Questions tagged [transcription]

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

Filter by
Sorted by
Tagged with
1
vote
1answer
72 views

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. ...
5
votes
1answer
92 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 ...
1
vote
3answers
6k views

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 ...
12
votes
2answers
2k views

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'? ...
0
votes
1answer
400 views

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 ...
3
votes
1answer
916 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' ...
3
votes
1answer
3k views

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-...
1
vote
1answer
78 views

Are microRNAs transcribed from the same DNA strand as their parent messenger RNAs?

I am new to micro RNAs. I have been trying to find the answer to the question if microRNAs are transcribed from the same DNA strand as the messenger RNAs encoded by the encompassing gene? From the ...
2
votes
2answers
379 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 ...
0
votes
1answer
69 views

DNA methylation in different positions

I'm trying to understand how does DNA methylation and histone methylation status of promoters differs given their position in a gene? Does position affect whether they are repressive or activating?
27
votes
2answers
8k views

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

I feel that I might have a complete misunderstanding here. If DNA has two strands, how does the machinery of RNA transcription determine which one to transcribe?
3
votes
2answers
1k 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 ...
12
votes
2answers
4k views

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 ...
1
vote
0answers
28 views

response elements in transcription regulation

I'm studying eukaryotic gene regulation and I want to know whether there are some instances where transcription factors don't need to bind to response elements to initiate transcription. RNA ...
0
votes
0answers
423 views

What are the causes of abortive initiation?

I was reading more about DNA transcription, and it mentioned abortive initiation. The article gave no explanation as to why the phenomenon occurs. The only explanation I can think of is that it is ...
10
votes
2answers
2k views

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?
3
votes
0answers
58 views

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 (...
4
votes
2answers
144 views

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 ...
0
votes
1answer
789 views

What is the meaning of the word 'bin' in the context of RNA-Seq?

I have a question from a book about RNA-Seq. I would like to know the meaning of the word "bin" in the below cited paragraph: RseQC has several nice features not found in the other programs: (a) ...
4
votes
2answers
4k views

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 ...
1
vote
0answers
34 views

Are RNA transcripts always synthesised from the same DNA strand? [duplicate]

The DNA is read 3'->5' (and RNA synthesized 5'->3'). But due to the DNA strands having to be complementary, it seems to me that the origin can only appear on the correct side of the ORF on one of the ...
1
vote
1answer
1k views

Hedgehog AP Bio question

Could someone please explain this AP Biology question? I know the answer is C but I do not understand why. Doesn't Smo prevent gene transcription? If you "block its activity" then wouldn't it cause ...
2
votes
0answers
22 views

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?
2
votes
1answer
89 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 ...
2
votes
2answers
201 views

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 ...
1
vote
0answers
94 views

Confusion about the role of capping and polyadenylation in nuclear transport

Before termination stage of transcription a GMP cap is added to the 5' end and poly-A tail to 3' end of mRNA. The link(http://sciencing.com/role-rna-polyadenylation-5434666.html) says: The poly(A) ...
2
votes
2answers
844 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 ...
9
votes
2answers
1k 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 ...
1
vote
0answers
36 views

Modifications of free nucleotides

We know that RNA can get modified post transcriptionally (RNA modification). So when the RNA is degraded, is it possible for such modifications to still be present on the individual nucleotides -- ...
2
votes
2answers
343 views

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 ...
4
votes
1answer
55 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 ...
1
vote
2answers
66 views

Division of proteins

This textbook states Proteins determined by a single gene may divide to form different proteins with various physiological actions. First how do proteins divide? Second if it's just fragmentation ...
7
votes
1answer
517 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 ...
1
vote
2answers
2k views

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 ...
0
votes
0answers
171 views

What is regulatory promoter?

I came across this term in University question paper. What is the difference between core promoter and regulatory promoter? I have googled (Web, Scholar and Books) it but couldn't find any ...
1
vote
0answers
546 views

Usage of the terms: Enhancer, Upstream activating sequence and Downstream activating sequence

From wikipedia An upstream activating sequence or upstream activation sequence (UAS) is a cis-acting regulatory sequence. It is distinct from the promoter and increases the expression of a ...
-1
votes
1answer
163 views

Why does RNA synthesis in E.coli begin with a Purine?

From Berg's Biochemistry: Most newly synthesized RNA chains carry a highly distinctive tag on the 5′ end: the first base at that end is either pppG or pppA. Is there a reason why the synthesis ...
1
vote
1answer
52 views

What does it mean to protect RNA polymerase?

From this paper However, based on the strong interaction between NusA and RNAP, we propose that the chaperone activity of NusA could provide more direct and concentrated protection for RNAP under ...
1
vote
0answers
91 views

Transcription by RNA polymerase in absence of inducer and activator

Does the presence of activator(CAP-cAMP complex) and inducer(lactose) only increase the likelihood that a particular gene(here operon) gets transcribed, i.e increases the rate of transcription of that ...
-1
votes
1answer
860 views

Mechanism of RNA synthesis by RNA polymerase [closed]

I want to study the mechanism involved in RNA polymerase's catalysis in E.coli. Things like: How does it bind to the promoter? How does it unwind the DNA? How does each component of the enzyme ...
2
votes
4answers
433 views

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, ...
1
vote
1answer
38 views

What regulates production of first transcription factors during development?

In my biochemistry class, we learned that transcription factors regulate the transcription of genes. However, transcription factors are also coded by genes, so what activates the transcription of ...
4
votes
2answers
186 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. ...
1
vote
3answers
809 views

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 ...
1
vote
2answers
78 views

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 ...
2
votes
1answer
753 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 ...
1
vote
2answers
2k views

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 ...
0
votes
0answers
1k views

Does prokaryotic transcription have activators / enhancer regions involved?

I am designing a biosensor, and I need to know whether prokaryotic transcription involves or can involve (if a gene needs to be regulated) enhancer regions. Also, where are enhancer regions located (...
3
votes
1answer
34 views

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 ...
1
vote
2answers
15k views

Multiple start and stop codons in mRNA and pre-mRNA [duplicate]

I have a main question that will lead to further questions depending upon the answer. In the process of transcription, will there be multiple start and stop codons in one sequence of pre-mRNA? If ...