Rockgo288
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1. What is the promoter region in DNA?

2. Epigenome is the chemical tags on DNA and histones. Are acetyl group and methyl group examples of it? If yes, is acetylation of histones and methylation of DNA examples of epigenetics?

3. Is siRNA effect on gene expression an example of epigenetics?
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randombiochemist
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1. Not sure what level (school- or degree-) of detail you'd like but it's basically the nucleotide sequence to which RNA polymerase binds to begin transcription of the gene(s) downstream.

2. Yes, histone acetylation (and other modifications) and DNA methylation are both typical mechanisms of epigenetics.

3. The most direct effect of siRNAs is to cause degradation of the mRNA transcript and prevent translation - this downregulation of gene expression is non-heritable and thus not an example of epigenetics. However, siRNAs can also result in chromatin remodelling, which falls under epigenetics.
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Rockgo288
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(Original post by randombiochemist)
1. Not sure what level (school- or degree-) of detail you'd like but it's basically the nucleotide sequence to which RNA polymerase binds to begin transcription of the gene(s) downstream.

2. Yes, histone acetylation (and other modifications) and DNA methylation are both typical mechanisms of epigenetics.

3. The most direct effect of siRNAs is to cause degradation of the mRNA transcript and prevent translation - this downregulation of gene expression is non-heritable and thus not an example of epigenetics. However, siRNAs can also result in chromatin remodelling, which falls under epigenetics.
1. So, is it true that the transcriptional factor always bind to promoter region to activate transcription?

2. So, the acetyl and methyl group are examples of the epigenome? that means the tags on DNA and histones?

3. All clear thanks!!!
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randombiochemist
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(Original post by Rockgo288)
1. So, is it true that the transcriptional factor always bind to promoter region to activate transcription?

2. So, the acetyl and methyl group are examples of the epigenome? that means the tags on DNA and histones?

3. All clear thanks!!!
1. Well.. Short answer: no. Longer answer: transcription factors are a diverse family of proteins functioning to regulate (initiate, activate, or suppress) transcription. Some bind to the promoter region (and/or to RNA polymerase itself) to activate transcription, others may e.g. bind at enhancer or silencer elements (both are also DNA sequences that can be located at a distance away from the coding region of the target gene) to promote or block the recruitment of RNA polymerase to particular genes.

2. Strictly speaking epigenome should only refer to the collective heritable chemical modifications made to a genome, so all the tags on an organism's DNA and histones as a whole are its epigenome. The individual acetyl/methyl groups are each an epigenetic modification.

3. No problem
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Rockgo288
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(Original post by randombiochemist)
1. Well.. Short answer: no. Longer answer: transcription factors are a diverse family of proteins functioning to regulate (initiate, activate, or suppress) transcription. Some bind to the promoter region (and/or to RNA polymerase itself) to activate transcription, others may e.g. bind at enhancer or silencer elements (both are also DNA sequences that can be located at a distance away from the coding region of the target gene) to promote or block the recruitment of RNA polymerase to particular genes.

2. Strictly speaking epigenome should only refer to the collective heritable chemical modifications made to a genome, so all the tags on an organism's DNA and histones as a whole are its epigenome. The individual acetyl/methyl groups are each an epigenetic modification.

3. No problem
For 2,
by epigenetic modification, do u mean acetyl and methyl groups are example of how epigenetics works? that means the mechanism of epigenetics? thanks!!!
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randombiochemist
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(Original post by Rockgo288)
For 2,
by epigenetic modification, do u mean acetyl and methyl groups are example of how epigenetics works? that means the mechanism of epigenetics? thanks!!!
Hi, yeah epigenetic modifications is just the term we use to refer to those acetyl and methyl groups, since they are chemical modifications to the genome and would constitute the epigenome. The acetylation/methylation processes (which are mediated by enzymes) that add those groups to DNA/histones are mechanisms of epigenetics.
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Rockgo288
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(Original post by randombiochemist)
Hi, yeah epigenetic modifications is just the term we use to refer to those acetyl and methyl groups, since they are chemical modifications to the genome and would constitute the epigenome. The acetylation/methylation processes (which are mediated by enzymes) that add those groups to DNA/histones are mechanisms of epigenetics.
thanks a lot!!! oh!! can you give me some examples of the tags on DNA and histones?? that is the epigenome? cause my book just kind of mentioned the epigenome is the tag so i’m kind of confused between epigenome and epigenetics...
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randombiochemist
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Sorry do you mean examples other than histone acetylation and DNA methylation?
In which case there are other modifications as well. Histone proteins can be methylated, phosphorylated, acetylated, ubiquitylated, and/or sumoylated, for example.
Now, epigenome vs. epigenetics - it's sort of like genome vs. genetics?
If you take a snapshot of the genome of an organism at a given instant in time, you will likely see various chemical tags on its DNA and histones, at different regions. Some genes may be heavily methylated, others may be rich in acetylated histones, etc. This particular pattern of marks is the organism's epigenome, which 'encodes' not only the types of tags present overall, but also 'which specific tags are where'. If you compare the collection of tags - the epigenome - between, say, two different developmental stages of the same organism, they will probably be different, even though the genome remains identical.
The term epigenetics, on the other hand, is used to refer to this field of study, the same way that genetics is broadly speaking the study of genes/heredity. We often use its adjective, epigenetic, to describe any process or entity that falls under it, like epigenetic modification/mechanism.
..Does that answer your question?
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Rockgo288
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(Original post by randombiochemist)
Sorry do you mean examples other than histone acetylation and DNA methylation?
In which case there are other modifications as well. Histone proteins can be methylated, phosphorylated, acetylated, ubiquitylated, and/or sumoylated, for example.
Now, epigenome vs. epigenetics - it's sort of like genome vs. genetics?
If you take a snapshot of the genome of an organism at a given instant in time, you will likely see various chemical tags on its DNA and histones, at different regions. Some genes may be heavily methylated, others may be rich in acetylated histones, etc. This particular pattern of marks is the organism's epigenome, which 'encodes' not only the types of tags present overall, but also 'which specific tags are where'. If you compare the collection of tags - the epigenome - between, say, two different developmental stages of the same organism, they will probably be different, even though the genome remains identical.
The term epigenetics, on the other hand, is used to refer to this field of study, the same way that genetics is broadly speaking the study of genes/heredity. We often use its adjective, epigenetic, to describe any process or entity that falls under it, like epigenetic modification/mechanism.
..Does that answer your question?
Thanks man!!! That was a clear explanation!!!
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randombiochemist
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(Original post by Rockgo288)
Thanks man!!! That was a clear explanation!!!
Good - glad to be of help All the best with your studies!
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