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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Strong activation of MAPK signaling pathway

I am reading a paper named "Mathematical models of protein kinase signal transduction". In that paper, I encountered a condition called "strongly activated pathways". In that ...
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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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What determines which strand of DNA is transcribed by RNA polymerase?

DNA has two strands. How does the machinery of RNA transcription determine which one to transcribe?
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Speed of cell signal to protein production

How long does a cell take to make a protein from the point of receiving the signal to produce the protein? Does the cell have stores of the protein ready to release or is the protein created in real-...
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Can the complement of the start sequence occur in a gene?

Put another way, I suppose I'm wondering if the start sequence of a gene always actually starts a gene. If so, I assume it means that the complement of the start sequence in one strand would always ...
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What is the enzyme production rate of a single E. Coli bacterium?

Suppose an E.Coli bacterium intakes a plasmid which encodes for an enzyme, if the promoter strength is known, is is possible to predict the rate at which the enzyme is produced? Is there an equation ...
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Anticodon Translation Question

Could somebody please explain the answer for (c). I assumed that since transcription started at the bolded/underlined T/A base pair, the second codon would be UCU? Thanks!
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Correct description of ALDH7A1 and other genes

A quote from a review paper: ALDH7A1 gene (discovered in 2006), which is located at chromosome 5q32.2, contains a transcript of 4964 base pairs and 539 amino acids divided among 18 exons [1,10,16,17]....
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If RNA transcription is 5' end to 3' end, what is the directionality of the promoter for?

I am confused. If RNA transcription always grows from the 5' end to the 3' end, what does the direction of the promoter do for the mRNA transcribed? From what i understand the RNA polymerase always ...
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Does a gene need to be transcribed for every single protein made? [duplicate]

There is one set of DNA in the nucleus and one instance of any particular gene. That gene is transcribed into mRNA and then it is translated by a ribosome. A cell has millions of ribosomes. So it ...
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What percentage of our DNA is never transcribable? What percent is never actually transcribed into RNA unless researchers force it to in a lab?

From what I gather, the vast majority (but not all) of the DNA in our genomes will transcribe and create an RNA, if only under certain conditions in a lab (forcibly unwound, among other steps). How ...
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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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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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Genes on the reverse strand of DNA indicated by (-) in GFF

In the transcription process, RNA is produced from the template strand of DNA (that is 3'-5') so the RNA molecule produced has the direction 5'-3'. When working with genes in bioinformatics, there are ...
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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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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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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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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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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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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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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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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 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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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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Are single-celled organisms capable of learning?

I've read that the amoeba is capable of learning. Since these protists have no nervous system, it's safe to assume that even highly simplified learning mechanisms of the Aplysia are miles off in the ...
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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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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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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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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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Why does the T7 RNA Polymerase require a reducing environment ie. DTT

Every bloody protocol suggests adding in DTT when doing in vitro RNA transcription. Why? The rationale seems to be that the cytoplasm traditionally has a reducing environment but as the only protein ...
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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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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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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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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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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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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 ...