A clarity on the Illumina TruSeq Small RNA prep kit manual

In the TruSeq® Small RNALibrary Prep Guide, below the Figure 1, there is a sentence: "The RNA 3' adapter is modified to target microRNAs and other small RNAs that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes." It's right, but could be very misleading if you are not clear of the diverse picture of transcriptome (scroll down for more detail). I want to emphasize that the 3' hydroxyl group (and the 5'-phosphate group) is NOT specific to microRNAs or any small RNAs. And it doesn't necessarily result from enzymatic cleavage by Dicer. Sonic fragmentation can also break the full length mRNA (with 5'-cap and 3'-polyA) into truncated RNA pieces with 5'-phosphate and 3' hydroxyl free ends. I just called Illumina to confirm that the 3' and 5' ligation steps don't guarantee the selection of miRNAs (but rather any RNAs with 5'-phosphate and 3' hydroxyl ends, if more accurately). The last step of gel purification is the key to select (or enrich, if more accurately) miRNAs.

OK. Here is what I learned from my colleagues about the different RNA species in the trancriptome:

There are 4 species in the transcriptome, where the later 3 are intermediates of transcription (or half product of degradation).

• me₇G_ppp-------------------------3' (1) 
•                 p------------- 3' (2) 
•                 OH-------------3' (3) 
•        ppp---------------------3' (4) 

Only group(2) will ligate to 5’adaptor. The 3' end can also have different format, at least two:

• 5' ----------------- AAAAAA (1) 
• 5' ---------- OH (2) 

Also note there are two enzymes used to repair the 5' ends: CIP and TAP. CIP (Calf Intestinal alkaline phosphatase) can remove the 5’ phosphate group of DNA strand. The TAP (Tobacco acid pyrophosphatase) is to remove the 5' cap structure (or 5'-5' triphosphate linkage) and leave a mono-phosphate at the 5' end. So, applying first CIP and then TAP will convert the above (2) and (4) to (3), then convert (1) to (2). That's one way to do capture the 5' cap structure, same purpose as CAGE (but CAGE use the type IIs restriction enzyme MmeI and type III restriction enzyme EcoP15I)