Certain chemical modifications in precursor RNA molecules can significantly affect splice site selection and ultimately impact the final mRNA isoforms produced during RNA processing. These modifications can alter the structure, stability, and recognition of splice sites by the splicing machinery, leading to the production of different mRNA isoforms.1. RNA editing: RNA editing is a process that introduces changes to the RNA sequence after transcription. One common type of RNA editing is the deamination of adenosine to inosine A-to-I editing , which can alter splice site recognition. Inosine is recognized as guanosine by the splicing machinery, and this change can lead to the inclusion or exclusion of specific exons, resulting in different mRNA isoforms.2. RNA methylation: Methylation of RNA molecules, such as the addition of a methyl group to the N6 position of adenosine m6A , can also impact splice site selection. The presence of m6A can influence the binding of splicing factors and other RNA-binding proteins, leading to changes in splice site recognition and the production of alternative mRNA isoforms.3. Pseudouridylation: Pseudouridine is a modified nucleotide found in various RNA molecules, including precursor mRNA. The presence of can stabilize RNA structures and affect the binding of splicing factors, ultimately influencing splice site selection and the generation of different mRNA isoforms.4. RNA secondary structure: Chemical modifications can also influence the secondary structure of precursor RNA molecules. For example, the presence of modified nucleotides can stabilize or destabilize RNA structures, affecting the accessibility of splice sites and the binding of splicing factors. This can lead to changes in splice site selection and the production of alternative mRNA isoforms.In summary, chemical modifications in precursor RNA molecules can impact splice site selection by altering the structure, stability, and recognition of splice sites by the splicing machinery. These changes can ultimately lead to the production of different mRNA isoforms, which can have significant consequences for gene expression and cellular function.