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

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Is DNA transcription inactive during mitosis ie no proteins are made? How does the cell survive?

I've read that during mitosis, DNA exists as heterochromatin, a form that is unable to be accessed for transcription. Does this mean no new proteins are made during what can be 20% of a cell's life? ...
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43 views

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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3answers
124 views

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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48 views

How does RNA polymerase achieve higher processivity?

DNA polymerase uses a sliding clamp in order to replicate DNA. RNA polymerase does not require one. What allows RNA polymerase to hold on to DNA just like DNA polymerase?
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32 views

Time needed for transcription of DNA [closed]

How much time would it take to complete the transcription of an average-sized human gene?
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34 views

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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25 views

Transcription of Genes: Are Specific Transcription Factors + Enhancers Necessary?

I learned about transcription in my AP Biology class and we discussed how transcription occurs, but I was wondering whether transcription always requires the enhancers, activators (specific ...
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15 views

Are both chromosomes transcribed and translated? [duplicate]

Or is it somehow regulated if both or only one chromosome is transcribed/translated?
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39 views

General transcription factors vs. DNA Binding transcription factors

I know that DNA binding transcription factors are trans-acting, but what about general transcription factors? Are they cis or trans acting?
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20 views

What is the difference between basal transcription and activated transcription?

My professor keeps mentioning these two forms of transcription and I'm completely confused as to what the difference is between them. I didn't even realise there were two different types of ...
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Why and how is DNA synthesis so much faster then RNA synthesis?

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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29 views

Transcription when Chromosomes are Condensed

Are genes transcribed just as well when chromosomes are condensed? I want to design a screen that depends on genes not transcribed when chromosomes are condensed (to identify cells that can't ...
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14 views

How many Stress Response Transcription Factors are there in yeast (and what are they)

I've Read that there are ~209 TFs in Yeast, but I'd like to know how many (and which) of these TFs are associated with Stress Responses? Is there a paper someone can link me to?
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1k views

How does RNA transcription know which half of the DNA to use?

I feel that I might have a complete misunderstanding here. If DNA has two strands, how does RNA transcription know which one to choose?
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97 views

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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63 views

TSS of a gene vs TSS of a transcript

I have an annotation from gencode.vM1.annotation of a mouse. Exons, genes, transcripts and UTR are listed there. For each feature a start and end positions are present. I need to find a TSS for each ...
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1answer
125 views

How do DNA-binding proteins determine that they're binding to 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 ...
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Will bacterial promoter without either -10 or -35 sequence allow no transcription?

I have a strong constitutive promoter on a plasmid inside of E.Coli, which expresses a gene. Having either -10 or -35 sequence modified to random sequence, will it ensure zero transcription from that ...
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1answer
14 views

What was the first gene(s) found to code for ncRNA

I could not find a source that states what the first gene found to code for ncRNA was. Someone told me, however, it was a gene that coded for either rRNA or tRNA. To this point in time I have had no ...
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63 views

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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15 views

translation rate regulated by transcription factors?

I'd like to know if there is in the litterature some examples of transcription factors capable to impact not just transcription but also translation rate so that both can be adjusted. I would be very ...
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1answer
94 views

What is the spacing between stop codon and transcription terminator?

When one tries to express a protein from a synthetic plasmid in E. coli, how many base pairs should there be between stop codon and the transcription terminator site?
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1answer
39 views

How does the MET gene work and what happens when the promoter region gets mutated?

I am doing research on inherited risk of Autism Spectrum Disorders(ASD) due to common Copy Number Variants(CNVs) One of the mutations is the 'CC' variant of Rs1858830 in the promoter region of the MET ...
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375 views

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 ...
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18 views

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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1answer
633 views

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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Are upstream activating factor (UAF) and upstream binding factor (UBF) the same thing?

During ribosome pre-40S and pre-60S synthesis, many sources state the importance of UAF or UBF in initiation complex of ribosome DNA transcription. None of the sources I've seen mentions the other ...
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2answers
1k 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 ...
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1answer
32 views

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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75 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?
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71 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 ...
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2answers
74 views

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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38 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
111 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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34 views

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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51 views

Are there U-rich transcriptional pause sites?

I've heard a statement in a talk that U-rich sequences cause transcriptional pausing. The intuitive explanation for this was that the UTP concentration is lower in the cell than the ATP concentration. ...
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100 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 ...
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1answer
166 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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1answer
130 views

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. ...
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2answers
1k 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 here or in ...
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1answer
217 views

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
170 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 ...
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How does Temperature influences the rate of protein turnover? [duplicate]

Question How (quantitatively speaking) does temperature influences rate of turnover of transcription factors? Which protein? As I am not looking for any accurate number I am talking about an ...
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1answer
99 views

How is the rate of transcription influenced by temperature?

How is the rate of transcription influenced by temperature? More precisely, I am looking for an article who quantitatively measured the rate of transcription of an "average gene" and show how this ...
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1answer
32 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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2answers
130 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 ...
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80 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 ...
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1answer
248 views

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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43 views

What is the suitable terminology to describe this study approach?

I need to know the correct term(s) which are usually used in the parlance of both biology and bioinformatics for this study approach: About 11 transcripts were investigated using qPCR for a number of ...
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1answer
2k views

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? ...