transcripts, transfrags, TARs, TUFs, ...

[doublehelix82]

Hello,
I am having trouble with understanding these (in the title). Let me try to explain my understanding and confusion and I would greatly appreciate it if anybody could comment on that.

transcript: An mRNA copy of a gene. This is the whole processed mRNA copy of the gene at hand.
transfrags (Transcribed fragment): A fragment that is found to be transcribed. (How?)
TAR (Transcriptionally active region): In the literature, I have seen TARs in the context of RNA-seq experiments, i.e., TAR is a region which is expressed according to an RNA-seq experiment.
TUF (Transcript of unknown function): A transcript in the cell whose function could not be determined. I am pretty confused about how these are discovered.

If these are correct, ESTs are, I think, transfrags (is that right?). But I do not understand the difference between TARs and TUFs. I think TARs are regions (without exact boundaries) that show transcriptional activity, but TUFs are actual mRNA sequences which are found in the cell (whose function could not be understood.) Most of the papers use the terms assuming that you already know what they are talking about. I would greatly appreciate it if you could elaborate on those or point me to some basic resources. Thanks!

DH.

[steven]

Hi,
As you pointed out, there is no clear standard for all this nomenclature, but here is my point of view:

A transcript is an RNA molecule. It can be mRNA, but also tRNA, miRNA, piRNA, PASR, lncRNA, tiRNA, etc. I would say TUF is used when the function of the transcript is unknown (usually non coding).

Transfrags is a term that was frequently used in the microarray world (i know it from tiling arrays). It is a genomic area identified by a microarray experiment where cellular RNA material is dumped on a chip. The signal indicates a genomic region with transcriptional activity, but you do not know the precise transcript structure. Different transfrags can belong to the same transcript (i.e. from different exons) but there is no connectivity information. Also, one transfrag can be generated by two overlapping exons from different isoforms -the signal is projected at the genomic level. Anyway.
I would say that TAR is the same, but was used in the context of RNA-seq. Again, this term describes a genomic region, not an RNA molecule. It may be a generic term.

ESTs are (not so) short sequences produced by "old-generation" transcript sequencing. They are supposed to indicate parts of mRNA.

Therefore, if you find ESTs, transfrags and RNA-seq reads over a genomic region, it is probably a TAR!

[bagdevi]

Thanks for the description of each term.