Hoatlin: CSF - Revision history

Maureen E. Hoatlin: /* Questions and Answers */

2012-01-24T04:19:07Z

Questions and Answers

←Older revision		Revision as of 04:19, 24 January 2012
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	*Cis elements- these are regulatory sequences on DNA. Can they be both enhancers and silencers? Does their proximity to the gene matter to still be considered "cis"?		*Cis elements- these are regulatory sequences on DNA. Can they be both enhancers and silencers? Does their proximity to the gene matter to still be considered "cis"?
	;Answer		;Answer
-	*Yes, they can be both enhancers and silencers, and can be very far away but on the same piece of DNA.	+	*Yes, they can be both enhancers and silencers, and can be very far away from the promoter, but on the same piece of DNA.
	;Question		;Question
	*Regarding constitutive and inducible enhancer elements, it was my understanding that enhancer refers to the DNA sequence, whereas activator refers to the DNA binding protein, so I’m not sure of what a constitutive and inducible enhancer is.		*Regarding constitutive and inducible enhancer elements, it was my understanding that enhancer refers to the DNA sequence, whereas activator refers to the DNA binding protein, so I’m not sure of what a constitutive and inducible enhancer is.

Maureen E. Hoatlin: /* Questions and Answers */

2012-01-23T19:36:36Z

Questions and Answers

←Older revision		Revision as of 19:36, 23 January 2012
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	*Are transcription factors, basal transcription factors, basal factors all the same thing?		*Are transcription factors, basal transcription factors, basal factors all the same thing?
	;Answer		;Answer
-	*Yes. (see pg 239 in your reading, Essential Cell Biology pg 239) and the lecture notes that describe initiation of transcription with the stepwise assembly of proteins at the promoter (the TFIIA, TFIIB etc plus RNA polymerase) and slide 24 of the last lecture where the first point is “Basal transcription factors: TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.” The basal transcription factors are a subset of all transcription factors.	+	* Yes. (see pg 239 in your reading, Essential Cell Biology pg 239) and the lecture notes that describe initiation of transcription with the stepwise assembly of proteins at the promoter (the TFIIA, TFIIB etc plus RNA polymerase) and slide 24 of the last lecture where the first point is “Basal transcription factors: TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.” The basal transcription factors are a subset of all transcription factors.

	;Question		;Question
	*It is not clear what the functional classes of transcription factors are.		*It is not clear what the functional classes of transcription factors are.
	;Answer		;Answer
-	* Slide 25 has the list of proteins that regulate transcription (as follows):	+	Transcription factors can be constitutively-active – present in all cells at all times or can be conditionally-active – requires activation (e.g., cell specific or signal-dependent).
		+
		+	* Slide 25 has the overview of the list of proteins that regulate transcription (as follows):
	**Basal transcription factors		**Basal transcription factors
	***TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.		***TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.

Maureen E. Hoatlin at 19:17, 23 January 2012

2012-01-23T19:17:55Z

←Older revision		Revision as of 19:17, 23 January 2012
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	***Histone modifying enzymes.		***Histone modifying enzymes.
	***Chromatin remodeling factors		***Chromatin remodeling factors
		+
		+	;Question
		+	*I was a bit confused with: Using a steroid receptor as an example, explain how gene expression can be regulated by hormonal signals.
		+	;Answer
		+	*Just a general description from the standpoint of transcription can be found in the related text and in the figure in the lecture notes: "Reciprocal regulation of transcription. In the absence of ligand, nuclear hormone receptors repress transcription through the action of co-repressor complexes with associated HDAC activity. Ligand-induced conformational changes lead to dissociation of co-repressor complexes with recruitment of co-activator/HAT complexes. (from Glass and Rosenfeld, Genes Dev. 14:121-41, 2000)"

	;Question		;Question

Maureen E. Hoatlin: /* Questions and Answers */

2012-01-23T18:17:56Z

Questions and Answers

←Older revision		Revision as of 18:17, 23 January 2012
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	*It is not clear what the functional classes of transcription factors are.		*It is not clear what the functional classes of transcription factors are.
	;Answer		;Answer
-	* Slide 25 has the list (as follows):	+	* Slide 25 has the list of proteins that regulate transcription (as follows):
	**Basal transcription factors		**Basal transcription factors
	***TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.		***TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.

Maureen E. Hoatlin: /* Questions and Answers */

2012-01-23T18:17:08Z

Questions and Answers

←Older revision		Revision as of 18:17, 23 January 2012
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	*Are transcription factors, basal transcription factors, basal factors all the same thing?		*Are transcription factors, basal transcription factors, basal factors all the same thing?
	;Answer		;Answer
-	*Yes. (see pg 239 in your reading, Essential Cell Biology pg 239) and the lecture notes that describe initiation of transcription with the stepwise assembly of proteins at the promoter (the TFIIA, TFIIB etc plus RNA polymerase) and slide 24 of the last lecture where the first point is “Basal transcription factors: TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.”	+	*Yes. (see pg 239 in your reading, Essential Cell Biology pg 239) and the lecture notes that describe initiation of transcription with the stepwise assembly of proteins at the promoter (the TFIIA, TFIIB etc plus RNA polymerase) and slide 24 of the last lecture where the first point is “Basal transcription factors: TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.” The basal transcription factors are a subset of all transcription factors.

	;Question		;Question

Maureen E. Hoatlin: /* Questions and Answers */

2012-01-23T03:33:23Z

Questions and Answers

←Older revision		Revision as of 03:33, 23 January 2012
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	*It is not clear what the functional classes of transcription factors are.		*It is not clear what the functional classes of transcription factors are.
	;Answer		;Answer
-	* ~~Please see the list on~~ Slide 25.	+	* Slide 25 has the list (as follows):
-	**Basal transcription factors: TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.	+	**Basal transcription factors
-	**DNA-Binding Factors Signal-regulated proteins: posttranslational modifications (phosphorylation). Nuclear Hormone Receptors: require ligand binding.	+	***TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.
-	**Co-regulatory protein complexes Interact with DNA binding proteins, but not (necessarily) with DNA TBP-Associated Factors (TAFs) Histone modifying enzymes. Chromatin remodeling factors	+	**DNA-Binding Factors
		+	***Signal-regulated proteins: posttranslational modifications (phosphorylation).
		+	***Nuclear Hormone Receptors: require ligand binding.
		+	**Co-regulatory protein complexes
		+	***Interact with DNA binding proteins, but not (necessarily) with DNA
		+	***TBP-Associated Factors (TAFs)
		+	***Histone modifying enzymes.
		+	***Chromatin remodeling factors

	;Question		;Question

Maureen E. Hoatlin: /* Questions and Answers */

2012-01-23T03:31:03Z

Questions and Answers

←Older revision		Revision as of 03:31, 23 January 2012
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	**Co-regulatory protein complexes Interact with DNA binding proteins, but not (necessarily) with DNA TBP-Associated Factors (TAFs) Histone modifying enzymes. Chromatin remodeling factors		**Co-regulatory protein complexes Interact with DNA binding proteins, but not (necessarily) with DNA TBP-Associated Factors (TAFs) Histone modifying enzymes. Chromatin remodeling factors

-	;Question	+	;Question
	*Cis elements- these are regulatory sequences on DNA. Can they be both enhancers and silencers? Does their proximity to the gene matter to still be considered "cis"?		*Cis elements- these are regulatory sequences on DNA. Can they be both enhancers and silencers? Does their proximity to the gene matter to still be considered "cis"?
-	;Answer	+	;Answer
	*Yes, they can be both enhancers and silencers, and can be very far away but on the same piece of DNA.		*Yes, they can be both enhancers and silencers, and can be very far away but on the same piece of DNA.
	;Question		;Question

Maureen E. Hoatlin: /* Questions and Answers */

2012-01-23T03:30:27Z

Questions and Answers

←Older revision		Revision as of 03:30, 23 January 2012
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	==Questions and Answers==		==Questions and Answers==
	*Taken from emailed questions:		*Taken from emailed questions:
		+	;Question
		+	*Are transcription factors, basal transcription factors, basal factors all the same thing?
		+	;Answer
		+	*Yes. (see pg 239 in your reading, Essential Cell Biology pg 239) and the lecture notes that describe initiation of transcription with the stepwise assembly of proteins at the promoter (the TFIIA, TFIIB etc plus RNA polymerase) and slide 24 of the last lecture where the first point is “Basal transcription factors: TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.”
		+
		+	;Question
		+	*It is not clear what the functional classes of transcription factors are.
		+	;Answer
		+	* Please see the list on Slide 25.
		+	**Basal transcription factors: TATA-binding protein TFIIB, TFIIA, TFIIE, TFIIH etc.
		+	**DNA-Binding Factors Signal-regulated proteins: posttranslational modifications (phosphorylation). Nuclear Hormone Receptors: require ligand binding.
		+	**Co-regulatory protein complexes Interact with DNA binding proteins, but not (necessarily) with DNA TBP-Associated Factors (TAFs) Histone modifying enzymes. Chromatin remodeling factors
		+
		+	;Question
		+	*Cis elements- these are regulatory sequences on DNA. Can they be both enhancers and silencers? Does their proximity to the gene matter to still be considered "cis"?
		+	;Answer
		+	*Yes, they can be both enhancers and silencers, and can be very far away but on the same piece of DNA.
		+	;Question
		+	*Regarding constitutive and inducible enhancer elements, it was my understanding that enhancer refers to the DNA sequence, whereas activator refers to the DNA binding protein, so I’m not sure of what a constitutive and inducible enhancer is.
		+	;Answer
		+	*The simplest answer is that an enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster. It is different than an promoter because it can act at great distances from the promoter and can act upstream or downstream of the promoter itself. A constitutive enhancer, is "on" all the time, versus an inducible enhancer that is conditionally able to influence transcription based on the presence of a particular protein (e.g., in a certain cell type or during a specific moment or location during development).
		+
	;Question		;Question
	*What is the difference between "alternative RNA Processing" and "alternative protein processing"?		*What is the difference between "alternative RNA Processing" and "alternative protein processing"?

Maureen E. Hoatlin: /* Questions and Answers */

2012-01-23T03:18:31Z

Questions and Answers

←Older revision		Revision as of 03:18, 23 January 2012
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	*What is the difference between "alternative RNA Processing" and "alternative protein processing"?		*What is the difference between "alternative RNA Processing" and "alternative protein processing"?
	;Answer		;Answer
-	*Alternative RNA processing is exhibited in the example of	+	*Alternative RNA processing is exhibited in the example of calcitonin and calcitonin gene related peptide. The same transcript is spliced in different ways to achieve different mRNAs and thus alternative proteins.
-	calcitonin and calcitonin gene related peptide. The same transcript is	+
-	spliced in different ways to achieve different mRNAs and thus alternative proteins.	+

-	*Alternative protein processing can refer to a number of things. Rather than confuse the	+	*Alternative protein processing can refer to a number of things. Rather than confuse the issue with examples, Let me know where the statement was in the notes so I can clarify.
-	issue with examples, Let me know where the statement was in the notes so I can clarify.	+

	;Question		;Question
-	*Can you shed some light on what is important about SINEs and LINEs,	+	*Can you shed some light on what is important about SINEs and LINEs, other than being transposons?
-	other than being transposons?	+
	;Answer		;Answer
-	*LINEs and SINEs are important to know about because (1) they	+	*LINEs and SINEs are important to know about because (1) they provide knowledge about a large part of the human genome (2) the role of SINEs and LINEs in genome evolution (e.g., via recombination) and (3) it is likely that a clearer picture of the activities of LINEs and SINEs in genomic stability and clinically-important influences will continue to emerge (see abstract for a recent review: http://www.ncbi.nlm.nih.gov/pubmed/20307669).
-	provide knowledge about a large part of the human genome (2) the role of	+
-	SINEs and LINEs in genome evolution (e.g., via recombination) and (3) it is	+
-	likely that a clearer picture of the activities of LINEs and SINEs in genomic	+
-	stability and clinically-important influences will continue to emerge (see	+
-	abstract for a recent review: http://www.ncbi.nlm.nih.gov/pubmed/20307669).	+

	;Question		;Question

Maureen E. Hoatlin: /* Questions and Answers */

2012-01-23T03:17:18Z

Questions and Answers

←Older revision		Revision as of 03:17, 23 January 2012
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	==Questions and Answers==		==Questions and Answers==
	*Taken from emailed questions:		*Taken from emailed questions:
-	Q: What is the difference between "alternative RNA Processing" and	+	;Question
-	"alternative protein processing"?	+	*What is the difference between "alternative RNA Processing" and "alternative protein processing"?
-	Alternative RNA processing is exhibited in the example of	+	;Answer
		+	*Alternative RNA processing is exhibited in the example of
	calcitonin and calcitonin gene related peptide. The same transcript is		calcitonin and calcitonin gene related peptide. The same transcript is
-	spliced	+	spliced in different ways to achieve different mRNAs and thus alternative proteins.
-	in different ways to achieve different mRNAs and thus alternative proteins.	+

-	Alternative protein processing can refer to a number of things~~, I'm not~~	+	*Alternative protein processing can refer to a number of things. Rather than confuse the
-	~~sure where in the notes/reading you fond this~~. Rather than confuse the	+	issue with examples, Let me know where the statement was in the notes so I can clarify.
-	issue with examples, Let me know where the statement was in the notes so I	+
-	can clarify.	+

-		+	;Question
-	Q: Can you shed some light on what is important about SINEs and LINEs,	+	*Can you shed some light on what is important about SINEs and LINEs,
-	other than being	+	other than being transposons?
-	transposons?	+	;Answer
-	LINEs and SINEs are important to know about because (1) they	+	*LINEs and SINEs are important to know about because (1) they
	provide knowledge about a large part of the human genome (2) the role of		provide knowledge about a large part of the human genome (2) the role of
-	SINEs	+	SINEs and LINEs in genome evolution (e.g., via recombination) and (3) it is
-	and LINEs in genome evolution (e.g., via recombination) and (3) it is	+	likely that a clearer picture of the activities of LINEs and SINEs in genomic
-	likely	+
-	that a clearer picture of the activities of LINEs and SINEs in genomic	+
	stability and clinically-important influences will continue to emerge (see		stability and clinically-important influences will continue to emerge (see
	abstract for a recent review: http://www.ncbi.nlm.nih.gov/pubmed/20307669).		abstract for a recent review: http://www.ncbi.nlm.nih.gov/pubmed/20307669).