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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Can the coding strand for an RNA act as the template for another?

Can the same strand of DNA act as a sense strand and an antisense strand at two different occasions of transcription and result in two different proteins?
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Is there a resource/paper containing information about which co-activators are often associated with a given transcription factor?

Given a list of human transcription factors, I would be interested in which co-activators they are often associated with. I imagine that one could combine co-expression, pull-down, and other kinds of ...
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How I can find the list of transcription factor proteins involved in transcription of a specific gene?

I want to get the list of transcription factor proteins involved in the transcription of the human SIRT1 gene. How can I access that?
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Human gene number distribution on different strands of the chromosomes

I cannot find an article that describes the gene distribution based on their appearances on different strands and if I find one, like this from 2007, there are some aspects which are confusing, for ...
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Why isn’t prokaryotic mRNA modified post-transcriptionally like eukaryotic mRNA?

Eukaryotic mRNA is subject to addition of a methyl-guanosine cap at the 5’ end, addition of 100-200 adenosines to the 3’ end, and splicing. Why don’t these occur in prokaryotes? Is it because there is ...
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If the AraC protein was a gene repressor when it binds arabinose, would there be high or low transcription levels when arabinose is present? [closed]

If the AraC protein were to function as a gene repressor when it binds arabinose, would there be high or low transcription levels when arabinose is present?
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How to memorize Transcription and Translation? [closed]

I often get confused between transcription and translation. Is there any way to memorize them easily like a mnemonic??
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Do transcription factors need to undergo extensive post-translational modification?

Some proteins need additional processing to become fully functional, for example NiFe-hydrogenases need to be cleaved by endopeptidases for some of their subunits to be active. Is it known whether ...
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What is the "anatomy" of transcriptional regulation in Archaea?

I want to know what are the DNA elements that are recognized by transcription factors in Archaea and so what is the "anatomy" of transcriptional regulation in this case. I found in this ...
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Does ribonuclease processing of pre-crRNAs happen co-transcriptionally?

I understand CRISPR-mediated bacterial immunity to occur in the following simplified steps: A CRISPR array is transcribed from promoters in the leader sequence to yield a precursor CRISPR RNA (pre-...
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How is it determined which parts of an mRNA precursor are to be spliced?

According to my textbook, the same pre-mRNA sequence can get spliced in multiple different ways. But how is this regulated by the cell? How are the introns and exons to be spliced determined?
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Can CNVs have a phenotypic effect unrelated to the direct modification of transcriptional units?

I'd like to know how (or if) copy number variations can have a phenotypic effect unrelated to the direct disruption/movement/duplication of sequences for coding regions, promoters, enhancers etc. I ...
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Why doesn't RNA polymerase just rotate?

I read A little help understanding DNA supercoiling , Understanding DNA supercoiling , and Why does underwinding create topological strain of DNA? , but there's still something I don't get. ...
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Is alternative splicing possible in the same cell?

I know alternative splicing is possible in different cell types of an organism, or within the same cell at different developmental stages. There are several examples like this. But are there any ...
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Does transcription terminate at the end of antibiotic resistance genes on the Duet expression plasmids?

I am working with the pETDuet and pRSFDuet plasmids to express RNAs under control of the T7 promoter. On these plasmids the antibiotic resistance genes (Amp for pET, and Kan for pRSF) are downstream ...
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Can the metatranscriptomics replace the approach of functional metatranscriptomics/functional metagenomics?

While metatranscriptomics reveals information about the expression of genes and their functions too, Functional metatranscriptomics (https://www.nature.com/articles/ismej201167) allows the ...
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Does the two-state gene expression model apply to constitutive genes?

Wikipedia defines constitutive genes as a gene that is transcribed continually as opposed to a facultative gene, which is only transcribed when needed. I don't have a strong theoretical background ...
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Explanation of "differential transcript usage" (DTU)

This paper describes differential transcript usage as Differential transcript usage (DTU) is a special case of alternative splicing in which a gene’s relative transcript abundance (RTA) profile, the ...
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Do RNA modification proteins bind to specific repeats on the RNA polymerase II CTD?

The C-terminal domain (CTD) of human RNA polymerase II has 52 repeats of a similar heptapeptide sequence. Will the RNA modification proteins only bind to some repeats at specific locations on this (e....
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Will a nucleic acid sequence deduced from a protein sequence be expressed from a plasmid?

I have a fasta file containing the amino acid sequence of glycogenin-1: https://www.rcsb.org/fasta/entry/6EQJ I want to create a plasmid that produces glycogenin-1. Is it possible to use the ...
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RNA polymerase Sigma subunit: transcription factor, coenzyme, or what?

Studying prokaryotic transcription, it seems that the α2ββ′ω core enzyme + the sigma (σ) subunit comprise the ‘holoenzyme’ required for prokaryotic transcription. In traditional enzyme nomenclature, ...
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What is the role of pyrophosphatase in RNA polymerization?

In Molecular Cell Biology (8th edition) there's a fragment in chapter 5.2 that says: The energetics of the polymerization reaction strongly favor the addition of ribonucleotides to the growing RNA ...
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Origins of transcription factors and RNA Polymerase

I was learning about transcription factors and RNA polymerase from Khan Academy to supplement Dr. Robert Sapolsky's lectures on Human Behavioral Biology. As I understand: RNA Polymerase transcribes ...
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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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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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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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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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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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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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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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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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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 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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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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