Publications

Select Publications from CNG researchers

RNA translation regulated by muscleblind proteins in myotonic dystrophy type 2
Zu, T, Cleary JD, Liu Y, Banez-Coronel M, Bubenik JL, Ayhan F, Ashizawa T, Xia G, Clark HB, Yachnis AT, Swanson MS, Ranum LPW (2017)  Neuron, Sep 13;95(6):1292-1305.e5. doi: 10.1016/j.neuron.2017.08.039.

Elimination of toxic microsatellite expansion RNA by RNA-targeting Cas9.
Batra R, Nelles DA, Pirie E, Blue S, Marina RJ, Wang H, Chaim AI, Thomas JD, Zhang N, Ngyuen V, Aigner S, Xia G, Swanson MS and Yeo G. 2017.  Cell Aug 24;170(5):899-912.e10. doi: 10.1016/j.cell.2017.07.010. Epub 2017 Aug 10.

Disrupted prenatal RNA processing and myogenesis in congenital myotonic dystrophy
Thomas JD, Sznajder LJ, Bardhi O, Aslam F, Anastasiadis Z, Scotti MM, Nishino I, Nakamori M, Wang ET, and Swanson MS. 2017. Genes Dev 31:1122-1133.

Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility.
deLorimier E, Hinman MN, Copperman J, Datta K, Guenza M, Berglund JA “The Journal of biological chemistry”>J Biol Chem. 2017 Mar 10;292(10):4350-4357. doi: 10.1074/jbc.M116.770768. Epub 2017 Jan 27. PMID:28130447

Dose-Dependent Regulation of Alternative Splicing by MBNL Proteins Reveals Biomarkers for Myotonic Dystrophy.
Wagner SD, Struck AJ, Gupta R, Farnsworth DR, Mahady AE, Eichinger K, Thornton CA, Wang ET, Berglund JA.  PLoS Genet. 2016 Sep 28;12(9):e1006316. doi: 10.1371/journal.pgen.1006316. PMCID: PMC5082313

Conservation of context-dependent splicing activity in distant Muscleblind homologs.
Oddo JC, Saxena T, McConnell OL, Berglund JA, Wang ET. Nucleic Acids Res. 2016 Sep 30;44(17):8352-62. doi:10.1093/nar/gkw735. PMCID: PMC5041496

C9orf72 BAC Mouse Model with Motor Deficits and Neurodegenerative Features of ALS/FTD.
Yuanjing Liu, Amrutha Pattamatta, Tao Zu, Tammy Reid, David R. Borchelt, Anthony T. Yachnis, Laura P.W. Ranum (2016) Neuron, 90:521–534

RAN translation in Huntington’s Disease.
Bañez-Coronel, M., F. Ayhan, A.D. Tarabochia, T. Zu, B.A. Perez, S.K. Tusi, O. Pletnikova, D.R. Borchelt, C.A. Ross, R.L. Margolis, A.T.Yachnis, J.C. Troncoso, L.P.W. Ranum (2015Neuron, 88:667-677.

Actinomycin D Specifically Reduces Expanded CUG Repeat RNA in Myotonic Dystrophy Models.
Siboni RB, Nakamori M, Wagner SD, Struck AJ, Coonrod LA, Harriott SA, Cass DM, Tanner MK, Berglund JA. Cell Rep. 2015 Dec 22;13(11):2386-94. doi: 10.1016/j.celrep.2015.11.028. Epub 2015 Dec 10. PMCID: PMC4691565

Biological Efficacy and Toxicity of Diamidines in Myotonic Dystrophy Type 1 Models.
Siboni RB, Bodner MJ, Khalifa MM, Docter AG, Choi JY, Nakamori M, Haley MM, Berglund JA. J Med Chem. 2015 Aug 13;58(15):5770-80. doi: 10.1021/acs.jmedchem.5b00356. Epub 2015 Jul 21.

MBNL sequestration by toxic RNAs and RNA mis-processing in the myotonic dystrophy brain.
Goodwin, M., Mohan, A., Batra, R., Lee, K-Y., Charizanis, K., Gómez, F.J.F., Eddarkaoui, S., Sergeant, N., Buée, L., Kimura, T., Clark, H.B., Dalton, J., Takamura, K., Weyn-Vanhentenryck, S., Zhang, C., Reid, T., Ranum, L.P.W., Day, J.W., and M. S. Swanson. (2015). Cell Rep. 12:
1159-1168.

Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins
Wang ET, Ward AJ, Cherone JM, Giudice J, Wang TT, Treacy DJ, Lambert NJ, Freese P, Saxena T, Cooper TA, Burge CB. Genome Res. 2015 Jun;25(6):858-71. doi: 10.1101/gr.184390.114. Epub 2015 Apr 16.

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model.
deLorimier E, Coonrod LA, Copperman J, Taber A, Reister EE, Sharma K, Todd PK, Guenza MG, Berglund JA.  (2014) Nucleic Acids Res.  Nov 10;42(20):12768-78. doi: 10.1093/nar/gku941. Epub 2014 Oct 10.

Reducing Levels of Toxic RNA with Small Molecules.
Coonrod LA, Nakamori M, Wang W, Carrell S, Hilton CL, Bodner MJ, Siboni RB, Docter AG, Haley MM, Thornton CA, Berglund JA. (2013) ACS Chem Biol. Nov 15;8(11):2528-37. doi: 10.1021/cb400431f. Epub 2013 Sep 27.

RAN proteins and RNA foci from antisense transcripts in C9ORF72 ALS and frontotemporal dementia.
Zu T, Y. Liu, M. Bañez-Coronel, T. Reid, O. Pletnikova, J. Lewis, T.M. Miller, M.B. Harms, A.E. Falchook, S.H. Subramony, L.W. Ostrow, J.D. Rothstein, J.C. Troncoso, L.P.W. Ranum (2013) Proc Natl Acad Sci U S A. 110:E4968-77. 1315438110.

Utilizing the GAAA tetraloop/receptor to facilitate crystal packing and structure determination of a CUG RNA helix.
Coonrod LA, Lohman JR, Berglund JA. (2012)  Biochemistry Oct 23;51(42):8330-7. doi: 10.1021/bi300829w. Epub 2012 Oct 12

Combinatorial Mutagenesis of MBNL1 Zinc Fingers Elucidates Distinct Classes of Splicing Regulatory Events.
Purcell J, Oddo JC, Wang ET, Berglund JA. (2012)  Mol Cell Biol. Oct;32(20):4155-67. Epub 2012 Aug 13.

Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins
Wang, Eric T, Cody, N. A. L., Jog, S., Biancolella, M., Wang, T. T., Treacy, D. J., Luo, S., Schroth, G. P., Housman, D. E., Reddy, S., Lecuyer, E., and Burge, C. B.(2012) Cell 150(4):710 24, Aug.

Frequency of KCNC3 DNA variants as causes of spinocerebellar ataxia 13 (SCA13).
Figueroa KP, Waters MF, Garibyan V, Bird TD, Gomez CM, Ranum LP, Minassian NA, Papazian DM, Pulst SM.
PLoS One. 2011 Mar 29;6(3):e17811.

Confirmation of the severe phenotypic effect of serine at codon 41 of the superoxide dismutase 1 gene.
Subramony SH, Ashizawa T, Langford L, McKenna R, Avvaru B, Siddique T, Vedanarayanan V.
Muscle Nerve. 2011 Mar 31. doi: 10.1002/mus.22117

Confirmation of the severe phenotypic effect of serine at codon 41 of the superoxide dismutase 1 gene.
Subramony SH, Ashizawa T, Langford L, McKenna R, Avvaru B, Siddique T, Vedanarayanan V.
Muscle Nerve. 2011 Mar 31. doi: 10.1002/mus.22117

Frequency of KCNC3 DNA variants as causes of spinocerebellar ataxia 13 (SCA13).
Figueroa KP, Waters MF, Garibyan V, Bird TD, Gomez CM, Ranum LP, Minassian NA, Papazian DM, Pulst SM.
PLoS One. 2011 Mar 29;6(3):e17811.

Non-ATG-initiated translation directed by microsatellite expansions.
Zu T, Gibbens B, Doty NS, Gomes-Pereira M, Huguet A, Stone MD, Margolis J, Peterson M, Markowski TW, Ingram MA, Nan Z, Forster C, Low WC, Schoser B, Somia NV, Clark HB, Schmechel S, Bitterman PB, Gourdon G, Swanson MS, Moseley M, Ranum LP.
Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):260-5. Epub 2010 Dec 20.**Selected as Editors Choice Article: Science Magazine 331:126-127 Jan 2011; **Selected as a Sci. Signal.Breakthrough of Year 2011. Sci. Signal., 5(205) pg eg1 Jan 2012

RNA gain-of-function in spinocerebellar ataxia type 8.
Daughters RS, Tuttle DL, Gao W, Ikeda Y, Moseley ML, Ebner TJ, Swanson MS, Ranum LPW. (2009) PLoS Genet. 5(8):e1000600.

Alternative isoform regulation in human tissue transcriptomes
Wang, Eric T, Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., and Burge, C. B. (2008)  Nature 456(7221):470{6, Nov.

Bidirectional expression of CUG and CAG expansion transcripts and intranuclear polyglutamine inclusions in spinocerebellar ataxia type 8
Moseley ML, Zu T, Ikeda Y, Gao W, Mosemiller AK, Daughters RS, Chen G, Weatherspoon MR, Clark HB, Ebner TJ, Day JW, Ranum LPW. (2006) . Nat. Genet. 38(7): 758-769.

Spectrin mutations cause spinocerebellar ataxia type 5.
Ikeda Y, Dick KA, Weatherspoon MR, Gincel D, Armbrust KR, Dalton JC, Stevanin G, Dürr A, Zühlke C, Bürk K, Clark HB, Brice A, Rothstein JD, Schut LJ, Day JW, Ranum LPW. (2006) Nature Genetics 38(2): 184-190.

 

Selected Review Articles

New developments in RAN translation: insights from multiple diseases
Cleary JD and Ranum LPW (2017) Curr Opin Genet Dev. 44:125-134

RNA mis-splicing in disease.
Scotti, M., and M.S. Swanson. (2016). Nat Rev. Genet. 17:19-32.

Global insights into alternative polyadenylation regulation
Batra, R., Manchanda, M., and M.S. Swanson. (2015). . RNA Biol. 12:597-602.

Rectifying RNA splicing errors in hereditary neurodegenerative disease.
Swanson, M.S. 2015. Proc. Natl. Acad. Sci. USA 112:2637-2638.

Alternative pre-mRNA splicing.
Wagner SD, Berglund JA. (2014)  Alternative pre-mRNA splicing.  Methods Mol Biol.;1126:45-54. doi: 10.1007/978-1-62703-980-24.

Repeat associated non-ATG (RAN) translation: new starts in microsatellite expansion disorders.
Cleary J.D., L.P.W. Ranum. (2014) Curr Opin Genet Dev. 26:6-15.  PMCID:PMC4237677

RNA-protein interactions in unstable microsatellite diseases
Mohan, A., Goodwin, M., and M.S. Swanson. (2014). . Brain Res., doi: 10.1016/j.brainres.2014.03.039. PMID: 24709120.

RNA-binding protein mis-regulation in microsatellite expansion disorders.
Goodwin M., and M.S. Swanson. (2014). Exp. Biol. Med. 825:353-388.

Repeat-associated non-ATG (RAN) translation in neurological disease
J.D. Cleary, L.P.W. Ranum. (2013) Hum Mol Genet. October 15; 22(R1): R45–R51. PMCID:PMC3782068