Decoding subcellular RNA localization one molecule at a time

Lécuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, et al. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell. 2007;131:174–87. https://doi.org/10.1016/j.cell.2007.08.003.

Article  CAS  PubMed  Google Scholar 

Wilk R, Hu J, Blotsky D, Krause HM. Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs. Genes Dev. 2016;30:594–609. https://doi.org/10.1101/gad.276931.115.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen L-L, et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 2023;24:430–47. https://doi.org/10.1038/s41580-022-00566-8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Davis BM, Mccurrach ME, Taneja KL, Singer RH, Housman DE. Expansion of a CUG trinucleotide repeat in the 3′ untranslated region of myotonic dystrophy protein kinase transcripts results in nuclear retention of transcripts. Proc Natl Acad Sci U S A. 1997;94:7388–93. https://doi.org/10.1073/pnas.94.14.7388.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fallini C, Zhang H, Su Y, Silani V, Singer RH, Rossoll W, et al. The survival of motor neuron (SMN) protein interacts with the mRNA-binding protein HuD and regulates localization of poly(A) mRNA in primary motor neuron axons. J Neurosci. 2011;31:3914–25. https://doi.org/10.1523/JNEUROSCI.3631-10.2011.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alami NH, Smith RB, Carrasco MA, Williams LA, Winborn CS, Han SSW, et al. Axonal transport of TDP-43 mRNA granules Is impaired by ALS-causing mutations. Neuron. 2014;81:536–43. https://doi.org/10.1016/j.neuron.2013.12.018.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Goering R, Hudish LI, Guzman BB, Raj N, Bassell GJ, Russ HA, et al. FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences. Elife. 2020;9:1–31. https://doi.org/10.7554/eLife.52621.

Article  Google Scholar 

Fernandopulle MS, Lippincott-Schwartz J, Ward ME. RNA transport and local translation in neurodevelopmental and neurodegenerative disease. Nat Neurosci. 2021;24:622–32. https://doi.org/10.1038/s41593-020-00785-2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

McGary K, Nudler E. RNA polymerase and the ribosome: the close relationship. Curr Opin Microbiol. 2013;16:112–7. https://doi.org/10.1016/j.mib.2013.01.010.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Van Treeck B, Protter DSW, Matheny T, Khong A, Link CD, Parker R. RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome. Proc Natl Acad Sci U S A. 2018;115:2734–9. https://doi.org/10.1073/pnas.1800038115.

Ripin N, Parker R. Formation, function, and pathology of RNP granules. Cell. 2023;186:4737–56. https://doi.org/10.1016/j.cell.2023.09.006.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mao YS, Zhang B, Spector DL. Biogenesis and function of nuclear bodies. Trends Genet. 2011;27:295–306. https://doi.org/10.1016/j.tig.2011.05.006.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shan L, Li P, Yu H, Chen LL. Emerging roles of nuclear bodies in genome spatial organization. Trends Cell Biol 2023:1–11. https://doi.org/10.1016/j.tcb.2023.10.012.

Gall JG, Bellini M, Wu Z, Murphy C. Assembly of the nuclear transcription and processing machinery: Cajal Bodies (Coiled Bodies) and transcriptosomes. Mol Biol Cell. 1999;10:4385–402. https://doi.org/10.1091/mbc.10.12.4385.

Article  CAS  PubMed  PubMed Central  Google Scholar 

West JA, Mito M, Kurosaka S, Takumi T, Tanegashima C, Chujo T, et al. Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization. J Cell Biol. 2016;214:817–30. https://doi.org/10.1083/jcb.201601071.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell. 2009;33:717–26. https://doi.org/10.1016/j.molcel.2009.01.026.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics. 2007;8:1–16. https://doi.org/10.1186/1471-2164-8-39.

Article  CAS  Google Scholar 

Dias AP, Dufu K, Lei H, Reed R. A role for TREX components in the release of spliced mRNA from nuclear speckle domains. Nat Commun. 2010;1:97. https://doi.org/10.1038/ncomms1103.

Article  CAS  PubMed  Google Scholar 

Spector DL, Lamond AI. Nuclear speckles. Cold Spring Harb Perspect Biol. 2011;3:a000646–a000646. https://doi.org/10.1101/cshperspect.a000646.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee ES, Smith HW, Wolf EJ, Guvenek A, Wang YE, Emili A, et al. ZFC3H1 and U1–70K promote the nuclear retention of mRNAs with 5’ splice site motifs within nuclear speckles. RNA. 2022;28:878–94. https://doi.org/10.1261/rna.079104.122.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, et al. Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature. 2024;629:1165–73. https://doi.org/10.1038/s41586-024-07429-6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pirrotta V, Li H-B. A view of nuclear Polycomb bodies. Curr Opin Genet Dev. 2012;22:101–9. https://doi.org/10.1016/j.gde.2011.11.004.

Article  CAS  PubMed  Google Scholar 

Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors—from names to functions. EMBO J. 2023;42:1–43. https://doi.org/10.15252/embj.2022112699.

Article  CAS  Google Scholar 

Van Koningsbruggen S, Gierliński M, Schofield P, Martin D, Barton GJ, Ariyurek Y, et al. High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Mol Biol Cell. 2010;21:3735–48. https://doi.org/10.1091/mbc.E10-06-0508.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ghetti A, Piñol-Roma S, Michael WM, Morandi C, Dreyfuss G. hnRNP I, the polypyrimidine tract-binding protein: distinct nuclear localization and association with hnRNAs. Nucleic Acids Res. 1992;20:3671–8. https://doi.org/10.1093/nar/20.14.3671.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen T, Boisvert FM, Bazett-Jones DP, Richard S. A role for the GSG domain in localizing Sam68 to novel nuclear structures in cancer cell lines. Mol Biol Cell. 1999;10:3015–33. https://doi.org/10.1091/mbc.10.9.3015.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang S. Review: perinucleolar structures. J Struct Biol. 2000;129:233–40. https://doi.org/10.1006/jsbi.2000.4247.

Article  CAS  PubMed  Google Scholar 

Dumbović G, Biayna J, Banús J, Samuelsson J, Roth A, Diederichs S, et al. A novel long non-coding RNA from NBL2 pericentromeric macrosatellite forms a perinucleolar aggregate structure in colon cancer. Nucleic Acids Res. 2018;46:5504–24.

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