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Many antisense sRNAs of miR399 and a few for miR827 were also detected, but they did not seem to be regulated by P. Intriguingly, the lowest expressed member, hvu-miR399k, had four-fold more antisense sRNAs than sense sRNAs, and furthermore under P sufficiency, the antisense sRNAs are more frequent than the sense sRNAs.
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Despite the fact that many fully complementary antisense sRNAs are currently known, the vast majority are found encoded on bacterial plasmids [70], [79].
In this study, by analysing expression profiles of miR399 and miR827, we identified 9 novel members of the miR399 family, and many isomirs and antisense sRNAs for both miR399 and miR827.
We also identified many other classes of sRNAs, including sense and antisense sRNAs, repeat-associated sRNAs, transfer RNA (tRNA -derived sRNAs and chloroplastRNA -derivedAsRNAsd some of which were ando significantly differentially expressed between the two P treatments.
Our study revealed a total of 35 antisense sRNAs showing perfect complementarity with annotated gene sequences.
A similar predominance for antisense sRNAs was described in cyanobacteria [71].
The CDSs displaying larger non-coding mapping ratios correspond to the antisense sRNAs we manually identified from the coverage signals (details are provided in Table S2).
Bacterial antisense sRNAs can furthermore be categorized as either cis-, or trans-encoded, depending on the genomic localization of their targets [6].
Of all the sRNAs identified, antisense sRNAs were the most abundant sRNA class in both P treatments.
Classification of sRNA candidates in putative trans-encoded sRNAs, cis-encoded antisense sRNAs, mRNA leader transcripts, and sense sRNAs overlapping coding regions is ambiguous.
In the classes of antisense sRNAs, mRNA leader transcripts, and sense sRNAs, only few known candidates were re-identified.
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