Human Disease

Management

Small RNA

DeAnnIso

Paper Link:

http://www.ncbi.nlm.nih.gov/pubmed/27179030

Website:

http://mcg.ustc.edu.cn/bsc/deanniso/index.html

Introduction

MicroRNAs (miRNAs), with average length of 22 nucleotides have emerged as key post-transcriptional regulators of gene expression in many developmental and cellular processes in eukaryotic organisms (1). Recent advances in high-throughput small RNA sequencing technology and algorithmic-based computational approaches have revealed the complex and dynamic repertoire of miRNAs -- a single miRNA locus can give rise to multiple distinct miRNA isoforms (isomiR) that differ in their length and sequence composition (2). It has been demonstrated that isomiRs were bona fide miRNA variants, which were originally dismissed as experimental artifacts (3,4). IsomiRs expression pattern can vary across different tissues, cell types or development time points (5).

Based on the sequences alignment with precusors, isomiRs can be divided into “templated” and “non-templated”, the main biogenesis of “templated” isomiRs most likely derives from variations in processing by the Drosha and/or Dicer enzymes (6). Non-templated isomiRs are mostly catalyzed by nucleotidyl transferases possessing 5’–3’ uridyltransferase and/or adenyltransferase activity, thereby causing an abundance of non-templated nucleotide extensions at 3’ rather than 5’ ends (7).

On the other hand, nucleotide variations detected in isomiRs may originate from SNPs in miRNA genes (8), or be resulted from enzymatic modification like A-I editing, which represents the most general miRNA editing types (9).

Regarding to the specific expression pattern and the heterogeneous nature of isomiRs, isomiRs have been demonstrated with differential functionality (2). 5’ isomiRs have different seed regions to their canonical miRNAs and therefore can stongly affect target selection, which is of great functional and evolutionary importance (10,11). 3’ uridylation and adenlylation isomiRs have opposing roles in plants by promoting the degradation and stability of isomiRs (12,13). A-to-I editing of has-miR-376 within the seed region generates a distinct set of predicted targets including PRPS1, contributes to tissue-specific regulation of uric-acid levels (14). Studies indicating differential functionality for isomiRs are currently confined to several specific variants, there are much more isomiRs with biological significance to be fully resolved.

Several tools, such as MODOMICS (15), SeqBuster (16), IsomiRex (17), miRanalyzer (18), isomiRID (19), IsomiRage (20) and CPSS (21) have been designed for the detection of RNA modifications from sRNA sequencing data. However, these tools mainly focus on the isomiR detection, and do not provide any comprehensive annotation information of the detected isomiR. Integrated tool(s) are required to precisely detect and systematically annotate isomiRs from sRNA sequencing data. To meet this demand, we are presenting an online tool, DeAnnIso (Detection and Annotation of IsomiRs from sRNA sequencing data). It is implemented on an algorithm that has been previously published (http://bioinformatics.oxfordjournals.org/content/28/14/1925.long)(21), and integrated a systematic annotation pipeline. Upon submission of the *.fa files, DeAnnIso can detect isomiRs in each uploaded sample and extract the isomiRs having differential expression between paired-samples. Once the isomiRs detection is accomplished, DeAnnIso will provide additional systematic annotation information to the users, including: 1) IsomiRs expression; 2) IsomiRs classification; 3) SNPs in isomiRs and 4) Tissue specific isomiR expression. Furthermore, DeAnnIso has the module of isomiR target prediction and enrichment analysis to help users further investigate the functionality of isomiRs.

In order to test the practicability of our tool, we applied DeAnnIso to sRNA sequencing data from testis of Spo11-/- and wild type mice. In both samples, the most abundant isomiRs detected by DeAnnIso was 3’ isomiRs, which is similar with former studies in other samples (22). The module of target analysis and enrichment analysis helped us screen out iso-miR-30a-5p with A to G modification in seed region, specifically targeting Polb, which might be related to the reproductive phenotype of Spo11-/- mice. This result indicates that DeAnnIso cannot only precisely detect isomiRs from sRNA sequencing data, but also provide systematically annotation information and target analysis that can help users to speculate the function of isomiRs.

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