Biogenesis of a 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation

Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants

Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at: www.mcr.org.in/diffisomirs.

Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants

microRNAs (miRNAs) play an important role as key regulators controlling the post-transcriptional events in plants across development, abiotic and biotic stress, tissue polarity and also in defining the evolutionary basis of the origin of the post-transcriptional machinery. Identifying patterns of regulated and co-regulated small RNAs, in particular miRNAs and their sequence variants with the availability of next generation sequencing approaches has widely demonstrated the role of miRNAs and their temporal regulation in maintaining plant development and their response to stress conditions. Although the role of canonical miRNAs has been widely explored and functional diversity is revealed, those works for isomiRs are still limited and urgent to be carried out across plants. This relative lack of information with respect to isomiRs might be attributed to the non-availability of large-scale detection of isomiRs across wide plant species. In the present research, we addressed this by developing Plant isomiR Atlas, which provides large-scale detection of isomiRs across 23 plant species utilizing 677 smallRNAs datasets and reveals a total of 98,374 templated and non-templated isomiRs from 6,167 precursors. Plant isomiR Atlas provides several visualization features such as species specific isomiRs, isomiRs and canonical miRNAs overlap, terminal modification classifications, target identification using psRNATarget and TargetFinder and also canonical miRNAs:target interactions. Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate to understand the functional role of isomiRs. Plant isomiR Atlas is available at www.mcr.org.in/isomir. One Sentence Summary  Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate the understanding and diversity of functional targets of plants isomiRs.