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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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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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23 votes
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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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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?
Benjamin Rogers-Newsome's user avatar
15 votes
2 answers
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Can methylation from DNA get copied to RNA during transcription?

Methylation on gene-body and 3'UTRs if copied to mRNA can potentially regulate post-transcription modifications or expression regulation. But I'm not sure if they are maintained after transcription or ...
Garima Kushwaha's user avatar
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4 answers
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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 ...
Dave Gerrard's user avatar
13 votes
1 answer
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How do CpG islands remain unmethylated?

In most of the genome CpG sites are pretty much always methylated, but CpG islands are instead often unmethylated. This has been linked to the fact that they often are associated to transcripted genes....
nico's user avatar
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12 votes
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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'? ...
Jewel Johnson's user avatar
12 votes
2 answers
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Modularity of transcription factors

I attended a seminar about neurogenesis that presented results for PAX6 as an important TF that contains 3 domains with very distinct patterns of downstream expression. The speaker ended up saying ...
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How does the stem-loop cause intrinsic transcription termination?

In this animation, towards the end (about three quarters) the process of transcription termination is shown. It states that the transcribed RNA forms a hairpin loop (or stem-loop), which halts the ...
arik-so's user avatar
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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 ...
SeanJ's user avatar
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11 votes
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determining genome-wide exogenous binding of pathogens to host genome?

I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice ...
yahoo301503's user avatar
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On which strand does the promoter sit?

My book keeps giving different indicators as to whether the promoters are on the coding or template strand. It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that ...
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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?
Laura kirkpatrick's user avatar
9 votes
2 answers
262 views

bi-directional transcription experiment

We suspect a bi-directional transcription event is happening at a locus in our organism where two genes are directly adjacent to each other. The annotation data is not well established. The intergenic ...
Damian Kao's user avatar
9 votes
2 answers
2k views

How do chromosome pairs get "paired up" for protein synthesis?

If my understanding is correct, during interphase a normal human cell will have 46 chromosomes scattered about in the cell nucleus. These chromosomes can be thought of as pairs: there are two copies ...
theQman's user avatar
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Number of transcription factor genes in the human genome

What is the number of the transcription factor genes present in the human genome? Does this value differ compared to Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, C. elegans and S. ...
Katz's user avatar
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How much does the distance between a transcription factor binding site and a promoter influence transcription?

Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
w128's user avatar
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2 answers
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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 ...
bobthejoe's user avatar
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Mutation That Loses Stop Codon

Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the ...
user4960003's user avatar
7 votes
1 answer
538 views

DNA & mRNA During Transcription

Just a simple, quick question: how are the mRNA and the template strand of the DNA structured during transcription? I've seen models and videos of them when they're both flat/straight (is that just ...
Alex P's user avatar
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Effect of histidine on the binding affinity of HisP

I was asked the following question by my teacher: A gene regulatory protein called HisP regulates the enzymes for histidine biosynthesis in the bacterium E. Coli. HisP is a protein whoes ...
Kirby's user avatar
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7 votes
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ChIP-seq vs ChIP-exo

I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites. As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this ...
Chris's user avatar
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Which factors besides the thermodynamic stability are important for the hairpin in intrinsic transcription termination?

Intrinsic termination (rho-independent) relies on a stable hairpin with a subsequent uridine repeat. The common explanation on how these sequences cause the termination of the transcription are based ...
Mad Scientist's user avatar
6 votes
3 answers
424 views

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. ...
Nav's user avatar
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6 votes
2 answers
812 views

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". ...
Noob's user avatar
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4 answers
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How many transcription factors are there?

In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to ...
hello_there_andy's user avatar
6 votes
1 answer
192 views

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. ...
eric_kernfeld's user avatar
6 votes
2 answers
7k views

Why is the DNA codon table "equal" to the RNA codon table

Before anything else please pay attention of the double quotes on the "equal" in the title - I know they are not equal, but you will understand in a bit. If I look at the DNA codon table ...
Sos's user avatar
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6 votes
2 answers
132 views

How predictably will RNA polymerase not transcribe repetitive sequences?

I am working on an (expensive) synthetic construct, which happens to have many "repetitive" sequences within it that are integral to its function. Primarily, the two sequences that are worrying me are:...
LanceLafontaine's user avatar
6 votes
1 answer
223 views

How can I tell if regulation is at the transcriptional or translational level?

I was reading a paper, http://www.pnas.org/content/109/8/E471.short, where the authors claim that (e475) Translation of the TfR (Transferrin Receptor) is regulated through sequences in the 3′ and 5′...
TMOTTM's user avatar
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Transcription and translation of prokaryotic operons

I'm taking a molecular genetics course, and we're currently discussing prokaryotic operons. The lacZ operon came up frequently for me as an undergraduate as an example for teaching regulatory control ...
Daniel Standage's user avatar
6 votes
1 answer
683 views

How can promoter binding sites be determined?

I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in Bacillus subtilis. I would expect it ...
StephUnna's user avatar
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5 votes
2 answers
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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?...
Seth H's user avatar
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5 votes
3 answers
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Do transcripts always start and end with exons?

I realized that in all cases of "RefSeq Genes" annotations of hg19 I looked at spliced transcripts start (and end) with an exon. From the annotation there is no evidence of any sequence upstream or ...
HerrJemine's user avatar
5 votes
3 answers
155 views

Can genes that activate transcription factors also called be called transcription factors?

If the sole known function of a gene is to activate a transcription factor, would that gene also be considered a transcription factor, or is there a word for such genes that are further upstream on ...
Atticus29's user avatar
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1 answer
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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 ...
Sharon's user avatar
  • 125
5 votes
2 answers
272 views

Is there selection against long proteins and long genes?

Background thought Titin and TTN Titin is the largest protein in the human genome with 33423 amino acids. Titin is coded by the gene TTN that must be at least $3 \cdot 33423 \approx 100kb$ long. ...
Remi.b's user avatar
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5 votes
2 answers
263 views

What are some atypical examples of positive transcriptional cooperativity?

Cooperativity in gene expression is an important feature of many regulatory networks. Described using the Hill function, the most common example is a transcription factor (TF) that when bound to its ...
boloyao's user avatar
  • 700
5 votes
1 answer
290 views

Bacterial chromatin binding data?

I'm looking for data - maybe CHP^2 data that shows chromatin binding to a prokaryotic genome under some specific conditions. Can anyone point me to a source?
shigeta's user avatar
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5 votes
1 answer
146 views

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 ...
Hawkeye's user avatar
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5 votes
1 answer
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What is the relation between plasmid concentration and mRNA levels?

Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene: One of the simplest ways to model GFP transcription is to use an ODE: $\frac{d [GFP_{mRNA}]}{dt} = a - ...
w128's user avatar
  • 511
5 votes
2 answers
74 views

tools to reconstruct the transcriptional regulatory circuits?

What are commonly used tools to reconstruct the transcriptional regulatory circuits that govern diverse cellular responses and what input data sets do they accept?
719016's user avatar
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5 votes
1 answer
209 views

Location of TFBS in genome

I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether ...
Alina's user avatar
  • 363
5 votes
1 answer
400 views

How do biologists infer correct ORF of a DNA sequence?

Each DNA (RNA) sequence has 6 possible Open Reading Frames(ORF). My question is: What are the theoretical bases of in vitro or in silico tries to find correct reading frame of a sequence? Is it just ...
MySky's user avatar
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5 votes
1 answer
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How is the transcription direction of RNA polymerase determined?

When transcription factors attach to the DNA strand - How do they know in which direction they have to initialize the transcription by rna polymerase? Is it always read in the same direction anyway? ...
Sprechblaseningenieur's user avatar
5 votes
2 answers
636 views

Why is 5S-rRNA is different from other rRNAs in place of transcription and usage of RNA polymerase?

While transcription of rRNAs happens in nucleolus mediated by RNA Polymerase-I, we see that 5S-rRNA is transcribed elsewhere by RNA Polymerase-III. What is the cause and why?
user avatar
5 votes
1 answer
457 views

Mechanism of Muscle Growth

According to this video (sorry for the poor reference but it represents my level of understanding in physiology), muscle grow as a consequence of repairing micro-lesions. How are these micro-lesions ...
Sulawesi's user avatar
  • 273
5 votes
1 answer
494 views

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 ...
Positron12's user avatar
4 votes
2 answers
19k views

Stop codons and exons?

If we had a hypotheical gene called gene exampleGene and this gene had 5 exons, labeled A, B, C, D, and E in that order on the chromosome, could it be the case that the stop codon for this gene be on ...
Ro Siv's user avatar
  • 1,289
4 votes
2 answers
380 views

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 ...
Chrystomath's user avatar