Three competing hypotheses emerged, each with their own prediction about the extent to which newly replicated DNA double helices contained old DNA strands versus newly synthesized material: semi-conservative replication, conservative replication, and dispersive replication.
Among 59 codons, 54 are found to be significantly different in leading strand versus lagging strand genes.
Additionally, we have found no obvious correlation between aggregation propensity and change in charge in amino acids that concentrate to a particular structure (beta strand versus non-beta strand regions, surface versus interior; see Supplementary Material, Fig. S1).
The miRNAs typically align to a ~ 21-nt region of the gene sequence with a preferential bias in the number of copies representing one strand versus the opposite strand, and thus, it result in relatively few different signatures.
We did not detect significant differences between these associations for genes coded on the sense strand versus those coded on the anti-sense strand, not even for any particular species, despite the differences between the nucleotide contents for these strands.
For example in viral RNA detection, the "+strand" is the viral genome, while the "- strand" RNA is indicative of active viral replication; therefore, stringent assays were designed to specifically detect one strand versus the other [ 3- 6].
By calculating the ratios of nat-siRNA reads on forward strand versus reverse strands, we found that the nat-siRNAs from 42 Bre cis-NATs and 66 Wut cis-NATs exhibited strand bias, with ratios greater than two-fold and p-value <0.01 (Additional file 4: Table S3, Additional file 5: Table S4).
