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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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2answers
362 views

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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752 views

Why are most transcription factors enhancing the expression rather than repressing?

One can classify the effects of Transcription Factors (TF) on gene expression into two types: it either enhance or repress the gene expression. I have always been told that most of transcription ...
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Gene silencing: relative or absolute number of methylated CpG sites?

CpG content varies a lot across the human genome. What does determine a promoter to be silenced through DNA methylation: the fraction of CpG sites that are methylated or the total number of methylated ...
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What triggers DNA to produce proteins?

What is the trigger for DNA to produce proteins or RNA? I have found enough material to study the inner workings of the cell and DNA; but, I can't find an explanation of the mechanics the cell uses ...
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RNA polymerase question

In this question we are examining a bacterial RNA polymerase that elongates at 20 codons per second. Question 1: How long will this RNA polymerase take to transcribe the Lac Z gene at 3510 base pairs? ...
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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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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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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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1answer
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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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1answer
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ATP required for cell processes [closed]

I haven't been able to find anything that tells me how much ATP is needed for DNA replication, transcription, and translation in humans, just papers that mention ATP used in those processes. I need ...
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660 views

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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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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Why don't housekeeping genes have TATA Box regions in their promoter sequences?

Housekeeping genes are genes that are continuously transcribed. Like all other genes they have promoter sequences, but they don't have TATA box sequences that are used to specify from where ...
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361 views

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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1answer
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How can I re-format my DNA motifs' position weight matrices?

I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites). The motifs belong to several species, and I wanted to cluster these ...
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1answer
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How would one determine whether a chemical will upregulate a certain class of proteins?

I'm trying to determine whether certain organic chemicals will upregulate classes of proteins that possess deacylase activity.  How would I go about this experiment? I'm assuming I would use some ...
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Remove RNAse from pipettes?

Our lab uses old Gilson Pipetman pipettes. I've been using some for making mRNA by in vitro transcription and started running into RNAse issues. I'm trying to clean everything up, including the ...
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1answer
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Process of Transcription

During the process of Conversion to Ribonucleoside Monophosphates the various ribonucleoside triphosphates break off their high energy bonds after linkage to the DNA.But the first ribonucleotide ...
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Transcription factor binding site located in intron

I have noticed that some TF binding sites are located in the introns of the genes. I am puzzled about whether the TF only binds to DNA in the initiation stage of transcription and will detach during ...
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1answer
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Why is there no U3 snRNP in the spliceosome complex of transcription initiation?

snRNP U1,U2,U4,U5,U6 are present in the spliceosome but there is no mention of U3.
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Is RNA polymerase affected by proteins bound to the coding sequence of a gene?

I am designing a synthetic gene construct to express genes in E. coli driven by either Ptet or PLacO. The construct would look like: -Ptet-(Gene1)-PLacO-(Gene2)- I want to express each gene using ...
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1answer
213 views

mRNA with Pseudouridine and 5-methylcytidine?

I am making mRNA by in vitro transcription for transfection purposes. There is a lot of literature about how protein expression is increased and innate immune activation is decreased by substituting ...
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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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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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Relationship of the DNA of a eukaryotic gene to the 5'-UTR of its mRNA

In eukaryote pre-mRNA I am having a little trouble grasping exactly what the 5 prime untranslated region is defined as. It seems that it could be defined as the difference in pre-mRNA between the ...
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2answers
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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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Is “TATA signal” synonymous with “TATA box”?

In the text I'm translating I have a diagram of an expression vector. It has a lot of marks, and one says "TATA signal". I googled and found the expression "TATA box". Are these expressions fully ...
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Are enhancers and silencers considered as epigenetic modifications?

Are enhancers and silencers considered as epigenetic modifications? I am confused as it seems like enhancers and silencers are sequences on the DNA and how they work is through binding with proteins, ...
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TFBS predictions for yeast and pombe?

Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (S. cerevisiae) and S. pombe genomes? Even if these are only de novo predictions, I would like ...
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1answer
560 views

What is the transcriptome in layman's term?

I am new to the bioinformatics field and am trying to understand a research paper that includes some terminology without definitions. The term transcriptome in particular is banded around in the ...
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8k views

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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2answers
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How much tissue is required to do RNA-seq analysis on a single organism?

How much tissue would be required to do RNA-seq analysis on a single organism? More specifically, if a person wanted an RNA-seq analysis of expression for a single organ, how much tissue would they ...
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2answers
615 views

How does rho-dependent termination occur?

Rho-dependent termination is not fully understood but there’s a brief description in almost every concerned book about it. In Snustard and Instant notes-Molecular Biology it is written that, the rho ...
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identifying which SNPs sit in TFBS (Yeast)

i have a set of ~11k SNPs for Saccharomyces cerevisiae, baker's yeast and i would like to identify which ones of these sit in transcription factor binding sites and if they do information on the ...
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1answer
86 views

Transcription rate expressed in microarray per hour

This article gives measurement of transcription rate and the unit they're using is microarray per hour. For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page ...
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1answer
352 views

Complementarity of cDNA

Strictly speaking, what is the definition of cDNA? This confuses me, since usually it is said to refer to DNA that is complementary to mRNA. Is this correct? Is it restricted to mature mRNA? I ...
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1answer
60 views

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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313 views

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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1answer
86 views

Finding Regulatory Elements: How Have People Been Doing This?

First up, I am NOT asking about how to search for and match regulatory elements using a database. I'm asking about how people found what to search for and match in a genome, how they built those ...
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1answer
193 views

Are both (partial) copies of DNA transcribed in S and G2 phases of cell cycle?

For a little less than half the cell cycle, a significant number of genes are represented twice (just before dividing). Does the cell differentiate between these DNA in any way or are transcription ...
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1answer
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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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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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Sense of rotation of DNA motors [closed]

DNA motor will rotate during transcription instead of reciprocal. What others will rotate? Does it rotate in a fixed sense? Why do they rotate?
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Multiple transcripts encoding for one protein

Trying to get a better understanding of the process of DNA to proteins. So when we have a gene, it is read from the 5' to 3' end, only translating the exons to mRNAs. A single gene can have multiple ...
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Link between macro lncRNA and DNA looping

I was wondering if anybody knows some publication about macro lncRNA (very long unspliced RNAs) or more generally a transcribed RNA that may lead to cis-DNA looping of genomic regions overlapped by ...
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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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Making sense out of the visual representation of transcription

Most people are familiar with the following diagram. Some genomic DNA with a promoter region, exons and introns. This is transcribed into RNA that is then translated into a polypeptide. When we look ...
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Are all prokaryotic promotor regions the same, or do they differ depending on the product of the transcript?

Are all prokaryotic promotor regions the same or do they differ depending on the protein encoded by the mRNA being transcribed? What I am thinking is that if activator proteins are a method of ...
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Is sigma factor a transcription factor?

After I googled 'sigma TF' I stumbled upon two papers(only). From a paper: Sigma factors (sigmas) are bacterial transcription factors that bind core RNA polymerase (RNAP) and direct transcription ...
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Relationship between DNA strands and mRNA

Does the sense strand or antisense strand of DNA code for the polypeptide product? I'm confused because I know the antisense strand is the template for mRNA but it has anti codons so I do not know how ...