Listed below are selected publications of interest from many of the labs affiliated with the U Penn RNA Group. Contact us to add your recent publication.


2016

A conserved virus-induced cytoplasmic TRAMP-like complex recruits the exosome to target viral RNA for degradation.
Molleston JM, Sabin LR, Moy RH, Menghani SV, Rausch K, Gordesky-Gold B, Hopkins KC, Zhou R, Jensen TH, Wilusz JE, Cherry S.

Genes Dev. 2016 Jul 15;30(14):1658-70. doi: 10.1101/gad.284604.116.

Cytoplasmic poly(A) binding protein-1 binds to genomically encoded sequences within mammalian mRNAs.
Kini HK, Silverman IM, Ji X, Gregory BD, Liebhaber SA.

RNA. 2016 Jan;22(1):61-74. doi: 10.1261/rna.053447.115.

A new view of transcriptome complexity and regulation through the lens of local splicing variations.
Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y.

Elife. 2016 Feb 1;5:e11752. doi: 10.7554/eLife.11752

2015

Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy.
Sotillo E, Barrett DM, Black KL, Bagashev A, Oldridge D, Wu G, Sussman R, Lanauze C, Ruella M, Gazzara MR, Martinez NM, Harrington CT, Chung EY, Perazzelli J, Hofmann TJ, Maude SL, Raman P, Barrera A, Gill S, Lacey SF, Melenhorst JJ, Allman D, Jacoby E, Fry T, Mackall C, Barash Y, Lynch KW, Maris JM, Grupp SA, Thomas-Tikhonenko A.

Cancer Discov. 2015 Dec;5(12):1282-95. doi: 10.1158/2159-8290.CD-15-1020.

Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins.
Kramer MC, Liang D, Tatomer DC, Gold B, March ZM, Cherry S, Wilusz JE.

Genes Dev. 2015 Oct 15;29(20):2168-82. doi: 10.1101/gad.270421.115.

2014

Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense.
Moy RH, Cole BS, Yasunaga A, Gold B, Shankarling G, Varble A, Molleston JM, tenOever BR, Lynch KW, Cherry S.

Cell. 2014 Aug 14;158(4):764-77. doi: 10.1016/j.cell.2014.06.023.

A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis.
Liu X, Zheng Q, Vrettos N, Maragkakis M, Alexiou P, Gregory BD, Mourelatos Z.

Mol Cell. 2014 Sep 18;55(6):868-79. doi: 10.1016/j.molcel.2014.07.017.

Transcriptome-wide RNA interaction profiling reveals physical and functional targets of hnRNP L in human T cells.
Shankarling G*, Cole BS*, Mallory MJ, Lynch KW.

Mol Cell Biol. 2014 Jan;34(1):71-83. doi: 10.1128/MCB.00740-13. Epub 2013 Oct 28.

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue.
Lovatt D, Ruble BK, Lee J, Dueck H, Kim TK, Fisher S, Francis C, Spaethling JM, Wolf JA, Grady MS, Ulyanova AV, Yeldell SB, Griepenburg JC, Buckley PT, Kim J, Sul JY, Dmochowski IJ, Eberwine J.

Nat Methods. 2014 Feb;11(2):190-6. doi: 10.1038/nmeth.2804. Epub 2014 Jan 12.

Specific enrichment of the RNA-binding proteins PCBP1 and PCBP2 in chief cells of the murine gastric mucosa.
Ghanem LR, Chatterji P, Liebhaber SA.

Gene Expr Patterns. 2014 Mar;14(2):78-87. doi: 10.1016/j.gep.2014.01.004. Epub 2014 Jan 28.

Serotonergic neuron regulation informed by in vivo single-cell transcriptomics.
Spaethling JM, Piel D, Dueck H, Buckley PT, Morris JF, Fisher SA, Lee J, Sul JY, Kim J, Bartfai T, Beck SG, Eberwine JH.

FASEB J. 2014 Feb;28(2):771-80. doi: 10.1096/fj.13-240267. Epub 2013 Nov 5.

Cytoplasmic poly(a) binding protein c4 serves a critical role in erythroid differentiation.
Kini HK, Kong J, Liebhaber SA.

Mol Cell Biol. 2014 Apr;34(7):1300-9. doi: 10.1128/MCB.01683-13. Epub 2014 Jan 27.

Cytoplasmic intron retention, function, splicing, and the sentinel RNA hypothesis.
Buckley PT, Khaladkar M, Kim J, Eberwine J.

Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):223-30. doi: 10.1002/wrna.1203. Epub 2013 Nov 4.

2013

In silico to in vivo splicing analysis using splicing code models.
Gazzara MR, Vaquero-Garcia J, Lynch KW, Barash Y.

Methods. 2013 Dec 7. pii: S1046-2023(13)00444-1. doi: 10.1016/j.ymeth.2013.11.006. [Epub ahead of print]

Adenosine-to-inosine RNA editing and human disease.
Slotkin W, Nishikura K.

Genome Med. 2013 Nov 29;5(11):105. [Epub ahead of print]

Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons.
Khaladkar M, Buckley PT, Lee MT, Francis C, Eghbal MM, Chuong T, Suresh S, Kuhn B, Eberwine J, Kim J.

PLoS One. 2013 Oct 3;8(10):e76194. doi: 10.1371/journal.pone.0076194. eCollection 2013.

A compendium of RNA-binding motifs for decoding gene regulation.
Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR.

Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.

Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn.
Martinez NM, Lynch KW.

Immunol Rev. 2013 May;253(1):216-36. doi: 10.1111/imr.12047.

Single-cell transcriptomics for drug target discovery.
Spaethling JM, Eberwine JH.

Curr Opin Pharmacol. 2013 Oct;13(5):786-90. doi: 10.1016/j.coph.2013.04.011. Epub 2013 May 29.

ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing.
Ota H, Sakurai M, Gupta R, Valente L, Wulff BE, Ariyoshi K, Iizasa H, Davuluri RV, Nishikura K.

Cell. 2013 Apr 25;153(3):575-89. doi: 10.1016/j.cell.2013.03.024.

Dendritic glutamate receptor mRNAs show contingent local hotspot-dependent translational dynamics.
Kim TK, Sul JY, Helmfors H, Langel U, Kim J, Eberwine J.

Cell Rep. 2013 Oct 17;5(1):114-25. doi: 10.1016/j.celrep.2013.08.029. Epub 2013 Sep 26.

AVISPA: a web tool for the prediction and analysis of alternative splicing.
Barash Y, Vaquero-Garcia J, González-Vallinas J, Xiong HY, Gao W, Lee LJ, Frey BJ.

Genome Biol. 2013;14(10):R114.

Antagonistic and stimulative roles of ADAR1 in RNA silencing: an editor's point-of-view.
Nishikura K, Sakurai M, Ariyoshi K, Ota H.

RNA Biol. 2013 Aug 1;10(8):1240-7. doi: 10.4161/rna.25947. Epub 2013 Jul 30.

αCP Poly(C) binding proteins act as global regulators of alternative polyadenylation.
Ji X, Wan J, Vishnu M, Xing Y, Liebhaber SA.

Mol Cell Biol. 2013 Jul;33(13):2560-73. doi: 10.1128/MCB.01380-12. Epub 2013 Apr 29.

X chromosome inactivation and epigenetic responses to cellular reprogramming.
Lessing D, Anguera MC, Lee JT.

Annu Rev Genomics Hum Genet. 2013;14:85-110. doi: 10.1146/annurev-genom-091212-153530. Epub 2013 May 6.

2012

Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes.
Anguera MC, Sadreyev R, Zhang Z, Szanto A, Payer B, Sheridan SD, Kwok S, Haggarty SJ, Sur M, Alvarez J, Gimelbrant A, Mitalipova M, Kirby JE, Lee JT.

Cell Stem Cell. 2012 Jul 6;11(1):75-90. doi: 10.1016/j.stem.2012.03.008.

Quantitative biology of single neurons.
Eberwine J, Lovatt D, Buckley P, Dueck H, Francis C, Kim TK, Lee J, Lee M, Miyashiro K, Morris J, Peritz T, Schochet T, Spaethling J, Sul JY, Kim J.

J R Soc Interface. 2012 Dec 7;9(77):3165-83. doi: 10.1098/rsif.2012.0417. Epub 2012 Aug 22.

An RNA-independent linkage of noncoding transcription to long-range enhancer function.
Yoo EJ, Cooke NE, Liebhaber SA.

Mol Cell Biol. 2012 May;32(10):2020-9. doi: 10.1128/MCB.06650-11. Epub 2012 Mar 19.

Perspectives on cell reprogramming with RNA.
Sul JY, Kim TK, Lee JH, Eberwine J.

Trends Biotechnol. 2012 May;30(5):243-9. doi: 10.1016/j.tibtech.2012.02.004. Epub 2012 Mar 27.

Alternative splicing networks regulated by signaling in human T cells.
Martinez NM, Pan Q, Cole BS, Yarosh CA, Babcock GA, Heyd F, Zhu W, Ajith S, Blencowe BJ, Lynch KW.

RNA. 2012 May;18(5):1029-40. doi: 10.1261/rna.032243.112. Epub 2012 Mar 27.

Interaction of PABPC1 with the translation initiation complex is critical to the NMD resistance of AUG-proximal nonsense mutations.
Peixeiro I, Inácio Â, Barbosa C, Silva AL, Liebhaber SA, Romão L.

Nucleic Acids Res. 2012 Feb;40(3):1160-73. doi: 10.1093/nar/gkr820. Epub 2011 Oct 11.

Drug targets: single-cell transcriptomics hastens unbiased discovery.
Bartfai T, Buckley PT, Eberwine J.

Trends Pharmacol Sci. 2012 Jan;33(1):9-16. doi: 10.1016/j.tips.2011.09.006. Epub 2011 Oct 25.

2011

The poly(rC)-binding protein alphaCP2 is a noncanonical factor in X. laevis cytoplasmic polyadenylation.
Vishnu MR, Sumaroka M, Klein PS, Liebhaber SA.

RNA. 2011 May;17(5):944-56. doi: 10.1261/rna.2587411. Epub 2011 Mar 28.

Single cell transcriptomics of hypothalamic warm sensitive neurons that control core body temperature and fever response Signaling asymmetry and an extension of chemical neuroanatomy.
Eberwine J, Bartfai T.

Pharmacol Ther. 2011 Mar;129(3):241-59. doi: 10.1016/j.pharmthera.2010.09.010. Epub 2010 Oct 21.

Signal- and development-dependent alternative splicing of LEF1 in T cells is controlled by CELF2.
Mallory MJ, Jackson J, Weber B, Chi A, Heyd F, Lynch KW.

Mol Cell Biol. 2011 Jun;31(11):2184-95. doi: 10.1128/MCB.05170-11. Epub 2011 Mar 28.

Transcriptome transfer provides a model for understanding the phenotype of cardiomyocytes.
Kim TK, Sul JY, Peternko NB, Lee JH, Lee M, Patel VV, Kim J, Eberwine JH.

Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11918-23. doi: 10.1073/pnas.1101223108. Epub 2011 Jul 5.

Cytoplasmic intron sequence-retaining transcripts can be dendritically targeted via ID element retrotransposons.
Buckley PT, Lee MT, Sul JY, Miyashiro KY, Bell TJ, Fisher SA, Kim J, Eberwine J.

Neuron. 2011 Mar 10;69(5):877-84. doi: 10.1016/j.neuron.2011.02.028.

X-chromosome epigenetic reprogramming in pluripotent stem cells via noncoding genes.
Kim DH, Jeon Y, Anguera MC, Lee JT.

Semin Cell Dev Biol. 2011 Jun;22(4):336-42. doi: 10.1016/j.semcdb.2011.02.025. Epub 2011 Mar 3.

Elucidating the inosinome: global approaches to adenosine-to-inosine RNA editing.
Wulff BE, Sakurai M, Nishikura K.

Nat Rev Genet. 2011 Feb;12(2):81-5. doi: 10.1038/nrg2915. Epub 2010 Dec 21.

Transcriptome analysis of single cells.
Morris J, Singh JM, Eberwine JH.

J Vis Exp. 2011 Apr 25;(50). pii: 2634. doi: 10.3791/2634.

An RNA-protein complex links enhanced nuclear 3' processing with cytoplasmic mRNA stabilization.
Ji X, Kong J, Liebhaber SA.

EMBO J. 2011 May 27;30(13):2622-33. doi: 10.1038/emboj.2011.171.

2010

Deciphering the splicing code.
Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ.

Nature. 2010 May 6;465(7294):53-9. doi: 10.1038/nature09000.

Functions and regulation of RNA editing by ADAR deaminases.
Nishikura K.

Annu Rev Biochem. 2010;79:321-49. doi: 10.1146/annurev-biochem-060208-105251.

Phosphorylation-dependent regulation of PSF by GSK3 controls CD45 alternative splicing.
Heyd F, Lynch KW.

Mol Cell. 2010 Oct 8;40(1):126-37. doi: 10.1016/j.molcel.2010.09.013.

Model-based detection of alternative splicing signals.
Barash Y, Blencowe BJ, Frey BJ.

Bioinformatics. 2010 Jun 15;26(12):i325-33. doi: 10.1093/bioinformatics/btq200.

Tsx produces a long noncoding RNA and has general functions in the germline, stem cells, and brain.
Anguera MC, Ma W, Clift D, Namekawa S, Kelleher RJ 3rd, Lee JT.

PLoS Genet. 2011 Sep;7(9):e1002248. doi: 10.1371/journal.pgen.1002248. Epub 2011 Sep 1.

Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency.
Iizasa H, Wulff BE, Alla NR, Maragkakis M, Megraw M, Hatzigeorgiou A, Iwakiri D, Takada K, Wiedmer A, Showe L, Lieberman P, Nishikura K.

J Biol Chem. 2010 Oct 22;285(43):33358-70. doi: 10.1074/jbc.M110.138362. Epub 2010 Aug 17.