Publications

2024

Peyda P, Lin CH, Onwuzurike K, Black DL. The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multi-part RNA regulatory modules. bioRxiv [Preprint]. 2024 Jul 16:2024.07.12.603345. doi: 10.1101/2024.07.12.603345. PMID: 39071271; PMCID: PMC11275806.

Xiao W, Halabi R, Lin CH, Nazim M, Yeom KH, Black DL. The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons. Genes Dev. 2024 May 21;38(7-8):294-307. doi: 10.1101/gad.351557.124. PMID: 38688681; PMCID: PMC11146593.

Nazim M, Lin CH, Feng AC, Xiao W, Yeom KH, Li M, Daly AE, Tan X, Vu H, Ernst J, Carey MF, Smale ST, Black DL. Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiation. Cell Stem Cell. 2024 May 2;31(5):754-771.e6. doi: 10.1016/j.stem.2024.04.001. PMID: 38701759; PMCID: PMC11126784.

Damianov A, Lin CH, Huang J, Zhou L, Jami-Alahmadi Y, Peyda P, Wohlschlegel J, Black DL. The splicing regulators RBM5 and RBM10 are subunits of the U2 snRNP engaged with intron branch sites on chromatin. Mol Cell. 2024 Apr 18;84(8):1496-1511.e7. doi: 10.1016/j.molcel.2024.02.039. Epub 2024 Mar 26. PMID: 38537639; PMCID: PMC11057915.

2023

Chen X, Yang HT, Zhang B, Phillips JW, Cheng D, Rigo F, Witte ON, Xing Y, Black DL. The RNA-binding proteins hnRNP H and F regulate splicing of a MYC-dependent HRAS exon in prostate cancer cells. Proc Natl Acad Sci U S A. 2023 Jul 11;120(28):e2220190120. doi: 10.1073/pnas.2220190120. Epub 2023 Jul 3. PMID: 37399401.

Xiao W, Yeom KH, Lin CH, Black DL. Improved enzymatic labeling of fluorescent in situ hybridization probes applied to the visualization of retained introns in cells. RNA. 2023 May 2:rna.079591.123. doi: 10.1261/rna.079591.123. Epub ahead of print. PMID: 37130703.

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

Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Mancia Leon WR, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Sabri S, Leonhardt H, Zheng S, Guttman M, Black DL, Plath K. 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.

Phillips JW, Pan Y, Tsai BL, Xie Z, Demirdjian L, Xiao W, Yang HT, Zhang Y, Lin CH, Cheng D, Hu Q, Liu S, Black DL, Witte ON, Xing Y. 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

Zhang Z, Pan Z, Ying Y, Xie Z, Adhikari S, Phillips J, Carstens RP, Black DL, Wu Y, Xing Y. 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

Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. 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.

Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. 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.

Yeom KH, Mitchell S, Linares AJ, Zheng S, Lin CH, Wang XJ, Hoffmann A, Black DL. 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.

Vuong CK, Wei W, Lee JA, Lin CH, Damianov A, de la Torre-Ubieta L, Halabi R, Otis KO, Martin KC, O’Dell TJ, Black DL. 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

Li Q, Zheng S, Han A, Lin CH, Stoilov P, Fu XD, Black DL. 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.

Ying Y, Wang XJ, Vuong CK, Lin CH, Damianov A, Black DL. 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.

Ke S, Pandya-Jones A, Saito Y, Fak JJ, Vågbø CB, Geula S, Hanna JH, Black DL, Darnell JE Jr, Darnell RB. 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.

Wang J, Rajbhandari P, Damianov A, Han A, Sallam T, Waki H, Villanueva CJ, Lee SD, Nielsen R, Mandrup S, Reue K, Young SG, Whitelegge J, Saez E, Black DL, Tontonoz P. 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

Vuong JK, Lin CH, Zhang M, Chen L, Black DL, Zheng S. 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.

Wongpalee SP, Vashisht A, Sharma S, Chui D, Wohlschlegel JA, Black DL. 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.

Zhang X, Chen MH, Wu X, Kodani A, Fan J, Doan R, Ozawa M, Ma J, Yoshida N, Reiter JF, Black DL, Kharchenko PV, Sharp PA, Walsh CA. 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.

Keppetipola NM, Yeom KH, Hernandez AL, Bui T, Sharma S, Black DL. 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.

Vuong CK, Black DL, Zheng S. 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.

Damianov A, Ying Y, Lin CH, Lee JA, Tran D, Vashisht AA, Bahrami-Samani E, Xing Y, Martin KC, Wohlschlegel JA, Black DL. 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

Lee JA, Damianov A, Lin CH, Fontes M, Parikshak NN, Anderson ES, Geschwind DH, Black DL, Martin KC. 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.

Linares AJ, Lin CH, Damianov A, Adams KL, Novitch BG, Black DL. 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.

Black D. 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

Sharma S, Wongpalee SP, Vashisht A, Wohlschlegel JA, Black DL. 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.

Han A, Stoilov P, Linares AJ, Zhou Y, Fu XD, Black DL. 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.

Li Q, Zheng S, Han A, Lin CH, Stoilov P, Fu XD, Black DL. 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

Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S, Massirer KB, Pratt GA, Black DL, Gray JW, Conboy JG, Yeo GW. 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.

Zheng S, Black DL. 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.

Babic I, Anderson ES, Tanaka K, Guo D, Masui K, Li B, Zhu S, Gu Y, Villa GR, Akhavan D, Nathanson D, Gini B, Mareninov S, Li R, Camacho CE, Kurdistani SK, Eskin A, Nelson SF, Yong WH, Cavenee WK, Cloughesy TF, Christofk HR, Black DL, Mischel PS. 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.

Zheng S, Damoiseaux R, Chen L, Black DL. 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.

Pandya-Jones A, Bhatt DM, Lin CH, Tong AJ, Smale ST, Black DL. 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

Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST. 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.

Keppetipola N, Sharma S, Li Q, Black DL. 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.

Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL. 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.

Gehman LT, Meera P, Stoilov P, Shiue L, O’Brien JE, Meisler MH, Ares M Jr, Otis TS, Black DL. 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.

Zheng S, Gray EE, Chawla G, Porse BT, O’Dell TJ, Black DL. 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

Pandya-Jones A. 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.

Gehman LT, Stoilov P, Maguire J, Damianov A, Lin CH, Shiue L, Ares M Jr, Mody I, Black DL. 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.

Tang ZZ, Sharma S, Zheng S, Chawla G, Nikolic J, Black DL. 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.

Sharma S, Maris C, Allain FH, Black DL. 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.

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