Table 1 Epigenetic alterations and RNA splicing.
From: The potential impact of RNA splicing abnormalities on immune regulation in endometrial cancer
Epigenetic alterations | Impact on RNA splicing | Examples |
|---|---|---|
DNA methylation | Directly affects the recognition of exons | EGFR, HPCAL1-SV and RNASET2-SV [39] The exon1 of the SFRP1 gene [40] The exon12 of the MBD1 gene [41] |
Indirectly affects the inclusion and exclusion of exons | The exon7 of the GCK gene [42] | |
Histone modification | Affects the identification of splice sites and the splicing efficiency | H3K36me3 and H3K27me3 [43] |
Affects the AS process | H3K36me—the intron2 retention in DVL2 mRNA [44] H3K36me3—the ES of IL-18 [45] | |
ncRNA | MiRNA targeted inhibition of SFs | MiR-30a-5p and miR-181a-5p—SRSF7 [26] MiR-802—SRSF9 [46] MiR-28 and miR-505—SRSF1 [47] MiR-10a and miR-10b—SRSF1 [48] MiR-10b—U6 snRNA [49] |
LncRNA influences the stability, subcellular localization, or interactions between SFs and pre-mRNAs | LncRNA CRNDE—SRSF6 [50] LncRNA H19—SRSF1 [51] LncRNA MALAT1 and LINC01133—SRSFs’ nuclear localization [52, 53] LncRNA CACClnc—YB1 and U2AF65 [54] LncRNA PLANE, MIR99AHG and LINC01089—hnRNPM and PTBP1 [55,56,57] | |
LncRNA encodes splicing regulatory protein | LncRNA LOC90024 —the “cancerous” Sp4 splice variant [58] | |
RNA modification | M6A readers participate in the regulation of AS | YTHDC1—lncHOXB-AS3 splice variant NR_033205.1 and RBM4-S variant [62, 63] HnRNPC—TAF8S subtype [65] |
Non-m6A modifications | 2’-O-methylation modification—U12-type intron splicing [66] | |
SNP | Disrupts splice sites | PKD1 (c.7866C > A) [67] TCHP (rs74416240) [68] FARP1 (rs677031-G) [69] PSMD13 (rs7128029 A < G) [70] ELP2 (rs1785932-T) [71] |
Creates new splice sites | PTEN (rs786204926-G) [72] GTPBP3 (c.809-1_809delinsA) [73] | |
Affects the splice adjustment elements | PKD1 (c.7866C > A,c.7960A > G, c.7979A > T, c.7987C > T, c.11346C > T and c.11393C > G) [67] ACADM (c.351A > C, c.325A > C, c.324T > C and c.326G > C) [74] IL7R (rs6897932) [75] | |
Alters RNA secondary structure | EGR1 (rs1995158) [76] |
