Team:Hong Kong HKUST/riboregulator/regulatory RNAs catalog

Some guidelines for categorizing RNA devices under this scheme:

1. Confirm it is non-coding RNA devices
2. Give category for “level of regulation”
3. List the natures of RNA devices currently under exam (the RNA devices)
4. Compare with the properties of different types of RNA devices with the RNA devices
5. Assign categories about “nature of part” to the RNA devices currently under exam only if the RNA device fulfils all the requirements listed for any type of RNA devices
1. Assign “//RNA/ncRNA/others” if no matches
2. Assign “//RNA/ncRNA/target_sequence” if it is target sequence of other ncRNA devices; Be sure also assign corresponding categories of ncRNA devices. For example, target sequence of sgRNA should be assigned for :
• //RNA/ncRNA/target_sequence
• //RNA/ncRNA/sgRNA
6. Assign categories of “function of part”. Note that it may not be limited to the two function listed above. Check the existing categories to assign appropriate categories.

siRNA VS miRNA

siRNA and miRNA are two very similar RNA devices. Both of them will be processed by Dicer and both of them will from a RISC complex to carry out their function. However there are substantial differences between the two.

First, siRNA are 20 to 25 nucleotides long; while miRNAs are 19-25 nucleotides long.

Second, siRNA usually fully complement with the target mRNA; while miRNA can be partially complement with target mRNA.As a result, siRNA usually target few mRNA while miRNA can target 250-500 different mRNAs. Last but not least, siRNAs usually stem from exogenous DNA; while miRNA usually stem from endogenous DNA.

siRNA / miRNA VS antisense RNA

Antisense RNAs refers to single stranded RNAs that are complementary to mRNA. Although no specific length requirement is imposed on antisense RNA, antisense RNA usually refers to RNA with longer length by historical reason. Whereas siRNA refers to short double stranded RNAs that are 20-25 nt long; miRNA usually refers to single stranded RNA that are 19-25 nt long. Antisense RNA form duplex with mRNA, which will blocks the access of ribosome to mRNA, also the duplex may be degraded by ribonuclease exist in the cell. Either functions of siRNA and miRNA depends on RISC.

Structural scaffold VS Stability control elements

Structural scaffold refers to the folding of RNA, which has the ability to recruit various molecules, mostly proteins. Scaffold may stabilize RNA devices and therefore a scaffold can also be stability control elements. While stability control elements refers to any RNA devices that contribute to the stability of RNA devices. It is not limited to RNA scaffold. One example is poly A tail elements for mRNA, it contributes to the stability of mRNA, however it is not a loop.

Case one: Spinach Aptamer

Case two: RNA_OUT