Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates
Fig 7
Unexpected patterns of 5' heterogeneity and processing of mirtrons.
(A) A 5'-tailed mirtron in Irak1 exhibits strong heterogeneity in its 5p species that differ in register by 2 nt; this is accompanied by strong heterogeneity in its 3p species. Inspection of this array of isomiR sequences suggests that distinct 5' ends of 5p species may instruct alternative Dicer cleavage. This may be accompanied by subsequent 3' resection of "long" 3p reads produced by Dicer cleavage closer to the terminal loop, and retention of 3'-uridylated 3p reads when the Dicer cleavage is further from the loop. (B) A counter-example in which broad 5' heterogeneity of 5p species, here distributed equally over three nucleotides, is not accompanied by 5’ heterogeneity of 3p species, which are extremely precisely-defined. All of these reads accumulate similarly in total and Ago-IP data. (C-E) Frequent 5' decapitation of select mirtron-5p reads defined by splicing. (C) Example of 3'-tailed mirtron (hsa-mir-4745) exhibiting nearly complete decapitation of 5'-G from its 5p reads (i.e., "xU" reads). These reads are present in multiple Ago-IP datasets. (D) Example of a conventional mirtron (hsa-mir-1236) exhibiting high frequency "xU" reads supported by Ago-IP evidence. (E) Summary of 5' heterogeneity amongst 5p reads from human conventional and 3'-tailed mirtrons, indicating that many mirtrons are subject to 5' decapitation.