Hoatlin: Fundamentals: Difference between revisions
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==Links for Maureen Hoatlin's | ==Links for Maureen Hoatlin's Fundamentals 2018 Class== | ||
== | ;Movies for Lecture. We will view several of these movies and discuss together. | ||
*[http://www.hhmi.org/biointeractive/dna-replication-advanced-detail DNA replication animation] | |||
*[https://www.youtube.com/watch?v=6O0qD6KCOVE DNA polymerase] | |||
*[http://www.youtube.com/watch?v=AJNoTmWsE0s telomere animation] | |||
*[http://www.youtube.com/watch?v=k4fbPUGKurI topoisomerase] | |||
*[https://www.youtube.com/watch?v=bePPQpoVUpM Helicase] | |||
*extra information if interested in telomeres [http://www.nature.com/scitable/topicpage/Telomeres-of-Human-Chromosomes-21041 Telomeres on Nature Network] | |||
;Materials for the Skills Session on XP | |||
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983582/ DNA repair diseases: What do they tell us about cancer and aging]. Scan before the XP session. | |||
*[http://www.ncbi.nlm.nih.gov/pubmed/22217736 J. DiGiovanna & K. Kraemer, “Shining a Light on Xeroderma Pigmentosum"]. J Invest Dermatol. (2012), 132, 785-96. Scan this review. This is for in-depth understanding, written by Ken Kraemer, an XP expert. | |||
*When the Lifeguard for the Gene Pool Goes on Strike. A January 2014 seminar by Ken Kraemer on XP. Shows patient cases and outcomes. Some of these slides will be shown during the introduction to the workshop. https://www.youtube.com/watch?v=_z0kEsvCw9k | |||
*NIH Summary of Xeroderma Pigmentosum. http://www.ncbi.nlm.nih.gov/books/NBK1397/ | |||
==Questions and Answers== | |||
*Taken from emailed questions over the years about topics I cover including transcription, chromosome and gene structure, DNA replication and DNA repair. Thank you to all students who have contributed these questions--we all benefit: | |||
* | ;Question | ||
* | *I had one question about the study guide. It says HATs acetylate and therefore neutralize a negative charge. I was taught that lysine is positive, and putting an acetyl group on it neutralized a positive charge. (note--this issue has been revised for clarification in the study guide as of 2014, but I left this q&A in because it may be informative). | ||
* | ;Answer | ||
* | *I think I see the confusion. In the sentence you got confused by (II. A.4a), the charge referred to is the negative charge on the DNA phosphate backbone. This is a problem with wording because the study guide and slides are so condensed that they make a general case for both HATs and HDACs. Other students had the same question. I hope this clears it up: | ||
* | Reversible modification of the ε-amino group of lysine by acetylation neutralizes a negative charge on DNA. | ||
* | *The longer version for the study guide that would be better is: | ||
*Histone tails contain amine groups on lysine and arginine. These positively charged residues interact with the negatively charged phosphate groups on the DNA phosphate backbone. Acetylation by HATs neutralizes the positive charges on the histone tails thus reducing histones binding to DNA, leading to chromatin expansion. HDACs remove acetyl groups resulting in a positive charge of histone tails increasing binding between the histones and DNA backbone, condensing chromatin. | |||
;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). | |||
*Lecture Slides have 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. Enhancers can even be located on a different chromosome than the promoter. Here’s a recent paper that is nteresting to scan briefly because it describes the complexities in transcription control. de Laat, W., & Duboule, D. (2013). Topology of mammalian developmental enhancers and their regulatory landscapes. Nature, 502(7472), 499–506. doi:10.1038/nature12753 | |||
;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 | ||
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;Comment | ;Comment | ||
* there | * there was a typo in lecture notes. the haploid human genome is 3x10^9 (billion) | ||
== Archived Links for previous Classes== | |||
*[http://www.youtube.com/watch?v=aVgwr0QpYNE Splicing animation] | |||
*[http://www.youtube.com/watch?v=SMtWvDbfHLo transcription animation] | |||
*[http://www.youtube.com/watch?v=4jtmOZaIvS0&feature=related DNA Replication] **note: mute the idiotic sound and voiceover and imagine instead the original soundtrack of a machine perking along. | |||
*[https://www.youtube.com/watch?v=ldXXGt8Ihss DNA polymerase animation] | |||
*[http://www.youtube.com/watch?v=AJNoTmWsE0s telomere animation] | |||
*[http://www.nature.com/scitable/topicpage/Telomeres-of-Human-Chromosomes-21041 Telomeres on Nature Network] | |||
*[http://www.youtube.com/watch?v=k4fbPUGKurI topoisomerase] | |||
*[https://www.youtube.com/watch?v=bePPQpoVUpM Helicase] | |||
*[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. | |||
Really. | |||
*[http://www.ted.com/talks/david_bolinsky_animates_a_cell.html Animation in Science Education] A TED talk to watch during a break from your studies. | |||
*Enjoy some [http://www.xvivo.net/zirus-antivirotics-condensed/ excellent animations]. The virology animation includes viral replication. Viral styles of replication are complex and fascinating, also providing a target for therapeutic intervention. | |||
*[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] | |||
==Other Stuff== | ==Other Stuff== |
Latest revision as of 11:10, 11 August 2018
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Links for Maureen Hoatlin's Fundamentals 2018 Class
Questions and Answers
Reversible modification of the ε-amino group of lysine by acetylation neutralizes a negative charge on DNA.
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)
Archived Links for previous Classes
Really.
Other Stuff |