A common class of transcripts with 5′-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification

Introns are found in 59 untranslated regions (59UTRs) for 35% of all human transcripts. These 59UTR introns are not randomly distributed: genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 59UTR introns tend to harbor specific RNA sequence elements in their early coding regions. Here we explored the connection between coding-region sequence and 59UTR intron status. We developed a classifier modeling this relationship that can predict 59UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 59proximal-intron-minus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. Members of this transcript class tend to exhibit differential RNA expression across many conditions. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure preceding the start codon, and near the 59cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the Exon Junction Complex (EJC) at non-canonical 59-proximal positions. Finally, N1-methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses reveal the existence of a distinct 5IM class comprising ~20% of human transcripts. This class is defined by depletion of 59proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N1-methyladenosines in the early coding region, and enrichment for non-canonical binding by the Exon Junction Complex.