931110.
The neurogenetics of alternative splicing. Nat Rev Neurosci. 2016 May;17(5):265-81. doi: 10.1038/nrn.2016.27. Review. PubMed PMID: 27094079; PubMed Central PMCID: PMC4861142.
Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR. Cell. 2016 Apr 21;165(3):606-19. doi: 10.1016/j.cell.2016.03.040. PubMed PMID: 27104978; PubMed Central PMCID: PMC4841943.
2015
Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes. Neuron. 2016 Jan 6;89(1):113-28. doi: 10.1016/j.neuron.2015.11.025. Epub 2015 Dec 10. PubMed PMID: 26687839; PubMed Central PMCID: PMC4858412.
The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation. Elife. 2015 Dec 24;4:e09268. doi: 10.7554/eLife.09268. PubMed PMID: 26705333; PubMed Central PMCID: PMC4755740.
Reflections on the RNA journal at 20 and its role in the question of splice site choice. RNA. 2015 Apr;21(4):497-9. doi: 10.1261/rna.050377.115. PubMed PMID: 25780111; PubMed Central PMCID: PMC4371253.
2014
Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly. Genes Dev. 2014 Nov 15;28(22):2518-31. doi: 10.1101/gad.248625.114. PubMed PMID: 25403181; PubMed Central PMCID: PMC4233244.
De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. PLoS Comput Biol. 2014 Jan;10(1):e1003442. doi: 10.1371/journal.pcbi.1003442. eCollection 2014 Jan. PubMed PMID: 24499931; PubMed Central PMCID: PMC3907290.
The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation. Elife. 2014;3:e01201. doi: 10.7554/eLife.01201. Epub 2014 Jan 21. PubMed PMID: 24448406; PubMed Central PMCID: PMC3896118.
2013
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol. 2013 Dec;20(12):1434-42. doi: 10.1038/nsmb.2699. Epub 2013 Nov 10. PubMed PMID: 24213538; PubMed Central PMCID: PMC3918504.
Alternative pre-mRNA splicing in neurons: growing up and extending its reach. Trends Genet. 2013 Aug;29(8):442-8. doi: 10.1016/j.tig.2013.04.003. Epub 2013 May 3. Review. PubMed PMID: 23648015; PubMed Central PMCID: PMC3959871.
EGFR mutation-induced alternative splicing of Max contributes to growth of glycolytic tumors in brain cancer. Cell Metab. 2013 Jun 4;17(6):1000-8. doi: 10.1016/j.cmet.2013.04.013. Epub 2013 May 23. PubMed PMID: 23707073; PubMed Central PMCID: PMC3679227.
A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing. Genome Res. 2013 Jun;23(6):998-1007. doi: 10.1101/gr.147546.112. Epub 2013 May 1. PubMed PMID: 23636947; PubMed Central PMCID: PMC3668367.
Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA. 2013 Jun;19(6):811-27. doi: 10.1261/rna.039081.113. Epub 2013 Apr 24. PubMed PMID: 23616639; PubMed Central PMCID: PMC3683915.
2012
Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell. 2012 Jul 20;150(2):279-90. doi: 10.1016/j.cell.2012.05.043. PubMed PMID: 22817891; PubMed Central PMCID: PMC3405548.
Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2. Crit Rev Biochem Mol Biol. 2012 Jul-Aug;47(4):360-78. doi: 10.3109/10409238.2012.691456. Epub 2012 Jun 2. PubMed PMID: 22655688; PubMed Central PMCID: PMC3422667.
The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA. 2012 May;18(5):1041-9. doi: 10.1261/rna.032912.112. Epub 2012 Mar 28. PubMed PMID: 22456266; PubMed Central PMCID: PMC3334691.
The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function. Genes Dev. 2012 Mar 1;26(5):445-60. doi: 10.1101/gad.182477.111. Epub 2012 Feb 22. PubMed PMID: 22357600; PubMed Central PMCID: PMC3305983.
PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2. Nat Neurosci. 2012 Jan 15;15(3):381-8, S1. doi: 10.1038/nn.3026. PubMed PMID: 22246437; PubMed Central PMCID: PMC3288398.
2011
Pre-mRNA splicing during transcription in the mammalian system. Wiley Interdiscip Rev RNA. 2011 Sep-Oct;2(5):700-17. doi: 10.1002/wrna.86. Epub 2011 May 2. Review. PubMed PMID: 21823230; PubMed Central PMCID: PMC3154077.
The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet. 2011 May 29;43(7):706-11. doi: 10.1038/ng.841. PubMed PMID: 21623373; PubMed Central PMCID: PMC3125461.
Regulation of the mutually exclusive exons 8a and 8 in the CaV1.2 calcium channel transcript by polypyrimidine tract-binding protein. J Biol Chem. 2011 Mar 25;286(12):10007-16. doi: 10.1074/jbc.M110.208116. Epub 2011 Jan 31. PubMed PMID: 21282112; PubMed Central PMCID: PMC3060452.
U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression. Mol Cell. 2011 Mar 4;41(5):579-88. doi: 10.1016/j.molcel.2011.02.012. PubMed PMID: 21362553; PubMed Central PMCID: PMC3931528.