MiRNA

What do you understand by miRNA(microRNA)? miRNA are the non-coding single-stranded RNA of ~22ntd(19-24ntd)which are derived from the endogenously produced pre-miRNA (precursor) of 75-80ntd having a hairpin (stem-loop) structure.

Which are the different types of non-coding small RNAs? The various small non-coding RNAs are listed below:

• siRNA (small interfering RNA): These are 21-28ntd RNAs produced from dsRNA. Endogenous siRNA are further classified into 3 classes:

1. 1. tasi RNA (trans-acting siRNA)- They act on mRNAs in trans to bring about mRNA cleavage.
   2. rasiRNA (repeat associated siRNA)- These siRNA match repetitive elements in sense or antisense orientation.
   3. scnRNA (small-scan RNA)- They scan DNA for genome rearrangement.

• tncRNA (tiny non-coding RNA)

• smRNA (small modulatory RNA)

What is the criteria that must be met before a small RNA can be classified as a miRNA? The following criteria:

1. Its expression should be confirmed by the hybridisation to a size fractionated RNA sample say by northern blotting, primer extension RPA assay or by microarray.
2. The small RNA sequence should be present in one arm of the hairpin precursor.
3. The sequence should be conserved across the species.
4. The precursor form should accumulate in the absence of dicer enzyme.

None of the above criteria is sufficient on its own for a small RNA to be classified as a miRNA. Usually it's 2 or more of the above points that need to be satisfied.

What is the principle behind miRNA nomenclature? miRNA nomenclature is explained in the following points:

• miRNAs are named as'miR-x'where x stands for any numeric value. This numeric value is assigned in a discovery dependent sequential manner. The conserved miRNAs across different species are assigned the same number.
• In order to distinguish miRNAs from one species to another, 'miR-X' nomenclature is preceded with a single alphabet initital from genus and two alphabet initial from species. For instance: a human miRNA would be named hsa-miR-29 (here hsa comes from homo sapiens).
• To distinguish 2 miRNAs which differ by a single base in the mature sequence, alphabets can be use like hsa-miR-29a, hsa-miR-29b & so on.
• There can also be instances where 2 miRNA have the same mature sequence but are derived from precursor sequence; in such a case, an additional numeric character is included in the name to mark this demarcation like hsa-miR-29a-1, hsa-miR-29a-2 & so on.

How do miRNA differ from siRNA? miRNA and siRNA are 2 classes of non-coding RNA that have revolutionized the way gene regulation was thought to be. miRNA alone have been shown to be regulation almost one-third of the human genes. There are a lot of similarities between these 2 classes of RNA like

• They are both derived from a precursor form
• They are both processed by Dicer & Drosha (RNAseIII enzymes)
• Both leads to the downregulation of the genes that they target

Despite these similarities, there are a lot of differences which make it imperative that these RNA classes be split into 2 different classes & not grouped into one. These differences are listed in the following points:

• Basis of origin: miRNA are derived from a typical hairpin or stemloop precursor whereas siRNA are derived from double stranded RNA fragments. Also, a number of siRNA can be generated from the ds precursor RNA whereas only a single miRNA result from the stemloop precursor. miRNAs originate from intergenic regions while no such information is known for siRNA.

• The genes that they target: In general, siRNA target the same transcript from which they have been derived but miRNAs can target any gene irrespective of the transcript from which they are derived.

• Conservation: miRNAs are more or less conserved across species. This conservation is more evident in case of mature miRNA and it decreases at the level of pre-miRNA. On the contrary, no such conservation is shown to occur in case of siRNA.

Do miRNAs always downregulate the gene expression? Till now only one report is there which shows the upregulation because of miRNA[http://pnas.org/cgi/content/full/105/5/1608. In this, miRNA 373 is shown increase the expession of E-cadherin & CSDC2.

What are the various online tools & sites related to miRNA? Such sites are innumerable. Which ones are worth trying is a million dollar question. Herein, I would be giving the list n try to make it as exhaustible as possible but it will take time. The list is as follows:

• miRbase: This gives the complete list of miRNAs[1]
• RegRNA: This software is designed to scan input RNA sequences for regulatory motifs and miRNA target sites. However, by simply plugging in promoter sequence, the software can also identify putative sites complementary to miRNAs in DNA strands.[2]