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

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110 views

Why analyse transcriptome instead of proteome?

Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (...
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2answers
132 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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0answers
8 views

Functional Difference between the Distal Promoter and Enhancer Region

According to the Wikipedia article on eukaryotic promoter regions, the distal promoter is: Anything further upstream (but not an enhancer or other regulatory region whose influence is positional/...
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0answers
14 views

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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0answers
23 views

Difference between TRN and GRN

I am little bit confused about what is the difference between Transcriptional Regulatory Networks (TRNs) vs Gene Regulatory Networks (GRNs). As far as know, both involve interactions of transcription ...
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0answers
11 views

How are siRNAs introduced to cells for RNAi experiments?

Specifically, can somebody explain how in-vitro transcription can synthesize siRNAs to conduct RNAi? I have been reading a number of research papers that discuss how to use siRNA and shRNA to conduct ...
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1answer
138 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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1answer
26 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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1answer
40 views

What is meant by Gene Expression Level?

I am new to BioInformatics, I want to know what is gene expression level and how it is determined.. Anyone who can answer this silly question.
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1answer
38 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. ...
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1answer
41 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 ...
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2answers
80 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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2answers
99 views

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?...
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2answers
1k 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'? ...
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1answer
104 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 ...
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1answer
129 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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1answer
54 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 ...
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0answers
47 views

Downstream Promoter Element’s Role

The promoters‘ role is to bind polymerase to get started transcription. And in fact: by Wikipedia “Like all core promoters, the DPE plays an important role in the initiation of gene transcription by ...
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1answer
52 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?
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0answers
18 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 ...
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0answers
208 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 ...
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0answers
44 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 (...
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2answers
69 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 ...
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1answer
225 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) ...
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2answers
1k 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 ...
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0answers
20 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 ...
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0answers
21 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?
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2answers
773 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?
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2answers
2k views

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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0answers
33 views

How are the coding and noncoding strands of DNA differentiated? [duplicate]

I know that DNA is made up of two complimentary strands, and that the one known as the coding strand contains the actual information used to make proteins. I also know that the noncoding strand is the ...
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0answers
43 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) ...
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0answers
29 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
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2answers
73 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 ...
2
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2answers
230 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 ...
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1answer
526 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 ...
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2answers
50 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 ...
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1answer
397 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 ...
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2answers
1k 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 ...
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0answers
96 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 ...
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0answers
348 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 ...
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2answers
727 views

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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0answers
64 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 ...
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1answer
46 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 ...
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2answers
241 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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1answer
61 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 ...
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1answer
373 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
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1answer
75 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
31 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 ...
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4answers
178 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, ...
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3answers
322 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 ...