Hoatlin: Fundamentals: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
|||
(20 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
{{HoatlinLab}} | {{HoatlinLab}} | ||
==Links for Maureen Hoatlin's CSF | ==Links for Maureen Hoatlin's CSF 2012 Class== | ||
*[http://www.youtube.com/watch?v=IMeJA_inoEM&feature=related Pharmacogenomics Video Lecture] | |||
*[http://www.genome.gov/SP2011/ Short Easy reading summary of genomics and medicine] | |||
==Bonus Materials== | ==Bonus Materials== | ||
Line 10: | Line 14: | ||
*[http://www.youtube.com/watch?v=k4fbPUGKurI topoisomerase] | *[http://www.youtube.com/watch?v=k4fbPUGKurI topoisomerase] | ||
*[http://www.youtube.com/watch?v=UWNhwceMjfk&p=C9FDF61276AE2050&index=6&playnext=3 Helicase] | *[http://www.youtube.com/watch?v=UWNhwceMjfk&p=C9FDF61276AE2050&index=6&playnext=3 Helicase] | ||
*[http://lifetech-it.hosted.jivesoftware.com/videos/1016 ion torrent video] | |||
*[http://www.youtube.com/watch?v=GLwCs370IGI Lectures on genomics] 13 week Series on Genomics 2012 on YouTube | |||
*[http://www.ted.com/talks/lang/eng/paul_rothemund_details_dna_folding.html Crazy Fun with DNA] A TED talk on DNA origami. | *[http://www.ted.com/talks/lang/eng/paul_rothemund_details_dna_folding.html Crazy Fun with DNA] A TED talk on DNA origami. | ||
Line 18: | Line 24: | ||
==Questions and Answers== | ==Questions and Answers== | ||
*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.” The basal transcription factors are a subset of all transcription factors. | |||
;Question | |||
*It is not clear what the functional classes of transcription factors are. | |||
;Answer | |||
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 | |||
***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 | |||
*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 | |||
*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 from the promoter, 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 | |||
*What is the difference between "alternative RNA Processing" and "alternative protein processing"? | |||
;Answer | |||
*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. | |||
*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. | |||
;Question | |||
*Can you shed some light on what is important about SINEs and LINEs, other than being transposons? | |||
;Answer | |||
*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). | |||
;Question | ;Question | ||
Line 23: | Line 77: | ||
;Answer: | ;Answer: | ||
*XP patients have a defect in one of the many genes involved in NER (nucleotide excision repair) e.g., XPA, XPC, XPC, XPG etc. Thus, XP patients cannot repair DNA damage (cyclobutane pyrimidine dimers) caused by exposure to sunlight. The XP-V patients have a different defect but the same phenotype. They have a defective bypass polymerase, called Pol eta. Normally, Pol eta can synthesize (error-free) past a thymine dimer by inserting two A residues. In XP-V patients, other bypass Pols are substituted that are not error-free for this lesion. Also, in XP-V patients, the upstream XPA-XPG proteins are functional and NER repair is intact. Only the bypass polymerase is defective. | *XP patients have a defect in one of the many genes involved in NER (nucleotide excision repair) e.g., XPA, XPC, XPC, XPG etc. Thus, XP patients cannot repair DNA damage (e.g., photoproducts like cyclobutane pyrimidine dimers) caused by exposure to sunlight. The XP-V patients have a different defect but the same phenotype. They have a defective bypass polymerase, called Pol eta. Normally, Pol eta can synthesize (error-free) past a thymine dimer by inserting two A residues. In XP-V patients, other bypass Pols are substituted that are not error-free for this lesion. Also, in XP-V patients, the upstream XPA-XPG proteins are functional and NER repair is intact. Only the bypass polymerase is defective. | ||
;Question | ;Question | ||
Line 53: | Line 107: | ||
;Comment | ;Comment | ||
* there | * there was a typo in lecture notes. the haploid human genome is 3x10^9 (billion) | ||
==Other Stuff== | ==Other Stuff== |
Revision as of 21:19, 23 January 2012
Home Projects Team Papers Contact Us Protocols Collaborations News Reagent Requests secret back door Hoatlin Lab Twitter
Links for Maureen Hoatlin's CSF 2012 ClassBonus Materials
Really.
Questions and Answers
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).
That's how PARP1 inhibitors are relatively selective in killing the HR deficient tumor cell but not the wild-type cell (which is competent for HR)
Other Stuff |