Complexity of Murine Cardiomyocyte miRNA Biogenesis, Sequence Variant Expression and Function

• DOI: 10.1371/journal.pone.0030933
• Publication Date: 2012-02-03T22:00:29Z
• Authors: David T. Humphreys; Carly J. Hynes; Hardip R. Patel; Grace H. Wei; Leah Cannon; Diane Fatkin; Catherine M. Suter; Jennifer L. Clancy; Thomas Preiss
• Keywords: MiRBase; Drosha; Dicer

microRNAs (miRNAs) are critical to heart development and disease. Emerging research indicates that regulated precursor processing can give rise an unexpected diversity of miRNA variants. We subjected small RNA from murine HL-1 cardiomyocyte cells next generation sequencing investigate the relevance such cardiac biology. ∼40 million tags were mapped known hairpin sequences as deposited in miRBase version 16, calling 403 generic miRNAs appreciably expressed. Hairpin arm bias broadly agreed with annotation, although 44 miR* unexpectedly abundant (>20% tags); conversely, 33 -5p/-3p annotated hairpins asymmetrically Overall, variability was infrequent at 5′ start but common 3′ end (5.2% 52.3% tags, respectively). Nevertheless, 105 showed marked isomiR expression tags). Among these miR-133a, a important functions, we demonstrated differential mRNA targeting by two its prevalent isomiRs. Analyses termini base-pairing patterns around Drosha Dicer cleavage regions confirmed towards uridine most position miRNAs, well supporting thermodynamic asymmetry rule for strand selection role local structural distortions fine tuning processing. further recorded appreciable 5 novel miR*, 38 extreme variants 8 antisense miRNAs. Analysis genome-mapped revealed 147 candidate In summary, pronounced sequence among knowledge which will underpin future into mechanisms involved biogenesis and, importantly, function, disease therapy.