Circular RNA (circRNA) molecules have critical functions during brain development and in brain-related disorders. Here, we identified and validated a circRNA, circHTT(2,3,4,5,6), stemming from the Huntington's disease (HD) gene locus that is most abundant in the central nervous system (CNS). We uncovered its evolutionary conservation in diverse mammalian species, and a correlation between circHTT(2,3,4,5,6) levels and the length of the CAG-repeat tract in exon-1 of HTT in human and mouse HD model systems. The mouse orthologue, circHtt(2,3,4,5,6), is expressed during embryogenesis, increases during nervous system development, and is aberrantly upregulated in the presence of the expanded CAG tract. While an IRES-like motif was predicted in circH TT (2,3,4,5,6), the circRNA does not appear to be translated in adult mouse brain tissue. Nonetheless, a modest, but consistent fraction of circHtt(2,3,4,5,6) associates with the 40S ribosomal subunit, suggesting a possible role in the regulation of protein translation. Finally, circHtt(2,3,4,5,6) overexpression experiments in HD-relevant STHdh striatal cells revealed its ability to modulate CAG expansion-driven cellular defects in cell-to-substrate adhesion, thus uncovering an unconventional modifier of HD pathology.

Board of Governor's Regenerative Medicine Institute Cedars Sinai Medical Center Los Angeles CA 90048 USA

Cellular Reprogramming Unit Fondazione IRCCS Casa Sollievo Della Sofferenza Viale dei Cappuccini 1 71013 San Giovanni Rotondo FG Italy

Institute of Biophysics Unit at Trento National Research Council CNR 38123 Trento Italy

Laboratory of RNA Regulatory Networks Department of Cellular Computational and Integrative Biology CIBIO University of Trento 38123 Trento Italy

Molecular Neurogenetics Unit Center for Genomic Medicine Massachusetts General Hospital Boston MA 02114 USA

NeuroEpigenetics Laboratory Department of Cellular Computational and Integrative Biology CIBIO University of Trento 38123 Trento Italy

Research Center PIGMOD Institute of Animal Physiology and Genetics Czech Academy of Science 277 21 Libechov Czech Republic

Section of Bioinformatics and Systems Cardiology University Hospital Heidelberg 69120 Heidelberg Germany

Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology Therapeutic Innovation Center Baylor College of Medicine Houston TX 77030 USA

See more in PubMed

McClung C.A., Nestler E.J. Neuroplasticity Mediated by Altered Gene Expression. Neuropsychopharmacology. 2008;33:3–17. doi: 10.1038/sj.npp.1301544. PubMed DOI

Blair J.D., Hockemeyer D., Doudna J.A., Bateup H.S., Floor S.N. Widespread Translational Remodeling during Human Neuronal Differentiation. Cell Rep. 2017;21:2005–2016. doi: 10.1016/j.celrep.2017.10.095. PubMed DOI PMC

Li Q., Lee J.-A., Black D.L. Neuronal regulation of alternative pre-mRNA splicing. Nat. Rev. Neurosci. 2007;8:819–831. doi: 10.1038/nrn2237. PubMed DOI

Su C.-H., D D., Tarn W.-Y. Alternative Splicing in Neurogenesis and Brain Development. Front. Mol. Biosci. 2018;5:12. doi: 10.3389/fmolb.2018.00012. PubMed DOI PMC

Raj B., Blencowe B.J. Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles. Neuron. 2015;87:14–27. doi: 10.1016/j.neuron.2015.05.004. PubMed DOI

Jeck W.R., Sorrentino J.A., Wang K., Slevin M.K., Burd C.E., Liu J., Marzluff W.F., Sharpless N.E. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA. 2013;19:141–157. doi: 10.1261/rna.035667.112. PubMed DOI PMC

Memczak S., Jens M., Elefsinioti A., Torti F., Krueger J., Rybak A., Maier L., Mackowiak S.D., Gregersen L.H., Munschauer M., et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495:333–338. doi: 10.1038/nature11928. PubMed DOI

Hansen T.B., Jensen T.I., Clausen B.H., Bramsen J.B., Finsen B., Damgaard C.K., Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495:384–388. doi: 10.1038/nature11993. PubMed DOI

Ashwal-Fluss R., Meyer M., Pamudurti N.R., Ivanov A., Bartok O., Hanan M., Evantal N., Memczak S., Rajewsky N., Kadener S. circRNA biogenesis competes with pre-mRNA splicing. Mol. Cell. 2014;56:55–66. doi: 10.1016/j.molcel.2014.08.019. PubMed DOI

Holdt L.M., Kohlmaier A., Teupser D. Molecular roles and function of circular RNAs in eukaryotic cells. Cell. Mol. Life Sci. 2018;75:1071–1098. doi: 10.1007/s00018-017-2688-5. PubMed DOI PMC

Abdelmohsen K., Panda A.C., Munk R., Grammatikakis I., Dudekula D.B., De S., Kim J., Noh J.H., Kim K.M., Martindale J.L., Gorospe M. Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1. RNA Biol. 2017;14:361–369. doi: 10.1080/15476286.2017.1279788. PubMed DOI PMC

Li Z., Huang C., Bao C., Chen L., Lin M., Wang X., Zhong G., Yu B., Hu W., Dai L., et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat. Struct. Mol. Biol. 2015;22:256–264. doi: 10.1038/nsmb.2959. PubMed DOI

Qin M., Wei G., Sun X. Circ-UBR5: An exonic circular RNA and novel small nuclear RNA involved in RNA splicing. Biochem. Biophys. Res. Commun. 2018;503:1027–1034. doi: 10.1016/j.bbrc.2018.06.112. PubMed DOI

Legnini I., Di Timoteo G., Rossi F., Morlando M., Briganti F., Sthandier O., Fatica A., Santini T., Andronache A., Wade M., et al. Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis. Mol. Cell. 2017;66:22–37.e9. doi: 10.1016/j.molcel.2017.02.017. PubMed DOI PMC

Rybak-Wolf A., Stottmeister C., Glažar P., Jens M., Pino N., Giusti S., Hanan M., Behm M., Bartok O., Ashwal-Fluss R., et al. Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed. Mol. Cell. 2015;58:870–885. doi: 10.1016/j.molcel.2015.03.027. PubMed DOI

Gruner H., Cortés-López M., Cooper D.A., Bauer M., Miura P. CircRNA accumulation in the aging mouse brain. Sci. Rep. 2016;6 doi: 10.1038/srep38907. PubMed DOI PMC

Gokool A., Anwar F., Voineagu I. The Landscape of Circular RNA Expression in the Human Brain. Biol. Psychiatry. 2020;87:294–304. doi: 10.1016/j.biopsych.2019.07.029. PubMed DOI

Licatalosi D.D., Darnell R.B. Splicing Regulation in Neurologic Disease. Neuron. 2006;52:93–101. doi: 10.1016/j.neuron.2006.09.017. PubMed DOI

Mehta S.L., Dempsey R.J., Vemuganti R. Role of circular RNAs in brain development and CNS diseases. Prog. Neurobiol. 2020;186 doi: 10.1016/j.pneurobio.2020.101746. PubMed DOI PMC

The Huntington’s Disease Collaborative Research Group A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington’s disease chromosomes. Cell. 1993;72:971–983. doi: 10.1016/0092-8674(93)90585-e. PubMed DOI

Wicht H., Lacalli T.C. The nervous system of amphioxus : structure, development, and evolutionary significance. Can. J. Zool. 2005;83:122–150.

Hinman V.F., Burke R.D. Embryonic neurogenesis in echinoderms. WIREs Dev. Biol. 2018;7 doi: 10.1002/wdev.316. PubMed DOI

Tartari M., Gissi C., Lo Sardo V., Zuccato C., Picardi E., Pesole G., Cattaneo E. Phylogenetic Comparison of Huntingtin Homologues Reveals the Appearance of a Primitive polyQ in Sea Urchin. Mol. Biol. Evol. 2008;25:330–338. doi: 10.1093/molbev/msm258. PubMed DOI

Candiani S., Pestarino M., Cattaneo E., Tartari M. Characterization, developmental expression and evolutionary features of the huntingtin gene in the amphioxus Branchiostoma floridae. BMC Dev. Biol. 2007;7:127. doi: 10.1186/1471-213X-7-127. PubMed DOI PMC

Iennaco R., Formenti G., Trovesi C., Rossi R.L., Zuccato C., Lischetti T., Bocchi V.D., Scolz A., Martínez-Labarga C., Rickards O., et al. The evolutionary history of the polyQ tract in huntingtin sheds light on its functional pro-neural activities. Cell Death Differ. 2022;29:293–305. doi: 10.1038/s41418-021-00914-9. PubMed DOI PMC

Labbadia J., Morimoto R.I. Huntington’s disease: underlying molecular mechanisms and emerging concepts. Trends Biochem. Sci. 2013;38:378–385. doi: 10.1016/j.tibs.2013.05.003. PubMed DOI PMC

Gil J.M., Rego A.C. Mechanisms of neurodegeneration in Huntington’s disease. Eur. J. Neurosci. 2008;27:2803–2820. doi: 10.1111/j.1460-9568.2008.06310.x. PubMed DOI

Bassi S., Tripathi T., Monziani A., Di Leva F., Biagioli M. Epigenetics of Huntington’s Disease. Adv. Exp. Med. Biol. 2017;978:277–299. doi: 10.1007/978-3-319-53889-1_15. PubMed DOI

Ayyildiz D., Bergonzoni G., Monziani A., Tripathi T., Döring J., Kerschbamer E., Di Leva F., Pennati E., Donini L., Kovalenko M., et al. CAG repeat expansion in the Huntington’s disease gene shapes linear and circular RNAs biogenesis. PLoS Genet. 2023;19 doi: 10.1371/journal.pgen.1010988. PubMed DOI PMC

Faber P.W., Barnes G.T., Srinidhi J., Chen J., Gusella J.F., MacDonald M.E. Huntingtin interacts with a family of WW domain proteins. Hum. Mol. Genet. 1998;7:1463–1474. doi: 10.1093/hmg/7.9.1463. PubMed DOI

Passani L.A., Bedford M.T., Faber P.W., McGinnis K.M., Sharp A.H., Gusella J.F., Vonsattel J.P., MacDonald M.E. Huntingtin’s WW domain partners in Huntington’s disease post-mortem brain fulfill genetic criteria for direct involvement in Huntington’s disease pathogenesis. Hum. Mol. Genet. 2000;9:2175–2182. doi: 10.1093/hmg/9.14.2175. PubMed DOI

Jiang Y.-J., Che M.-X., Yuan J.-Q., Xie Y.-Y., Yan X.-Z., Hu H.-Y. Interaction with polyglutamine-expanded huntingtin alters cellular distribution and RNA processing of huntingtin yeast two-hybrid protein A (HYPA) J. Biol. Chem. 2011;286:25236–25245. doi: 10.1074/jbc.M110.216333. PubMed DOI PMC

Sathasivam K., Neueder A., Gipson T.A., Landles C., Benjamin A.C., Bondulich M.K., Smith D.L., Faull R.L.M., Roos R.A.C., Howland D., et al. Aberrant splicing of HTT generates the pathogenic exon 1 protein in Huntington disease. Proc. Natl. Acad. Sci. USA. 2013;110:2366–2370. doi: 10.1073/pnas.1221891110. PubMed DOI PMC

Lin L., Park J.W., Ramachandran S., Zhang Y., Tseng Y.-T., Shen S., Waldvogel H.J., Curtis M.A., Faull R.L.M., Troncoso J.C., et al. Transcriptome sequencing reveals aberrant alternative splicing in Huntington’s disease. Hum. Mol. Genet. 2016;25:3454–3466. doi: 10.1093/hmg/ddw187. PubMed DOI PMC

Wilusz J.E. Repetitive elements regulate circular RNA biogenesis. Mob. Genet. Elements. 2015;5:1–7. doi: 10.1080/2159256X.2015.1045682. PubMed DOI PMC

Hughes A.C., Mort M., Elliston L., Thomas R.M., Brooks S.P., Dunnett S.B., Jones L. Identification of Novel Alternative Splicing Events in the Huntingtin Gene and Assessment of the Functional Consequences Using Structural Protein Homology Modelling. J. Mol. Biol. 2014;426:1428–1438. doi: 10.1016/j.jmb.2013.12.028. PubMed DOI

Labadorf A.T., Myers R.H. Evidence of Extensive Alternative Splicing in Post Mortem Human Brain HTT Transcription by mRNA Sequencing. PLoS One. 2015;10 doi: 10.1371/journal.pone.0141298. PubMed DOI PMC

Chung D.W., Rudnicki D.D., Yu L., Margolis R.L. A natural antisense transcript at the Huntington’s disease repeat locus regulates HTT expression. Hum. Mol. Genet. 2011;20:3467–3477. doi: 10.1093/hmg/ddr263. PubMed DOI PMC

Maass P.G., Glažar P., Memczak S., Dittmar G., Hollfinger I., Schreyer L., Sauer A.V., Toka O., Aiuti A., Luft F.C., Rajewsky N. A map of human circular RNAs in clinically relevant tissues. J. Mol. Med. 2017;95:1179–1189. doi: 10.1007/s00109-017-1582-9. PubMed DOI PMC

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., et al. A guide to naming eukaryotic circular RNAs. Nat. Cell Biol. 2023;25:1–5. doi: 10.1038/s41556-022-01066-9. PubMed DOI PMC

Rahimi K., Venø M.T., Dupont D.M., Kjems J. Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons. Nat. Commun. 2021;12:4825. doi: 10.1038/s41467-021-24975-z. PubMed DOI PMC

Kohany O., Gentles A.J., Hankus L., Jurka J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinf. 2006;7:474. doi: 10.1186/1471-2105-7-474. PubMed DOI PMC

Sugathan A., Biagioli M., Golzio C., Erdin S., Blumenthal I., Manavalan P., Ragavendran A., Brand H., Lucente D., Miles J., et al. CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors. Proc. Natl. Acad. Sci. USA. 2014;111:E4468–E4477. doi: 10.1073/pnas.1405266111. PubMed DOI PMC

Trettel F., Rigamonti D., Hilditch-Maguire P., Wheeler V.C., Sharp A.H., Persichetti F., Cattaneo E., MacDonald M.E. Dominant phenotypes produced by the HD mutation in STHdhQ111 striatal cells. Hum. Mol. Genet. 2000;9:2799–2809. doi: 10.1093/hmg/9.19.2799. PubMed DOI

Cattaneo E., Conti L. Generation and characterization of embryonic striatal conditionally immortalized ST14A cells. J. Neurosci. Res. 1998;53:223–234. doi: 10.1002/(SICI)1097-4547(19980715)53:2<223::AID-JNR11>3.0.CO;2-7. PubMed DOI

Dodbele S., Mutlu N., Wilusz J.E. Best practices to ensure robust investigation of circular RNAs: pitfalls and tips. EMBO Rep. 2021;22 doi: 10.15252/embr.202052072. PubMed DOI PMC

Wang K., Bai X., Xue Y., Luo X., Dong J., Yang G., Ma K., Huang L., Zhou J., Wang J. Absolute quantification of circRNA using digital reverse transcription-hyperbranched rolling circle amplification. Sensor. Actuator. B Chem. 2023;375 doi: 10.1016/j.snb.2022.132893. DOI

Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31:3406–3415. doi: 10.1093/nar/gkg595. PubMed DOI PMC

Menalled L.B., Kudwa A.E., Miller S., Fitzpatrick J., Watson-Johnson J., Keating N., Ruiz M., Mushlin R., Alosio W., McConnell K., et al. Comprehensive Behavioral and Molecular Characterization of a New Knock-In Mouse Model of Huntington’s Disease: zQ175. PLoS One. 2012;7 doi: 10.1371/journal.pone.0049838. PubMed DOI PMC

Neueder A., Landles C., Ghosh R., Howland D., Myers R.H., Faull R.L.M., Tabrizi S.J., Bates G.P. The pathogenic exon 1 HTT protein is produced by incomplete splicing in Huntington’s disease patients. Sci. Rep. 2017;7:1307. doi: 10.1038/s41598-017-01510-z. PubMed DOI PMC

Southwell A.L., Smith-Dijak A., Kay C., Sepers M., Villanueva E.B., Parsons M.P., Xie Y., Anderson L., Felczak B., Waltl S., et al. An enhanced Q175 knock-in mouse model of Huntington disease with higher mutant huntingtin levels and accelerated disease phenotypes. Hum. Mol. Genet. 2016;25:3654–3675. doi: 10.1093/hmg/ddw212. PubMed DOI PMC

Wheeler V.C., Auerbach W., White J.K., Srinidhi J., Auerbach A., Ryan A., Duyao M.P., Vrbanac V., Weaver M., Gusella J.F., et al. Length-dependent gametic CAG repeat instability in the Huntington’s disease knock-in mouse. Hum. Mol. Genet. 1999;8:115–122. doi: 10.1093/hmg/8.1.115. PubMed DOI

Piwecka M., Glažar P., Hernandez-Miranda L.R., Memczak S., Wolf S.A., Rybak-Wolf A., Filipchyk A., Klironomos F., Cerda Jara C.A., Fenske P., et al. Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science. 2017;357 doi: 10.1126/science.aam8526. PubMed DOI

Hollensen A.K., Thomsen H.S., Lloret-Llinares M., Kamstrup A.B., Jensen J.M., Luckmann M., Birkmose N., Palmfeldt J., Jensen T.H., Hansen T.B., Damgaard C.K. circZNF827 nucleates a transcription inhibitory complex to balance neuronal differentiation. Elife. 2020;9 doi: 10.7554/eLife.58478. PubMed DOI PMC

Venø M.T., Hansen T.B., Venø S.T., Clausen B.H., Grebing M., Finsen B., Holm I.E., Kjems J. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. Genome Biol. 2015;16:245. doi: 10.1186/s13059-015-0801-3. PubMed DOI PMC

Humbert S. Is Huntington disease a developmental disorder? EMBO Rep. 2010;11:899. doi: 10.1038/embor.2010.182. PubMed DOI PMC

Lee J.K., Mathews K., Schlaggar B., Perlmutter J., Paulsen J.S., Epping E., Burmeister L., Nopoulos P. Measures of growth in children at risk for Huntington disease. Neurology. 2012;79:668–674. doi: 10.1212/WNL.0b013e3182648b65. PubMed DOI PMC

Nopoulos P.C., Aylward E.H., Ross C.A., Mills J.A., Langbehn D.R., Johnson H.J., Magnotta V.A., Pierson R.K., Beglinger L.J., Nance M.A., et al. Smaller intracranial volume in prodromal Huntington’s disease: evidence for abnormal neurodevelopment. Brain. 2011;134:137–142. doi: 10.1093/brain/awq280. PubMed DOI PMC

Barnat M., Capizzi M., Aparicio E., Boluda S., Wennagel D., Kacher R., Kassem R., Lenoir S., Agasse F., Braz B.Y., et al. Huntington’s disease alters human neurodevelopment. Science. 2020;369:787–793. doi: 10.1126/science.aax3338. PubMed DOI PMC

Qin X., Jiang Y., Tse Y.C., Wang Y., Wong T.P., Paudel H.K. Early Growth Response 1 (Egr-1) Regulates N-Methyl-d-aspartate Receptor (NMDAR)-dependent Transcription of PSD-95 and α-Amino-3-hydroxy-5-methyl-4-isoxazole Propionic Acid Receptor (AMPAR) Trafficking in Hippocampal Primary Neurons. J. Biol. Chem. 2015;290:29603–29616. doi: 10.1074/jbc.M115.668889. PubMed DOI PMC

Kaur P., Karolina D.S., Sepramaniam S., Armugam A., Jeyaseelan K. Expression Profiling of RNA Transcripts during Neuronal Maturation and Ischemic Injury. PLoS One. 2014;9 doi: 10.1371/journal.pone.0103525. PubMed DOI PMC

Seeler S., Andersen M.S., Sztanka-Toth T., Rybiczka-Tešulov M., Van Den Munkhof M.H., Chang C.-C., Maimaitili M., Venø M.T., Hansen T.B., Pasterkamp R.J., et al. A Circular RNA Expressed from the FAT3 Locus Regulates Neural Development. Mol. Neurobiol. 2023;60:3239–3260. doi: 10.1007/s12035-023-03253-7. PubMed DOI PMC

Dudekula D.B., Panda A.C., Grammatikakis I., De S., Abdelmohsen K., Gorospe M. CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol. 2016;13:34–42. doi: 10.1080/15476286.2015.1128065. PubMed DOI PMC

Ray D., Kazan H., Cook K.B., Weirauch M.T., Najafabadi H.S., Li X., Gueroussov S., Albu M., Zheng H., Yang A., et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013;499:172–177. doi: 10.1038/nature12311. PubMed DOI PMC

Weirauch M.T., Yang A., Albu M., Cote A.G., Montenegro-Montero A., Drewe P., Najafabadi H.S., Lambert S.A., Mann I., Cook K., et al. Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity. Cell. 2014;158:1431–1443. doi: 10.1016/j.cell.2014.08.009. PubMed DOI PMC

Chen C.-K., Cheng R., Demeter J., Chen J., Weingarten-Gabbay S., Jiang L., Snyder M.P., Weissman J.S., Segal E., Jackson P.K., Chang H.Y. Structured elements drive extensive circular RNA translation. Mol. Cell. 2021;81:4300–4318.e13. doi: 10.1016/j.molcel.2021.07.042. PubMed DOI PMC

Stefani G., Fraser C.E., Darnell J.C., Darnell R.B. Fragile X Mental Retardation Protein Is Associated with Translating Polyribosomes in Neuronal Cells. J. Neurosci. 2004;24:7272–7276. doi: 10.1523/JNEUROSCI.2306-04.2004. PubMed DOI PMC

Kramer M.C., Liang D., Tatomer D.C., Gold B., March Z.M., Cherry S., Wilusz J.E. Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes Dev. 2015;29:2168–2182. doi: 10.1101/gad.270421.115. PubMed DOI PMC

Reis S.A., Thompson M.N., Lee J.-M., Fossale E., Kim H.-H., Liao J.K., Moskowitz M.A., Shaw S.Y., Dong L., Haggarty S.J., et al. Striatal neurons expressing full-length mutant huntingtin exhibit decreased N-cadherin and altered neuritogenesis. Hum. Mol. Genet. 2011;20:2344–2355. doi: 10.1093/hmg/ddr127. PubMed DOI PMC

Singer E., Walter C., Weber J.J., Krahl A.-C., Mau-Holzmann U.A., Rischert N., Riess O., Clemensson L.E., Nguyen H.P. Reduced cell size, chromosomal aberration and altered proliferation rates are characteristics and confounding factors in the STHdh cell model of Huntington disease. Sci. Rep. 2017;7 doi: 10.1038/s41598-017-17275-4. PubMed DOI PMC

Tran N.L., Adams D.G., Vaillancourt R.R., Heimark R.L. Signal transduction from N-cadherin increases Bcl-2. Regulation of the phosphatidylinositol 3-kinase/Akt pathway by homophilic adhesion and actin cytoskeletal organization. J. Biol. Chem. 2002;277:32905–32914. doi: 10.1074/jbc.M200300200. PubMed DOI

Zheng J.Y., Han S.P., Chiu Y.-J., Yip A.K., Boichat N., Zhu S.W., Zhong J., Matsudaira P. Epithelial Monolayers Coalesce on a Viscoelastic Substrate through Redistribution of Vinculin. Biophys. J. 2017;113:1585–1598. doi: 10.1016/j.bpj.2017.07.027. PubMed DOI PMC

Jin Y.N., Yu Y.V., Gundemir S., Jo C., Cui M., Tieu K., Johnson G.V.W. Impaired Mitochondrial Dynamics and Nrf2 Signaling Contribute to Compromised Responses to Oxidative Stress in Striatal Cells Expressing Full-Length Mutant Huntingtin. PLoS One. 2013;8 doi: 10.1371/journal.pone.0057932. PubMed DOI PMC

Patop I.L., Wüst S., Kadener S. Past, present, and future of circ RNA s. EMBO J. 2019;38 doi: 10.15252/embj.2018100836. PubMed DOI PMC

Wang P.L., Bao Y., Yee M.-C., Barrett S.P., Hogan G.J., Olsen M.N., Dinneny J.R., Brown P.O., Salzman J. Circular RNA Is Expressed across the Eukaryotic Tree of Life. PLoS One. 2014;9 doi: 10.1371/journal.pone.0090859. PubMed DOI PMC

Liu C.-X., Chen L.-L. Circular RNAs: Characterization, cellular roles, and applications. Cell. 2022;185:2016–2034. doi: 10.1016/j.cell.2022.04.021. PubMed DOI

Wright G.E.B., Collins J.A., Kay C., McDonald C., Dolzhenko E., Xia Q., Bečanović K., Drögemöller B.I., Semaka A., Nguyen C.M., et al. Length of Uninterrupted CAG, Independent of Polyglutamine Size, Results in Increased Somatic Instability, Hastening Onset of Huntington Disease. Am. J. Hum. Genet. 2019;104:1116–1126. doi: 10.1016/j.ajhg.2019.04.007. PubMed DOI PMC

Mühlau M., Winkelmann J., Rujescu D., Giegling I., Koutsouleris N., Gaser C., Arsic M., Weindl A., Reiser M., Meisenzahl E.M. Variation within the Huntington’s Disease Gene Influences Normal Brain Structure. PLoS One. 2012;7 doi: 10.1371/journal.pone.0029809. PubMed DOI PMC

Muniz L., Nicolas E., Trouche D. RNA polymerase II speed: a key player in controlling and adapting transcriptome composition. EMBO J. 2021;40 doi: 10.15252/embj.2020105740. PubMed DOI PMC

Zhang Y., Xue W., Li X., Zhang J., Chen S., Zhang J.-L., Yang L., Chen L.-L. The Biogenesis of Nascent Circular RNAs. Cell Rep. 2016;15:611–624. doi: 10.1016/j.celrep.2016.03.058. PubMed DOI

Kiliszek A., Kierzek R., Krzyzosiak W.J., Rypniewski W. Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases. Nucleic Acids Res. 2010;38:8370–8376. doi: 10.1093/nar/gkq700. PubMed DOI PMC

Belotserkovskii B.P., Liu R., Tornaletti S., Krasilnikova M.M., Mirkin S.M., Hanawalt P.C. Mechanisms and implications of transcription blockage by guanine-rich DNA sequences. Proc. Natl. Acad. Sci. USA. 2010;107:12816–12821. doi: 10.1073/pnas.1007580107. PubMed DOI PMC

Lin Y., Dent S.Y.R., Wilson J.H., Wells R.D., Napierala M. R loops stimulate genetic instability of CTG·CAG repeats. Proc. Natl. Acad. Sci. USA. 2010;107:692–697. doi: 10.1073/pnas.0909740107. PubMed DOI PMC

Reddy K., Tam M., Bowater R.P., Barber M., Tomlinson M., Nichol Edamura K., Wang Y.-H., Pearson C.E. Determinants of R-loop formation at convergent bidirectionally transcribed trinucleotide repeats. Nucleic Acids Res. 2011;39:1749–1762. doi: 10.1093/nar/gkq935. PubMed DOI PMC

Nakamori M., Pearson C.E., Thornton C.A. Bidirectional transcription stimulates expansion and contraction of expanded (CTG)•(CAG) repeats. Hum. Mol. Genet. 2011;20:580–588. doi: 10.1093/hmg/ddq501. PubMed DOI PMC

Mason M.A., Gomez-Paredes C., Sathasivam K., Neueder A., Papadopoulou A.-S., Bates G.P. Silencing Srsf6 does not modulate incomplete splicing of the huntingtin gene in Huntington’s disease models. Sci. Rep. 2020;10 doi: 10.1038/s41598-020-71111-w. PubMed DOI PMC

Schilling J., Broemer M., Atanassov I., Duernberger Y., Vorberg I., Dieterich C., Dagane A., Dittmar G., Wanker E., Van Roon-Mom W., et al. Deregulated Splicing Is a Major Mechanism of RNA-Induced Toxicity in Huntington’s Disease. J. Mol. Biol. 2019;431:1869–1877. doi: 10.1016/j.jmb.2019.01.034. PubMed DOI

Anderson R., Das M.R., Chang Y., Farenhem K., Schmitz C.O., Jain A. CAG repeat expansions create splicing acceptor sites and produce aberrant repeat-containing RNAs. Mol. Cell. 2024;84:702–714.e10. doi: 10.1016/j.molcel.2024.01.006. PubMed DOI PMC

Gantley L., Stringer B.W., Conn V.M., Ootsuka Y., Holds D., Slee M., Aliakbari K., Kirk K., Ormsby R.J., Webb S.T., et al. Functional Characterisation of the Circular RNA, circHTT(2-6), in Huntington’s Disease. Cells. 2023;12:1337. doi: 10.3390/cells12091337. PubMed DOI PMC

Jarlstad Olesen M.T., S Kristensen L. Circular RNAs as microRNA sponges: evidence and controversies. Essays Biochem. 2021;65:685–696. doi: 10.1042/EBC20200060. PubMed DOI

Das A., Sinha T., Shyamal S., Panda A.C. Emerging Role of Circular RNA–Protein Interactions. ncRNA. 2021;7:48. doi: 10.3390/ncrna7030048. PubMed DOI PMC

Fan X., Yang Y., Chen C., Wang Z. Pervasive translation of circular RNAs driven by short IRES-like elements. Nat. Commun. 2022;13:3751. doi: 10.1038/s41467-022-31327-y. PubMed DOI PMC

Li H., Xie M., Wang Y., Yang L., Xie Z., Wang H. riboCIRC: a comprehensive database of translatable circRNAs. Genome Biol. 2021;22:79. doi: 10.1186/s13059-021-02300-7. PubMed DOI PMC

Case L.B., Baird M.A., Shtengel G., Campbell S.L., Hess H.F., Davidson M.W., Waterman C.M. Molecular mechanism of vinculin activation and nanoscale spatial organization in focal adhesions. Nat. Cell Biol. 2015;17:880–892. doi: 10.1038/ncb3180. PubMed DOI PMC

Johnson R.P., Craig S.W. F-actin binding site masked by the intramolecular association of vinculin head and tail domains. Nature. 1995;373:261–264. doi: 10.1038/373261a0. PubMed DOI

Chen H., Choudhury D.M., Craig S.W. Coincidence of Actin Filaments and Talin Is Required to Activate Vinculin. J. Biol. Chem. 2006;281:40389–40398. doi: 10.1074/jbc.M607324200. PubMed DOI

Pendergrass W., Wolf N., Poot M. Efficacy of MitoTracker GreenTM and CMXrosamine to measure changes in mitochondrial membrane potentials in living cells and tissues. Cytometry Pt A. 2004;61A:162–169. doi: 10.1002/cyto.a.20033. PubMed DOI

Dai Y., Wang H., Lian A., Li J., Zhao G., Hu S., Li B. A comprehensive perspective of Huntington’s disease and mitochondrial dysfunction. Mitochondrion. 2023;70:8–19. doi: 10.1016/j.mito.2023.03.001. PubMed DOI

Pamudurti N.R., Patop I.L., Krishnamoorthy A., Ashwal-Fluss R., Bartok O., Kadener S. An in vivo strategy for knockdown of circular RNAs. Cell Discov. 2020;6:52. doi: 10.1038/s41421-020-0182-y. PubMed DOI PMC

Gao X., Ma X.-K., Li X., Li G.-W., Liu C.-X., Zhang J., Wang Y., Wei J., Chen J., Chen L.-L., Yang L. Knockout of circRNAs by base editing back-splice sites of circularized exons. Genome Biol. 2022;23:16. doi: 10.1186/s13059-021-02563-0. PubMed DOI PMC

Li X., Yang L., Chen L.-L. The Biogenesis, Functions, and Challenges of Circular RNAs. Mol. Cell. 2018;71:428–442. doi: 10.1016/j.molcel.2018.06.034. PubMed DOI

Li S., Li X., Xue W., Zhang L., Yang L.-Z., Cao S.-M., Lei Y.-N., Liu C.-X., Guo S.-K., Shan L., et al. Screening for functional circular RNAs using the CRISPR–Cas13 system. Nat. Methods. 2021;18:51–59. doi: 10.1038/s41592-020-01011-4. PubMed DOI

Pierattini B., D’Agostino S., Bon C., Peruzzo O., Alendar A., Codino A., Ros G., Persichetti F., Sanges R., Carninci P., et al. SINEUP non-coding RNA activity depends on specific N6-methyladenosine nucleotides. Mol. Ther. Nucleic Acids. 2023;32:402–414. doi: 10.1016/j.omtn.2023.04.002. PubMed DOI PMC

Carrieri C., Cimatti L., Biagioli M., Beugnet A., Zucchelli S., Fedele S., Pesce E., Ferrer I., Collavin L., Santoro C., et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature. 2012;491:454–457. doi: 10.1038/nature11508. PubMed DOI

D’Agostino S., Tettey-Matey A., Volpe M., Pierattini B., Ansaloni F., Lau P., Bon C., Peruzzo O., Braccia C., Armirotti A., et al. Internal Ribosome Entry Sites act as Effector Domain in linear and circular antisense long non-coding SINEUP RNAs. Mol. Biol. 2023 doi: 10.1101/2023.05.25.542260. DOI

White J.K., Auerbach W., Duyao M.P., Vonsattel J.P., Gusella J.F., Joyner A.L., MacDonald M.E. Huntingtin is required for neurogenesis and is not impaired by the Huntington’s disease CAG expansion. Nat. Genet. 1997;17:404–410. doi: 10.1038/ng1297-404. PubMed DOI

Beaudoin G.M.J., Lee S.-H., Singh D., Yuan Y., Ng Y.-G., Reichardt L.F., Arikkath J. Culturing pyramidal neurons from the early postnatal mouse hippocampus and cortex. Nat. Protoc. 2012;7:1741–1754. doi: 10.1038/nprot.2012.099. PubMed DOI

Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Pietzsch T., Preibisch S., Rueden C., Saalfeld S., Schmid B., et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods. 2012;9:676–682. doi: 10.1038/nmeth.2019. PubMed DOI PMC

Ershov D., Phan M.-S., Pylvänäinen J.W., Rigaud S.U., Le Blanc L., Charles-Orszag A., Conway J.R.W., Laine R.F., Roy N.H., Bonazzi D., et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat. Methods. 2022;19:829–832. doi: 10.1038/s41592-022-01507-1. PubMed DOI

Stringer C., Wang T., Michaelos M., Pachitariu M. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods. 2021;18:100–106. doi: 10.1038/s41592-020-01018-x. PubMed DOI

Tatomer D.C., Liang D., Wilusz J.E. In: mRNA Processing Methods in Molecular Biology. Shi Y., editor. Springer; 2017. Inducible Expression of Eukaryotic Circular RNAs from Plasmids; pp. 143–154. PubMed DOI

Gagnon K.T., Li L., Janowski B.A., Corey D.R. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nat. Protoc. 2014;9:2045–2060. doi: 10.1038/nprot.2014.135. PubMed DOI PMC

Agarwal V., Bell G.W., Nam J.-W., Bartel D.P. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4 doi: 10.7554/eLife.05005. PubMed DOI PMC

Kozomara A., Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucl. Acids Res. 2014;42:D68–D73. doi: 10.1093/nar/gkt1181. PubMed DOI PMC

Glažar P., Papavasileiou P., Rajewsky N. circBase: a database for circular RNAs. RNA. 2014;20:1666–1670. doi: 10.1261/rna.043687.113. PubMed DOI PMC

Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., Haussler D. The human genome browser at UCSC. Genome Res. 2002;12:996–1006. doi: 10.1101/gr.229102. PubMed DOI PMC

Li J.-H., Liu S., Zhou H., Qu L.-H., Yang J.-H. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42:D92–D97. doi: 10.1093/nar/gkt1248. PubMed DOI PMC

Bernabò P., Tebaldi T., Groen E.J.N., Lane F.M., Perenthaler E., Mattedi F., Newbery H.J., Zhou H., Zuccotti P., Potrich V., et al. In Vivo Translatome Profiling in Spinal Muscular Atrophy Reveals a Role for SMN Protein in Ribosome Biology. Cell Rep. 2017;21:953–965. doi: 10.1016/j.celrep.2017.10.010. PubMed DOI PMC

Lauria F., Bernabò P., Tebaldi T., Groen E.J.N., Perenthaler E., Maniscalco F., Rossi A., Donzel D., Clamer M., Marchioretto M., et al. SMN-primed ribosomes modulate the translation of transcripts related to spinal muscular atrophy. Nat. Cell Biol. 2020;22:1239–1251. doi: 10.1038/s41556-020-00577-7. PubMed DOI PMC