As you may know from previous courses, gene transcription begins with the assemb

Question

As you may know from previous courses, gene transcription begins with the assembly of the transcriptional machinery (TFIIA-H proteins) at the core promoter of genes. Where do you think core promoters are more likely to be located? Nucleosome DNA or Linker DNA?

Go ahead and formulate a hypothesis on the more likely location of core promoters of genes in DNA, and defend it with molecular biology arguments (in other words, why would one or the other be a preferred location for core promoters, based on what you know about nucleosome DNA and linker DNA?).

Then, I want you to imagine that you have access to a standard molecular genetics lab, and I want you to propose an experimental test of your hypothesis. You don’t need to get too technical, just a description of how you would design an experiment that tests your hypothesis, indicating samples, treatments, and the measurements or readouts that that you plan to take. Your imaginary lab has the following equipment:

1)  Antibodies for immunoprecipitation: these are molecules that can bind to several kinds of proteins, and allow you to physically pull them down (along with anything that is bound to them). In this case, imagine that you have access to antibodies that allow you to separate any proteins bound to DNA and isolate them along with any DNA bound to them!!

2)DNA sequencer: a machine that allows you to “read” the sequence of a given DNA sample.

3)Core promoter sequences: Information about what a typical core promoter sequence looks like.

So go ahead and design an experiment using any combination of one or more of the resources listed above, and do not forget to describe what results you expect to see, should your hypothesis be correct.

Your submission should be 200 words or fewer,

Explanation / Answer

Nucleosome DNA

Promoters are sequences which bind the RNA polymerase to initiate transcription. these promoters are present upstream to gene am may be regulated by protein binding or epigentic mechasnism to express the genes they control differentially.Linker DNA on the other hand may have sequences which may act as promoters in cases where nucleosomes are absent. The linker DNA are responsible from chromatin folding etc. and structure of chromatin, they are also responsible for the separation of the nucleosomes.

We can test this hypotheis using the available materials in the lab.

Within the nucleuosome, octamer of Histone proteins H2A, H2B H3 and H4 form the core of the nucleosome are which the DNA is wrapped, to replicate a DNA has to be free of these histones so the it can de-condense and the DNA polymerase can be loaded on the parent DNA sequence to start replication.

Here we have been given the information about core promoter sequence and we can use this after we have deciphered the nucleotide sequence using a sequencer to test our hypothesis

Procedure:

1) Treat your DNA sample with antibodies against the four histone proteins. These antibodies will target the histone proteins and remove them from the nucleosome and not from linker DNA as linker DNA has a different histone protein histone H1

2) Once you have removed the histone proteins, the DNA wrapped around the nucleosome is free and can now be read as a sequencer

3) the sequencer will start reading the DNA strand, assemble the nucleotide sequence and then span the fragments for the promoters using the promoter sequence information

If the hypothesis is correct, in the DNA sequence of the nucleosome, we will find a region that will resemble a core promoter

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