Acknowledgement
This study was supported by the National Research Foundation of Korea (NRF) grant funded by the South Korea government (MSIT) [RS-2023-00212894], Learning & Academic research institution for Master's·Ph.D. students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education [RS-2023-00301914], Korea Institute for Advancement of Technology funded by the Ministry of Trade, Industry and Energy [P0025489], and Korean Environment Industry & Technology Institute (KEITI) through Core Technology Development Project for Environmental Diseases Prevention and Management funded by Korean Ministry of Environment (MOE) (no. 2022003310001).
References
- Albulescu LO, Sabet N, Gudipati M, Stepankiw N, Bergman ZJ, Huffaker TC, Pleiss JA (2012) A quantitative, high-throughput reverse genetic screen reveals novel connections between Pre-mRNA splicing and 5' and 3' end transcript determinants. PLOS Genet 8:e1002530.
- Bruderer R, Tatham MH, Plechanovova A, Matic I, Garg AK, Hay RT (2011) Purification and identification of endogenous polySUMO conjugates. EMBO Rep 12:142-148.
- Cao Y, Huang C, Zhao X, Yu J (2023) Regulation of SUMOylation on RNA metabolism in cancers. Front Mol Biosci 10:1137215.
- Choi H, Kang M, Lee KH, Kim YS (2023) Elevated level of PLRG1 is critical for the proliferation and maintenance of genome stability of tumor cells. BMB Rep 56:612-617.
- Choi J, Ryoo ZY, Cho DH, Lee HS, Ryu HY (2021) Trans-tail regulation-mediated suppression of cryptic transcription. Exp Mol Med 53:1683-1688.
- De Conti L, Baralle M, Buratti E (2013) Exon and intron definition in pre-mRNA splicing. Wiley Interdiscip Rev RNA 4:49-60.
- Karijolich J, Yu YT (2010) Spliceosomal snRNA modifications and their function. RNA Biol 7:192-204.
- Kitamura-Abe S, Itoh H, Washio T, Tsutsumi A, Tomita M (2004) Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs. J Bioinform Comput Biol 02:309-331.
- Lee S, Jung H, Choi S, Cho N, Kim EM, Kim KK (2023) Intron retention decreases METTL3 expression by inhibiting mRNA export to the cytoplasm. BMB Rep 56:514-519.
- Li SJ, Hochstrasser M (2000) The yeast ULP2 (SMT4) gene encodes a novel protease specific for the ubiquitin-like Smt3 protein. Mol Cell Biol 20:2367-2377.
- Liu Y, Park JM, Lim S, Duan R, Lee DY, Choi D, Choi DK, Rhie BH, Cho SY, Ryu HY, Ahn SH (2024) Tho2-mediated escort of Nrd1 regulates the expression of aging-related genes. Aging Cell e14203.
- Melchior F (2000) SUMO--nonclassical ubiquitin. Annu Rev Cell Dev Biol 16:591-626.
- Pozzi B, Bragado L, Will CL, Mammi P, Risso G, Urlaub H, Luhrmann R, Srebrow A (2017) SUMO conjugation to spliceosomal proteins is required for efficient pre-mRNA splicing. Nucleic Acids Res 45:6729-6745.
- Ryu HY (2022) SUMO pathway is required for ribosome biogenesis. BMB Rep 55:535-540.
- Ryu HY, Ahn SH, Hochstrasser M (2020a) SUMO and cellular adaptive mechanisms. Exp Mol Med 52:931-939.
- Ryu HY, Hochstrasser M (2021) Histone sumoylation and chromatin dynamics. Nucleic Acids Res 49:6043-6052.
- Ryu HY, Lopez-Giraldez F, Knight J, Hwang SS, Renner C, Kreft SG, Hochstrasser M (2018) Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease. Nat Commun 9:5417.
- Ryu HY, Su D, Wilson-Eisele NR, Zhao D, Lopez-Giraldez F, Hochstrasser M (2019) The Ulp2 SUMO protease promotes transcription elongation through regulation of histone sumoylation. The EMBO J 38:e102003.
- Ryu HY, Wilson NR, Mehta S, Hwang SS, Hochstrasser M (2016) Loss of the SUMO protease Ulp2 triggers a specific multichromosome aneuploidy. Genes Dev 30:1881-1894.
- Ryu HY, Zhao D, Li J, Su D, Hochstrasser M (2020b) Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation. Nucleic Acids Res 48:12151-12168.
- Sakharkar MK, Chow VTK, Kangueane P (2004) Distributions of exons and introns in the human genome. In Silico Biology 4:387-393.
- Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative CT method. Nat Protoc 3:1101-1108.
- Singh R (2002) RNA-protein interactions that regulate pre-mRNA splicing. Gene Expr 10:79-92.
- Stajich JE, Dietrich FS, Roy SW (2007) Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biol 8:R223.
- Xie J, Wang L, Lin RJ (2023) Variations of intronic branchpoint motif: Identification and functional implications in splicing and disease. Commun Biol 6:1142.