RNA interference
RNAinterference (RNAi) is an evolutionary conserved, gene silencing mechanism mediated through small non-coding RNA. It plays a significant role in the development of organism and also maintains the integrity of the genome. The RNAi pathway is complex that is triggered by double stranded RNA (dsRNA). The enzyme Dicer process the dsRNA to generate 20-25 bp fragments and one of the two strand of the fragment bind to the RISC (RNA-induced silencing complex) that subsequently bind to the mRNA in sequence specific manner to degrade the mRNA. The short 20-25 bp fragments are known as small interfering RNA (siRNA) when they are produced from dsRNA and microRNA (miRNA) when they are produced endogenously as hairpin loop structure.
RNAi has become a valuable research tool to knock down a specific gene to study the function of a gene. In addition to research applications it is also emerging as a novel therapeutic intervention to suppress disease causing genes.
To use this natural mechanism for human benefit it is crucial to understand the basic mechanism of RNAi and its associated components.
Information about resources, which can be utilized to make RNAi technology more effective are given below:
Database of miRNA
These are some database, which provide information about miRNA gene, and its expression profile in different tissues.
| Database |
Description |
| miRBase |
A database of miRNA, provide names for novel miRNA genes prior to
publication. Also predicted miRNA targets in animals by using the tools,
MIRNANDA and TARGETSCAN. |
| miRNAMap |
A database of experimental verified microRNAs and its target genes in human, mouse, rat, and other
metazoan genomes. Also provides expression profile of miRNA in tissue specific
and differential expression in cancer/normal cell. |
| ASRP |
Repository for sequences of small RNAs (microRNAs and siRNA) cloned from various Arabidopsis thaliana genotypes and tissues. |
| miRNApath | A database of miRNAs, target genes and metabolic pathways. |
| miRGen |
A database of cluster of miRNA, genomics and their targets. |
| miRex | Serves an online repository for microRNA gene expression data and also analyses the microRNA expression data. |
| ARGONAUTE2 | A database on mammalian microRNAs and their function in gene and pathway regulation. |
Database of miRNA target
| Databases | Description |
|---|
|
TarBase | A database of experimentally supported animal microRNA targets. |
siRNA design
These are some tools, which can be helpful to design siRNA for a specific gene.
| Academic |
Description |
| siRNA at Whitehead | It helps in selecting siRNAs to knock down the gene of interes. |
| siRNA selector | program evaluates siRNA FUNCTIONALITY and SPECIFICITY |
| siDirect | highly effective, target specific siRNA online design site |
| Commercial |
Description |
| Ambion | siRNA Target Finder |
| Dharmacon siDESIGN | an advanced, user-friendly siRNA design tool, which significantly improves the likelihood of identifying functional siRNA. |
| QIAGEN | Products and services for life science research, molecular diagnostics, genomics, and gene therapy |
miRNA predition tool
These are some tools, which can be used to predict the potential miRNA precursors.
| Tools |
Description |
i|
TripletSVM | Predict whether the query hairpin structure is a real miRNA precursor or not. |
| miR-abela |
miRNA gene prediction. |
| MIRScan |
Predict miRNA precursors. |
| MiRAlign | Predict hairpin containing mature miRNA in animals and plants. |
| RNAmicro |
Predict microRNA precursors in comparative genomics data. |
| findMIRNA |
Predicting miRNA precursor candidates in A. thaliana. |
| BayesmiRNAfind |
miRNA target prediction tools
| Tools |
Description |
|
miRacle |
miRNA target prediction. |
|
miRanda |
Predict miRNA targets and also provides the expression profile of miRNA in various tissues. |
|
RNAhybrid |
Hybridize a long and a short RNA. |
|
TragetScan |
Predict miRNA (miRNA family) target in vertebrates, worm, and fly. |
|
MicroInspector |
Detect miRNA binding sites in an mRNA sequence. |
|
Pic Tar |
Predict miRNA target in vertebrates , flies, and nematodes. |
|
miRNA-Target predict |
Predict Drosophila miRNA targets. |
|
DIANA Micro Test |
miRNA target prediction. |
|
miRU |
Predict plant miRNA target. |
|
TargetBoost |
Predict miRNA target in C.elegans. |
|
RNA22 |
A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes.
|
