Recent multi-omics studies using a large-scale genome, transcriptome, and epigenome data produced by massively parallel sequencing techniques or next generation sequencing techniques provide an opportunity for us to investigate new territories in genomes and lead to novel functional insights into noncoding DNAs, intergenic regions, and introns. In the present review, we first introduce some studies showing what molecular characteristics of introns cannot be explained by a simple random mutational process that real junk DNAs may have undergone. Subsequently, we summarize the functional characteristics of introns that have been studied providing clues about the adaptive significance of introns in genomes. We divide the functional roles of introns into two different categories, i.e., direct roles and indirect roles in Table 1 [15262728293031323334353637383940414243444546], and demonstrate the details in the Results section.
