Cardiogenesis energy (MFE) and distinction between real pre-miRNAs


Cardiogenesis is known to be a complex process,
the transcriptomics of which shows striking similarities with failing heart.
microRNAs (non-coding RNAs of ~22 nucleotide) are one of the key regulatory
elements controlling both heart development and diseases through
post-transcriptional modification. However, very little is known about their
sequences, expression, molecular pathways they regulate and their target genes in
both fetal cardiac development as well as heart diseases. In the present study,
we identified and characterized putative novel miRNAs isolated from fetal heart
tissue using chicken as model system. We sequenced six small RNA libraries
prepared from different developmental stages of the chicken heart using next
generation sequencing. The identified sequences were mapped against the chicken
genome and aligned with existing miRNA sequences in miRBase (v.19.0). Nearly, 1056
putative miRNA sequences were detected, out of which 353 sequences were aligned
with known miRNAs, while 703 miRNAs did not align with any of the sequences. An
in-depth in-silico analysis was
performed to characterize and functionally validate the putative novel fetal
heart miRNAs. A total of 55 putative novel miRNAs were sorted and selected on
the basis of their abundance in various development stages. They were further
characterized on the basis of their secondary structures, minimum free energy
(MFE) and distinction between real pre-miRNAs and pseudo pre-miRNAs. Out of 55
putative miRNAs, 18 miRNAs were real pre-miRNAs, with ideal MFE, forming miRNA
like secondary structure as well as not aligning with any published or reported
miRNA sequences. Expression analysis of selected candidate miRNAs showed differential
expression in different developmental stages. Target genes prediction and their
functional classification revealed that majority of the target genes were
co-expressed, involved in cellular process such as catalytic and receptor
activities (signaling), metabolic and developmental processes, and part of different
protein classes (transcription factors and nucleic acid binding proteins).
Interestingly, we observed that many of the target genes expressed during fetal
development contributes to severe heart disease progression. In conclusion, our
study attempted to provide an understanding of putative novel miRNAs in cardiogenomics,
which may be playing a critical role in cardiac development and supports a
novel potential therapeutic approach towards modulate fetal gene expression
cardiovascular diseases. 

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