2024
Scacchetti, A., Shields, E.J., Trigg, N.A., Wilusz, J.E., Conine, C.C., and Bonasio, R. (2024) A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3’ termini. Mol Cell.
Morandell, J., Monziani, A., Lazioli, M., Donzel, D., Döring, J., Pegorar, C.O., D’Anzi, A., Pellegrini, M., Mattiello, A., Bortolotti, D., Bergonzoni, G., Tripathi, T., Mattis, V.B., Kovalenko, M., Rosati, J., Dieterich, C., Dassi, E., Wheeler, V.C., Ellederová, Z., Wilusz, J.E., Viero, G., and Biagioli, M. (2024) CircHTT(2,3,4,5,6) – co-evolving with the HTT CAG-repeat tract – modulates Huntington’s disease phenotypes. Mol Ther Nucleic Acids 35: 102234.
Wright, B.L. and Wilusz, J.E. (2024) An unexpected path for Malat1 in neurons: Trafficking out of the nucleus for translation. Genes Dev 38: 291-293.
Du, C., Waltzer, W.C., Wilusz, J.E., Spaliviero, M., Darras, F., and Romanov, V. (2024) Circular STAG2 RNA modulates bladder cancer progression via miR-145-5p/TAGLN2 and is considered as a biomarker for recurrence. Cancers 16: 978.
Xiao, M.-S. and Wilusz, J.E. (2024) Purification of circular RNAs using poly(A) tailing followed by RNase R digestion. Methods Mol Biol 2765: 3-19.
Fuchs Wightman, F., Lukin, J., Giusti, S., Soutschek, M., Bragado, L., Pozzi, B., Gonzalez, P., Fededa, J.P., Schratt, G., Fujiwara, R., Wilusz, J.E., Refojo, D., and de la Mata, M. (2024) Influence of RNA circularity on target RNA-directed microRNA degradation. Nucleic Acids Res.
2023
Lu, F., Park, B.J., Fujiwara, R., Wilusz, J.E., Gilmour, D.S., Lehmann, R., and Lionnet, T. (2023) Integrator-mediated clustering of poised RNA polymerase II synchronizes histone transcription. BioRxiv.
Stringer, B.W., Gabryelska, M., Marri, S., Clark, L., Lin, H., Gantley, L., Liu, R., Wilusz, J.E., Conn, V.M., and Conn, S.J. (2023) Versatile toolkit for highly-efficient and scarless overexpression of circular RNAs. BioRxiv.
Scacchetti, A., Shields, E.J., Trigg, N.A., Wilusz, J.E., Conine, C.C., and Bonasio, R. (2023) A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3’ termini. BioRxiv.
Fujiwara, R., Zhai, S.-N., Liang, D., Shah, A.P., Tracey, M., Ma, X.-K., Fields, C.J., Mendoza-Figueroa, M.S., Meline, M.C., Tatomer, D.C., Yang, L., and Wilusz, J.E. (2023) IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events. Mol Cell 83: 4445-4460.
Chen, L.L., Bindereif, A., Bozzoni, I., Chang, H.Y., Matera, A.G., Gorospe, M., Hansen, T.B., Kjems, J., Ma, X.-K., Pek, J.W., Rajewsky, N., Salzman, J., Wilusz, J.E., Yang, L., Zhao, F. (2023) A guide to naming eukaryotic circular RNAs. Nat Cell Biol 25: 1-5.
Mattick, J.S., Amaral, P.P., Carninci, P., Carpenter, S., Chang, H.Y., Chen, L.L., Chen, R., Dean, C., Dinger, M.E., Fitzgerald, K.A., Gingeras, T.R., Guttman, M., Hirose, T., Huarte, M., Johnson, R., Kanduri, C., Kapranov, P., Lawrence, J.B., Lee, J.T., Mendell, J.T., Mercer, T.R., Moore, K.J., Nakagawa, S., Rinn, J.L., Spector, D.L., Ulitsky, I., Wan, Y., Wilusz, J.E., and Wu, M. (2023) Long non-coding RNAs: Definition, functions, challenges and recommendations. Nat Rev Mol Cell Biol 24: 430-447.
2022
Antony, C., George, S.S., Blum, J., Somers, P., Thorsheim, C.L., Wu-Corts, D.J., Ai, Y., Gao, L., Lv, K., Tremblay, M.G., Moss, T., Tan, K., Wilusz, J.E., Ganley, A.R.D., Pimkin, M., and Paralkar, V.R. (2022) Control of ribosomal RNA synthesis by hematopoietic transcription factors. Mol Cell 82: 3826-3839. View Publication
Yang, L., Wilusz, J.E., and Chen, L.L. (2022) Biogenesis and regulatory roles of circular RNAs. Annu Rev Cell Dev Biol 38: 263-289.
Ai, Y., Liang, D., and Wilusz, J.E. (2022) CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells. Nucleic Acids Res. 50: e65.
2021
Cable, J., Heard, E., Hirose, T., Prasanth, K.V., Chen, L.L., Henninger, J.E., Quinodoz, S.A., Spector, D.L., Diermeier, S.D., Porman, A.M., Kumar, D., Feinberg, M.W., Shen, X., Unfried, J.P., Johnson, R., Chen, C.K., Wilusz, J.E., Lempradl, A., McGeary, S.E., Wahba, L., Pyle, A.M., Hargrove, A.E., Simon, M.D., Marcia, M., Przanowska, R.K., Chang, H.Y., Jaffrey, S.R., Contreras, L.M., Chen, Q., Shi, J., Mendell, J.T., He, L., Song, E., Rinn, J.L., Lalwani, M.K., Kalem, M.C., Chuong, E.B., Maquat, L.E., and Liu, X. (2021) Noncoding RNAs: biology and applications—a Keystone Symposia report. Ann NY Acad Sci 1506: 118-141.
Chen, L.L. and Wilusz, J.E. (2021) Methods for circular RNAs. Methods 196: 1-2.
Liang, D., Tatomer, D.C., and Wilusz, J.E. (2021) Use of circular RNAs as markers of readthrough transcription to identify factors regulating cleavage/polyadenylation events. Methods 196: 121-128.
Dodbele, S., Mutlu, N., and Wilusz, J.E. (2021) Best practices to ensure robust investigation of circular RNAs: pitfalls and tips. EMBO Rep 22: e52072.
Meganck, R.M., Liu, J., Hale, A.E., Simon, K.E., Fanous, M.M., Vincent, H.A., Wilusz, J.E., Moorman, N.J., Marzluff, W.F., Asokan, A. (2021) Engineering highly efficient backsplicing and translation of synthetic circRNAs. Mol Ther Nucleic Acids 23: 821-834.
He, C., Bozler, J., Janssen, K.A., Wilusz, J.E., Garcia, B.A., Schorn, A.J., and Bonasio, R. (2021) TET2 chemically modifies tRNAs and regulates tRNA fragment levels. Nat Struct Mol Biol 28: 62-70.
Tatomer, D.C., Liang, D., and Wilusz, J.E. (2021) RNAi screening to identify factors that control circular RNA localization. Methods Mol Biol 2209: 321-332.
2020
Mendoza-Figueroa, M.S., Tatomer, D.C., and Wilusz, J.E. (2020) The Integrator complex in transcription and development. Trends Biochem Sci 45: 923-934.
Dodbele, S. and Wilusz, J.E. (2020) Ending on a high note: Downstream ORFs enhance mRNA translational output. EMBO J. 39: e105959.
Tatomer, D.C. and Wilusz, J.E. (2020) Attenuation of eukaryotic protein-coding gene expression via premature transcription termination. Cold Spring Harb Symp Quant Biol 84: 83-93.
Xiao, M.S., Ai, Y., and Wilusz, J.E. (2020) Biogenesis and functions of circular RNAs come into focus. Trends Cell Biol 30: 226-240.
2019
Elrod, N.D., Henriques, T., Huang, K.L., Tatomer, D.C., Wilusz, J.E., Wagner, E.J., and Adelman, K. (2019) The Integrator complex attenuates promoter-proximal transcription at protein-coding genes. Mol Cell 76: 738-752.
Fujiwara, R., Damodaren, N., Wilusz, J.E., and Murakami, K. (2019) The capping enzyme facilitates promoter escape and assembly of a follow-on pre-initiation complex for re-initiation. Proc Natl Acad Sci USA. 116: 22573-22582.
Tatomer, D.C., Elrod, N.D., Liang, D., Xiao, M.S., Jiang, J.Z., Jonathan, M., Huang, K.L., Wagner, E.J., Cherry, S., and Wilusz, J.E. (2019) The Integrator complex cleaves nascent mRNAs to attenuate transcription. Genes Dev 33: 1525-1538.
Garikipati, V.N.S., Verma, S.K., Cheng, Z., Liang, D., Truongcao, M.M., Cimini, M., Yue, Y., Huang, G., Wang, C., Benedict, C., Mallaredy, V., Ibetti, J., Grisanti, L., Schumacher, S.M., Gao, E., Rajan, S., Wilusz, J.E., Goukassian, D., Houser, S., Koch, W.J., and Kishore, R. (2019) Circular RNA circFNDC3b modulates cardiac repair after myocardial infarction via FUS-1/VEGF-A axis. Nat Commun. 10: 4317.
Xiao, M.S. and Wilusz, J.E. (2019) An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3’ ends. Nucleic Acids Res. 47: 8755-8769.
Kearse, M.G., Goldman, D.H., Choi, J., Nwaezeapu, C., Liang, D., Green, K.M., Goldstrohm, A.C., Todd, P.K., Green, R., and Wilusz, J.E. (2019) Ribosome queuing enables non-AUG translation to be resistant to multiple protein synthesis inhibitors. Genes Dev 33: 871-885.
Wilusz, J.E. (2019) Circle the wagons: Circular RNAs control innate immunity. Cell 177: 797-799.
2018
Meganck, R.M., Borchardt, E.K., Castellanos Rivera, R.M., Scalabrino, M.L., Wilusz, J.E., Marzluff, W.F. and Asokan, A. (2018) Tissue-dependent expression and translation of circular RNAs with recombinant AAV vectors in vivo. Mol Ther Nucleic Acids 13: 89-98.
Huang, C., Liang, D., Tatomer, D.C., and Wilusz, J.E. (2018) A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs. Genes Dev 32: 639-644.
Wilusz, J.E. (2018) A 360° view of circular RNAs: From biogenesis to functions. Wiley Interdiscip Rev RNA 9: e1478.
2017
Liang, D., Tatomer, D.C., Luo, Z., Wu, H., Yang, L., Chen, L.L., Cherry, S., and Wilusz, J.E. (2017) The output of protein-coding genes shifts to circular RNAs when the pre-mRNA processing machinery is limiting. Mol Cell 68: 940-954.
Kearse, M.G. and Wilusz, J.E. (2017) Non-AUG translation: a new start for protein synthesis in eukaryotes. Genes Dev 31: 1717-1731.
Tatomer, D.C., Liang, D., and Wilusz, J.E. (2017) Inducible expression of eukaryotic circular RNAs from plasmids. Methods Mol Biol 1648: 143-154.
Chen, Y.G., Kim, M.V., Chen, X., Batista, P.J., Aoyama, S., Wilusz, J.E., Iwasaki, A., and Chang, H.Y. (2017) Sensing self and foreign circular RNAs by intron identity. Mol Cell 67: 228-238.
Tatomer, D.C. and Wilusz, J.E. (2017) An unchartered journey for ribosomes: Circumnavigating circular RNAs to produce proteins. Mol Cell 66: 1-2.
2016
He, C., Sidoli, S., Warneford-Thomson, R., Tatomer, D.C., Wilusz, J.E., Garcia, B.A., and Bonasio, R. (2016) High-resolution mapping of RNA-binding regions in the nuclear proteome of embryonic stem cells. Mol Cell 64: 416-430.
Wilusz, J.E. (2016) Circular RNAs: Unexpected outputs of many protein-coding genes. RNA Biol 14: 1007-1017.
Molleston, J.M., Sabin, L.R., Moy, R.H., Menghani, S.V., Rausch, K., Gordesky-Gold, B., Hopkins, K.C., Zhou, R., Jensen, T.H., Wilusz, J.E., and Cherry, S. (2016) A conserved virus-induced cytoplasmic TRAMP-like complex recruits the exosome to target viral RNA for degradation. Genes Dev 30: 1658-1670.
2015
Doucet, A.J., Wilusz, J.E., Miyoshi, T., Liu, Y., and Moran, J.V. (2015) A 3’ poly(A) tract is required for LINE-1 retrotransposition. Mol Cell 60: 728-741.
Kramer, M.C., Liang, D., Tatomer, D.C., Gold, B., March, Z.M., Cherry, S., and Wilusz, J.E. (2015) Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes Dev 29: 2168-2182.
Wilusz, J.E. (2015) Removing roadblocks to deep sequencing of modified RNAs. Nat Methods 12: 821-822.
Wilusz, J.E. (2015) Long noncoding RNAs: Re-writing dogmas of RNA processing and stability. Biochim Biophys Acta 1859: 128-138.
Wilusz, J.E. (2015) Repetitive elements regulate circular RNA biogenesis. Mob Genet Elements 5: 1-7. doi: 10.1080/2159256X.2015.1045682.
Wilusz, J.E. (2015) Controlling translation via modulation of tRNA levels. Wiley Interdiscip Rev RNA 6: 453-470.
Kuhn, C.-D., Wilusz, J.E., Zheng, Y., Beal, P.A., and Joshua-Tor, L. (2015) On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. Cell 160: 644-658.
2014
Wilusz, J.E. and Wilusz, J. (2014) Nonsense-mediated RNA decay: At the ‘cutting-edge’ of regulated snoRNA production. Genes Dev 28: 2447-2449.
Liang, D. and Wilusz, J.E. (2014) Short intronic repeat sequences facilitate circular RNA production. Genes Dev 28: 2233-2247.
2013
Wilusz, J.E. and Sharp, P.A. (2013) A circuitous route to noncoding RNA. Science 340: 440-441.
Wilusz, J.E. (2013) Noncoding RNA. In: Maloy, S. and Hughes, K. (eds.) Brenner’s Online Encyclopedia of Genetics. 2nd edn.
2012-2005
Wilusz, J.E., JnBaptiste, C.K., Lu, L.Y., Kuhn, C.-D., Joshua-Tor, L., and Sharp, P.A. (2012) A triple helix stabilizes the 3’ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 26: 2392-2407.
Wilusz, J.E., Whipple, J.M., Phizicky, E.M., and Sharp, P.A. (2011) tRNAs marked with CCACCA are targeted for degradation. Science 334: 817-821.
Wilusz, J.E. and Spector, D.L. (2010) An unexpected ending: non-canonical 3’ end processing mechanisms. RNA 16: 259-266.
Wilusz, J.E., Sunwoo, H., and Spector, D.L. (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23: 1494-1504.
Sunwoo, H., Dinger, M.E., Wilusz, J.E., Amaral, P.P., Mattick, J.S., and Spector, D.L. (2009) MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19: 347-359.
Wilusz, J.E., Freier, S.M., and Spector, D.L. (2008) 3’ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135: 919-932.
Wilusz, J.E. and Beemon, K.L. (2006) The negative regulator of splicing element of Rous sarcoma virus promotes polyadenylation. J. Virol. 80: 9634-9640.
Wilusz, J.E., Devanney, S.C., and Caputi, M. (2005) Chimeric peptide nucleic acid compounds modulate splicing of the bcl-xgene in vitro and in vivo. Nucleic Acids Res 33: 6547-6554.
