What do we call a transcript?

Question

[Riku]

Dear all,

I looked up the exact meaning of the word transcript, but I couldn't understnad it. I now understand the words in Central Dogma as shown in the figure below. Which of these words do you call a transcript? Also, which substruct sequences can be obtained by RNAseq? Please point out to me if my understanding is wrong in the first place.

Thank you for reading.

[lieven.sterck]

One apparent 'problem' with the diagram you post here is that the usage of 'gene' in this is not correct. It should read 'exon' not 'gene' (for simplicity I neglect the very few exceptions on this 'rule')

2 genes can not be joined/spliced together to form an isoform. This on the other hand is exactly how exon are used: they are stitched together to form a gene (isoform 1 or isoform 2 ).

but as clearly stated here already by other people this is basic (molecular) biology and most of it can be figured out by doing some literature study (or searching around) .

On the other hand I do agree with you that a clear definition or at least usage of the correct term is key when talking to peers, just to get everyone to understand. (if you would do the explanation of the diagram to me in a conversation I would not know what you were talking about ;) since the usage of gene does not make sense here)

[Mensur Dlakic]

I think you have been on this site long enough to know that this is not a bioinformatics question. It is also a question that can be answered with minimal effort using search engines.

[Riku]

Thank you for your suggestions and advice.

I also understand that this question is basical. However, these words:for example, transcript, unigene, isoform etc, are unclearly understood, so I thought they should be clearly and graphically understood for bioinformatics analysis.

If this is an inappropriate question, I will remove this question.

[seidel]

As Mensur Dlakic says, you should just do some reading, use google and pubmed, survey some literature, distill some ideas, and if you still have specific questions try asking on biology stack exchange. The most basic answer, is that a "transcript" is an RNA product of RNA polymerase in association with a DNA template. Beyond that, there are myriad ways to qualify various kinds of transcripts. Without a specific purpose or question in mind, there are too many forms for a simple diagram to represent, bioinformatically related or not.

[Riku]

Thank you for kind explaining.

You're right, it can be difficult to simply understand graphically, considering the various processes involved.

I apologize for asking the question in the wrong place and for my lack of study.

Answer 1

[liorglic]

When people say transcript they usually mean a mature mRNA molecule (or sequence in the context of bioinformatics). Although this is not always correct, in many cases the words transcript, mRNA, cDNA and isoform mean the same thing, that is the mRNA sequence of a specific splice variant of a given gene.

[Riku]

Thank you very much all for your answers.

I can understand these words weren't clearly defined, it is difficult to define them because their process is complex. It is good for me to understand that these words are taken in a minimal mean in Bioinformatics.

It seems that I need to have the knowledge to understand the correct meaning of these words whenever I encounter them. I will study more.

Answer 2

[Carlo Yague]

By definition, a transcript is the end product of the transcription process. So it can be most kind of RNA really, not just mRNA, but also tRNA, rRNA, ncRNA, etc...

So, all RNA are transcripts ?

No, because some RNA are not synthetized by DNA-dependent RNA polymerase, and are therefore not (edit: see comments) transcribed. For instance, RNA genome replicated by RNA-dependent RNA polymerases are not, by definition, transcripts. siRNA amplified by RDRC are not transcripts either.

Also, cDNA, obviously, are not transcripts (and I strongly disagree with liorglic's answer on this point). From a biological perspective, they are even the opposite of transcripts since they are the product of reverse-transcription.

What about the distinction between pre-mRNA and mRNA ?

In my opinion, both pre-mRNA and mRNA are considered as "transcripts". To make a distinction, we can use the term 'primary transcripts', that denotes pre-mRNA (but also pre-tRNA, pre-tRNA, pre-rRNA, etc...) but not mature mRNA.

[benformatics]

Why would the production of mRNA from RNA-dependent RNA polymerase not be considered transcription... I think that is just an over simplification where "transcription" usually means "DNA transcription". Probably a relic from the central dogma which - as we can all agree - is not a hard and fast set of rules.

I would be hard-pressed to agree that mRNA production from a virus with an RNA-genome is not considered transcription.

https://academic.oup.com/nar/article/48/16/9285/5891572

[Carlo Yague]

This is a valid point. To clarify my (over-simplified) view can be summarized as:

• RNA to DNA: transcription
• DNA to RNA: reverse-transcription
• DNA to DNA: replication
• RNA to RNA: replication

And it doesn't hold to your exemple because the viral genome (RNA) is both transcribed (to mRNA) and replicated (to RNA). So I guess I will have to update my definition. Any suggestion ?

[benformatics]

Also some siRNA can be produced from endogenously transcribed mRNA hairpins... those siRNA would still inherent their parental state of being transcripts by your own definition.

[Carlo Yague]

They are, that is why I wrote "many siRNA" not "all siRNA".