This paper describes the ALISA tool, which implements a lightly supervised method for sentence-level alignment of speech with imperfect transcripts.
"Even if a transcript is imperfect, it gives the user an approximate idea of what was said".
If the complimentarity of the miR to an mRNA transcript is imperfect, translation is repressed through a variety of mechanisms.
It is possible that these transcripts arose from imperfect fidelity of Pol II transcriptional machinery due to stochastic components governing fundamental interactions between molecules within the cell.
Analysis of the gene ontology of differentially expressed transcripts, while imperfect, provides insight to the potential interactions that underlie the fate determination that drives the mesodermal subpopulation of differentiating mESCs along a cardiac lineage.
In mammalian cells, typical miRNAs are first produced as imperfect hairpins within longer transcripts.
More recently, methodologies used to profile genome wide RISC occupancy have revealed extensive RISC binding to transcripts with imperfect or nonexistent seed matches [ 18- 21].
This takes place when the miRNA targets the 3′- untranslated region (3′-UTR) of transcripts by imperfect base pairing and functions to inhibit translation.
An alternative scenario is that nuclear-accumulated sense transcripts form imperfect hairpin structures, which resemble miRNA precursors, are processed into small RNAs and function as a trigger for RNA degradation via RDR-catalyzed synthesis of dsRNA, resulting in PTGS [ 32].
Reasons for "off-target" effects may be (i) the siRNA-induced RNA cleavage of transcripts with imperfect homology to the siRNA [ 52, 53], (ii) a possible competition with endogenously expressed micro RNAs (miRNAs), which may be involved in the control of, for instance, cell differentiation, for RISC protein components [ 54], and (iii) the induction of an interferon response [ 45, 55].
