UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; RNA Therapeutics Institute

Publication Date


Document Type



Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Genetics and Genomics


Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with > 80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5' proximal-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. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N1-methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising approximately 20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N1-methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC.


5′-UTR introns, N1-methyladenosine, exon junction complex, random forest

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© 2017 Cenik et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society. Freely available online through the RNA Open Access option.

DOI of Published Version



RNA. 2017 Mar;23(3):270-283. doi: 10.1261/rna.059105.116. Epub 2016 Dec 19. Link to article on publisher's site

Journal/Book/Conference Title

RNA (New York, N.Y.)

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Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.