Final answer:
Alternative RNA splicing is a key gene regulation mechanism involving cassette exons and intron retention. Cassette exons contribute to protein diversity by including or excluding specific exons, while intron retention can alter protein function by maintaining introns in the mRNA. Both processes are utilized by eukaryotic organisms and potentially some archaea.
Step-by-step explanation:
Alternative RNA splicing is the general gene regulation mechanism involving cassette exons and intron retention. This process allows for the generation of multiple protein isoforms from a single gene. Cassette exons, also known as exon skipping, involve the selective inclusion or exclusion of specific exons during the splicing process, leading to various mRNA variants. On the other hand, intron retention occurs when an intron that is typically spliced out of pre-mRNA is retained, potentially altering the mRNA stability or the encoded protein's function.
While both cassette exon inclusion and intron retention contribute to the diversity of the proteome, they are different in the final mRNA and protein they produce. Cassette exons result in the inclusion or omission of entire exons, possibly resulting in different protein domains, whereas intron retention can lead to a non-functional protein or altered protein function due to the maintained intron sequence. Both mechanisms are used by eukaryotic organisms, but it's important to note that alternative splicing is more complex and diverse in higher eukaryotes. Moreover, recent studies suggest that certain archaea also exhibit the capability to splice their pre-mRNA, indicating that alternative splicing mechanisms may not be exclusive to eukaryotes.