Questions tagged [transcription]

The process that produces a complementary strand of RNA from a section of DNA or (rarely) other RNA.

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Is it possible to distinguish between coding and template strands from the sequence?

Let’s say you have the following DNA sequence fragment: 5’-ACCAGTACTTCGT-3’ 3’-TGGTCATGAAGCA-5’ Is there any way to determine which strand is the template ...
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Why is thymine not incorporated into mRNA?

I am aware that in transcription uracil bonds to adenine and not thymine. But what is it that actually prevents thymine from bonding to adenine in transcription, that is not present in replication?
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Does Remdesivir interfere with human transcription?

Remdesivir is metabolized into a nucleotide analogue. It is incorporated in the viral genomes causing either termination of transcription or a dysfunctional genome. Thus, the new viral particles ...
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why does translation occur more frequently than transcription?

In our textbook it says that translation occurs more in a cell than transcription but I couldn't find anything that explains why it happens
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Is there any current knowledge of how DNA polymerase is “motivated” to perform error corrections during transcription?

I was trying to understand the process of how polymerase performs error corrections on DNA. Every paper on this topic mentions what happens during the process, but there's no mention of how it happens....
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Does RNA polymerase move around DNA or does DNA rotate beneath the polymerase?

I'm thinking of the human genome specifically, but more general answers are welcome. As RNA polymerase moves along the DNA helix it follows a single strand. The two DNA strands are unwound locally ...
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pacbio adapters

It's my fist time using pacbio data. We're using long reads to assembly a transcriptome of reference for a non-model organism. We've sequenced our data at an external sequencing core facility. They ...
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How to estimate mRNA counts from Relative Promoter Units (RPU) or RNAP per second (PoPS) in E. coli?

I need a rough estimate on how to translate RPU or Polymerases Per Second (PoPS) to mRNA count (or even better protein count) in E. coli. I understand that any number we come up with will be a very ...
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Why isn't there a standard unit of promoter strength?

Sometimes in synthetic biology, we need to know rates of transcription of one promoter in relation to others (particularly inducible vs constitutive) in order to perform tasks like balancing ...
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How do enhancers induce transcription?

DNA response elements are DNA sequences that are could be found upstream, downstream of genes that regulate gene expression at the transcriptional level. One type -Enhancers- bind specific ...
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Why majority of synthesized mRNAs are halted at Nuclear Pore Complex?

I was reading about mRNA export process. I came to know that only 36% of synthesized mRNA transport events at Nuclear Pore Complexes(NPC) of the nuclear membrane get successful in crossing to the ...
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From which end of mRNA does transcription start?

The book "Understanding bioinformatics", says that "RNA polymerase transcribes the anticoding strand in the direction from 3' to 5', so that the mRNA strand is produced from the 5' to the 3' end". ...
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How to find the amino acid in the DNA protein

3' A T A G T A C C G C A T G T A C G G G C G A G A C A T T C G A G C A T T C A T 5' This a Template DNA. How to find the number of amino acids amino acids ...
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How do cells relocate transmembrane proteins from one side of the cell to the other? Is it possible?

Is there a process by which cells can relocate proteins residing on the cell membrane in areas of low demand to that of a high demand location somewhere else in on the cell? What's that process called?...
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How do eukaryotes terminate transcription? (clarification on Campbell Biology)

I'm having trouble understanding how eukaryotes terminate transcription. Studying Campbell Biology (pg. 342, 10th ed.), I read: In eukaryotes, RNA polymerase II transcribes the polyadenylation ...
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How do DNA, enzymes, hormones etc. reach their proper cellular locations?

I was trying to understand DNA transcription from this chapter, and there seems to be no explanation on how exactly the proteins, enzymes and other molecules manage to find each other inside the cell. ...
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Why are there inverted repeats in response elements?

The following picture shows an inverted repeat sequence in a response element. Response element sequences for glucocorticoids, estrogen, and thyroid hormone show that they all contain inverse repeats. ...
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What makes/breaks the hydrogen bonds between DNA and RNA during transcription?

So I know that RNA polymerase catalyzes the phosphodiester bonds that hold the sugar backbones of a growing mRNA molecule together during transcription. However, I'm less sure about the hydrogen bonds ...
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Control of gene expression

Eukaryotes have many genes, so how does RNA polymerase recognize a gene needed to be transcripted?
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Are there any particular chemicals that initiate either DNA replication or Transcription ? [closed]

When does the nucleus of a cell "know" when to bind DNA nucleotides ( for Replication ) or RNA nucleotides ( for Transcription ). From what i read, they're both structurally different and free ...
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Why analyse transcriptome instead of proteome?

Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (...
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Does the complimentary base pairing of rRNA with itself play a role in its transcription?

I have read that the termination of the transcription of mRNA involves a termination sequence in the form of a stem loop. As the structure of ribosomal RNA involves extensive internal base pairing, I ...
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How does transcription end?

In rho-dependent termination in prokaryotes, how does RNA polymerase “know” that it has reached the end of a gene and that it has to stop so that the rho-factor can bind mRNA’s rut site? Is there a ...
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On which DNA strand is TATA box present?

My book (Snustard and Simmons) mentions that TATA box is present on the non-coding DNA strand but that was for the promoter of mouse thymidine kinase gene. I have tried to find out more information ...
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Functional Difference between the Distal Promoter and Enhancer Region

According to the Wikipedia article on eukaryotic promoter regions, the distal promoter is: Anything further upstream (but not an enhancer or other regulatory region whose influence is positional/...
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Sequence between PolyA signal and PolyA tail

Between the polyadenylation (PolyA) signal (AAUAAA in humans) and the start of the polyA tail, there is a short sequence of about 10~20 (G/U rich) bases, is there a special term for it? Image credit: ...
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RNA polymerase and DNA helicase

Is DNA helicase or RNA polymerase responsible for breaking the hydrogen bond between the 2 strands during transcription for eukaryotic cells? My textbook (WJEC Biology for AS level) says it is DNA ...
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The role of GC content in promoting or hindering transcription

This is quite a specific question, and I'm hoping someone might be able to assist in a literature hunt I've been engaged in for ages. I study some long bacterial operons, and have noticed that the GC%...
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What is meant by Gene Expression Level?

I am new to BioInformatics, I want to know what is gene expression level and how it is determined.. Anyone who can answer this silly question.
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How does cell detect if a RNA polymerase II is stalled during transcription and in turn deploy the proper transcription-coupled repair factors?

When a segment of the template strand of DNA is damaged due to factors such as UV radiation, a lesion is created that would effectively block the passage of RNA polymerase II during transcription. ...
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How do cells determine RNA types?

I was reading about the different types of RNA polymerases, and I am confused as to how a cell determines which type of RNA it is transcribing. According to this nature article: RNA pol I ...
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difference between transcriptional activator and general transcription factors?

What is the difference between transcriptional activator and general transcription factors? Are they same or different, and do the transcriptional activators first attract general transcription ...
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Why aren't 'exons' named 'introns'?

Why are introns called 'introns' when they are the actual ones who are getting spliced out from the pre-mRNA. Shouldn't exons be named introns as they are the ones that are 'in' and are not 'exiting'? ...
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Questions about RNA Polymerase

I'm confused about the terminology and directions described in processing DNA to proteins in this paragraph. RNA polymerase reads a DNA template in the 3’ to 5’ direction to synthesize RNA in the ...
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Terminology of the sequences of promoters in relation to DNA strands

I'm studying molecular biology and I'm trying to understand an experiment which shows the importance of promoters in the relative transcription level (RT). The image below comes from Rolf Knippers' ...
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How do DNA-binding proteins recognize the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?" He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-...
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Are microRNAs transcribed from the same DNA strand as their parent messenger RNAs?

I am new to micro RNAs. I have been trying to find the answer to the question if microRNAs are transcribed from the same DNA strand as the messenger RNAs encoded by the encompassing gene? From the ...
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How does alternative splicing work?

I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens... Thank you in ...
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DNA methylation in different positions

I'm trying to understand how does DNA methylation and histone methylation status of promoters differs given their position in a gene? Does position affect whether they are repressive or activating?
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How does RNA transcription determine which half of the DNA to use?

I feel that I might have a complete misunderstanding here. If DNA has two strands, how does the machinery of RNA transcription determine which one to transcribe?
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DNA methylation on the forward vs reverse strand?

I'm wondering if there are meant to be differences in DNA methylation between the forward and the reverse strand of the gene? I'm wondering because in primer design for bisulfite pyrosequencing one ...
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Why and how is DNA synthesis so much faster then RNA synthesis in bacteria?

DNA synthesis in E. coli is 20x faster than RNA synthesis at 1000nt/s vs 50nt/s. (Mirkin'05) I find that perplexing since DNA polymerization has better proofreading than the RNA variety, which ...
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response elements in transcription regulation

I'm studying eukaryotic gene regulation and I want to know whether there are some instances where transcription factors don't need to bind to response elements to initiate transcription. RNA ...
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What are the causes of abortive initiation?

I was reading more about DNA transcription, and it mentioned abortive initiation. The article gave no explanation as to why the phenomenon occurs. The only explanation I can think of is that it is ...
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When does histone synthesis occur in relation to DNA replication?

Do histones have to be synthesized before DNA is replicated to allow the DNA to coil around histones?
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What is the reason for occurence of introns in eukaryotic mRNA? [duplicate]

After transcription of the Template strand of DNA, in prokaryotes, the translation process begins immediately. But in eukaryotes the mRNA transcript has both non coding (introns) as well as coding (...
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Do all RNA polymerase in Eukaryotes share the same transcription factors?

I know that TFII proteins bind to cis elements in DNA and help initiate transcription for RNA polymerase II. But do RNA polymerase I and III also use these proteins when transcribing genes? Also, do ...
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What is the meaning of the word 'bin' in the context of RNA-Seq?

I have a question from a book about RNA-Seq. I would like to know the meaning of the word "bin" in the below cited paragraph: RseQC has several nice features not found in the other programs: (a) ...
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Is the transcription starting site located before or after the promoter?

It's maybe a stupid question, but I really want to know the answer. The definition of Promoter (From Wikipedia): In genetics, a promoter is a region of DNA that initiates transcription of a ...
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Are RNA transcripts always synthesised from the same DNA strand? [duplicate]

The DNA is read 3'->5' (and RNA synthesized 5'->3'). But due to the DNA strands having to be complementary, it seems to me that the origin can only appear on the correct side of the ORF on one of the ...