CH391L/S2013

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Office: MBB 3.422AA
Office: MBB 3.422AA
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Syllabus (need to upload)
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[[Media:2013_Spring_CH391L_Syllabus.pdf|Syllabus]]
[[:Category:CH391L_S2013 | Index of All CH391/S2013 Pages]]
[[:Category:CH391L_S2013 | Index of All CH391/S2013 Pages]]
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= Assignments =
= Assignments =
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[[CH391L/S2012/Assignments|Class Assignments]]
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[[CH391L/S13/WikiEditing| A Wiki Editing Tutorial borrowed from (The Other) CH391L]]
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[[:Category:CH391L_S2013 | Index of All CH391/S2013 Pages]]
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[[Special:RecentChangesLinked/Category:CH391L_S2013 | View Recent Changes to CH391/S2013 Pages]]
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= Grading =
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== Due January 23, 2013 ==
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# Alesha S:  [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1038%2Fng2051 Spontaneous DNA breakage in single living Escherichia coli cells.]
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## First oral presentation
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## [[Wiki article -- first draft]]
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# Tanya R:  [http://www.ncbi.nlm.nih.gov/pubmed/23273981 Activation of DSB Processing Requires Phosphorylation of CtIP by ATR.]
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## First oral presentation
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## Wiki article -- first draft
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###[[CH391L/S2013 Tanya Raymond Jan 23 2013]]
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# Hala Ouzon:  [http://www.ncbi.nlm.nih.gov/pubmed/20729832 Purified human BRCA2 stimulates RAD51-mediated recombination.]
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## First oral presentation
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## Wiki article -- first draft
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###[[CH391L/S2013 Hala Ouzon Jan 23 2013]]
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Final grades will be assigned by a straight scale (no curve) based on how many points you accumulate. Grades will be assigned based on the following ruberick:
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== Due January 30, 2013 ==
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# Alesha S:  [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1038%2Fng2051 Spontaneous DNA breakage in single living Escherichia coli cells.]
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## Second oral presentation 
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## Wiki article -- final draft
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      *[[CH391L/S2013 Alesha Stewart Jan 30 2013]]
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# Tanya R:  [http://www.ncbi.nlm.nih.gov/pubmed/23273981 Activation of DSB Processing Requires Phosphorylation of CtIP by ATR.]
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## Second oral presentation
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## Wiki article -- '''final''' draft
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###[[CH391L/S2013 Tanya Raymond Jan 30 2013]]
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# Hala Ouzon: [http://www.ncbi.nlm.nih.gov/pubmed/20729832 Purified human BRCA2 stimulates RAD51-mediated recombination.]
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## Second oral presentation
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## Wiki article -- final draft
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###[[CH391L/S2013 Hala Ouzon Jan 30 2013]]
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# Logan M:  [http://www.ncbi.nlm.nih.gov/pubmed/18483401 Activation of the cellular DNA damage Response in the Absence of DNA Lesions.]
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## First oral presentation
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## Wiki article -- first draft
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### [[CH391L/S2013 Logan R Myler Jan 30 2013]]
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{|  class="wikitable" width="300"
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== Due February 6, 2013 ==
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!Topic
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# Tanya R: [http://www.nature.com/nature/journal/v493/n7431/full/nature11676.html Recombination-restarted replication makes inverted chromosome fusions at inverted repeats]
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!Points
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## First Oral Presentation
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|-
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## Wiki article -- first draft
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|Written Reports (wiki) || 400
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###[[CH391L/S2013 Tanya Raymond Feb 6 2013]]
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|-
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# Taylor Pursell: [http://www.nature.com/nature/journal/v491/n7423/full/nature11598.html]
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|Oral Presentations || 300
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## First Oral Presentation
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|-
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## Wiki Article First Draft: [[CH391L/S2013 Taylor Pursell Feb 6/Feb 13 2013]]
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|Participation (Class/Wiki) || 300
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|-
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| '''Total''' || '''1000'''
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|}
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== Due February 13, 2013 ==
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# Alesha S:  [http://www.ncbi.nlm.nih.gov/pubmed/19285961 Regulation of DNA repair by parkin]
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## First oral presentation
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## Wiki article -- first draft: [[CH391L/S2013 Alesha Stewart Feb 13 2013]]
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# Hala Ouzon:  [http://www.sciencedirect.com/science/article/pii/S0092867411008488# Linking RNA Polymerase Backtracking to Genome Instability in E. coli]
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## First oral presentation
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## Wiki article -- first draft: [http://openwetware.org/wiki/User_talk:Hala_Ouzon-Shubeita#CH391L.2FS2013_Hala_Ouzon_Feb_13_2013 Hala_Ouzon_Feb_13_2013]
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# Taylor Pursell: [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1038%2Fnature11598 Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA.]
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##Second Oral Presentation
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## Final Wiki Article: [[CH391L/S2013 Taylor Pursell Feb 13 2013]]
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#  Tanya R: [http://www.nature.com/nature/journal/v493/n7431/full/nature11676.html Recombination-restarted replication makes inverted chromosome fusions at inverted repeats]
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##Second Oral Presentation
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##Final Wiki Article [[CH391L/S2013 Tanya Raymond Feb 13 2013]]
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== Due February 20, 2013 ==
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# Logan M: [http://www.ncbi.nlm.nih.gov/pubmed/19965384| The Fanconi anemia pathway promotes replication-dependent DNA interstrand cross-link repair.]
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## Wiki article -- first draft
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# Alesha S:  [http://www.ncbi.nlm.nih.gov/pubmed/19285961 Regulation of DNA repair by parkin]
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## Second oral presentation
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## Wiki article -- final draft: [[CH391L/S2013 Alesha Stewart Feb 13 2013]]
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{| width="300"
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== Due February 27, 2013 ==
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!Points
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#Taylor P: [http://www.ncbi.nlm.nih.gov/pubmed/23352430 Identification of Early Replicating Fragile Sites that Contribute to Genome Instability.]
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!Grade
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##Article:[[CH391L/S2013 Taylor Pursell Feb 27 2013]]
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#Tanya R: [http://www.sciencedirect.com/science/article/pii/S1097276512003504 Atl1 regulates choice between global genome repair and  transcription-coupled repair of O(6)-alkylguanines]
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|>900 || A
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##First Oral presentation
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|-
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##[[CH391L/S2013 Tanya Raymond February 27 2013]]
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| 801-900 || B
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#Logan M: [http://www.ncbi.nlm.nih.gov/pubmed/19965384| The Fanconi anemia pathway promotes replication-dependent DNA interstrand cross-link repair].
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|-
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##Final Oral presentation
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| 701-800 || C
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##[[CH391L/S2013 Logan Myler February 27 2013]]
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| 601-700 || D
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|<600 || F
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|}
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= Class Structure =
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== Due March 20, 2013 ==
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# Hala Ouzon: Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair [http://ac.els-cdn.com/S0092867411006623/1-s2.0-S0092867411006623-main.pdf?_tid=921aee16-8ce7-11e2-a5d9-00000aab0f26&acdnat=1363293879_768a6b1d3ff346ba78b08601158f13df]
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## First oral presentation
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## Wiki article -- first draft: [[CH391L/S2013 Hala Ouzon March 20 2013]]
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# Alesha S: [http://www.ncbi.nlm.nih.gov/pubmed/16497933 Structure of a DNA glycosylase searching for lesions.]
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## First oral presentation
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## Wiki article -- first draft: [[CH391L/S2013 Alesha Stewart Mar 20 2013]]
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#Taylor P: [http://www.ncbi.nlm.nih.gov/pubmed/23352430 Identification of Early Replicating Fragile Sites that Contribute to Genome Instability.]
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##Final Article:[[CH391L/S2013 Taylor Pursell March 20 2013]]
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#Tanya R: [http://www.sciencedirect.com/science/article/pii/S1097276512003504 Atl1 regulates choice between global genome repair and  transcription-coupled repair of O(6)-alkylguanines]
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##Wiki article -- final draft: [[CH391L/S2013 Tanya Raymond Mar 20 2013]]
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Each class time will be split into two halves with a 10-15 minute break between them.
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== Due March 27, 2013 ==
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#Logan M: [http://www.ncbi.nlm.nih.gov/pubmed/23012240 Single-molecule imaging reveals target-search mechanisms during DNA mismatch repair.]
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##First Oral presentation
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##First Draft -- [[CH391L/S2013 Logan Myler March 27 2013]]
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# Alesha S: [http://www.ncbi.nlm.nih.gov/pubmed/16497933 Structure of a DNA glycosylase searching for lesions.]
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## Second oral presentation
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## Wiki article -- Final draft: [[CH391L/S2013 Alesha Stewart Mar 27 2013]]
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# Hala Ouzon: Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair [http://ac.els-cdn.com/S0092867411006623/1-s2.0-S0092867411006623-main.pdf?_tid=921aee16-8ce7-11e2-a5d9-00000aab0f26&acdnat=1363293879_768a6b1d3ff346ba78b08601158f13df]
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## First oral presentation
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## Wiki article -- final draft: [[CH391L/S2013 Hala Ouzon March 20 2013]]
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== First Section — New Topics ==
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== Due April 3, 2013 ==
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In the first half of each class, 3-5 participants will have 15 to 20 minutes each to individually present new topics. To prepare for these oral presentations, you are required to complete a written report by creating a new page on the [http://openwetware.org/wiki/CH391L/2013 course web site] that is an in-depth discussion of the topic (aim for ~1000 words, ≥3 citations to scientific reviews and research papers, and explanatory figures.)
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#Taylor: [http://www.nature.com/nature/journal/v464/n7288/pdf/nature08802.pdf Heteroplasmic mitochondrial DNA mutations in normal and tumour cells]
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##First Oral Presentation
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## First Draft: [[CH391L/S2013 Taylor Pursell April 3 2013]]
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This Wiki report should be finished by the day of your presentation. Presentations should be kept simple. They may contain figures from the literature ''(with proper attribution)'' and a verbal description of the background, experimental methods, results, and future directions in a research area.
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==Due April 10, 2013==
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# Alesha S: [http://www.nature.com/onc/journal/vaop/ncurrent/pdf/onc20136a.pdf p53 promotes repair of heterochromatin DNA by regulating JMJD2b and SUV39H1 expression]
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## First oral presentation
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## Wiki article -- first draft: CH391L/S2013 Alesha Stewart Apr 10 2013
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# Hala Ouzon: Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta [http://www.sciencemag.org/content/318/5852/967.long]
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## First oral presentation
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## Wiki article -- first draft: [[CH391L/S2013 Hala Ouzon April 10 2013]]
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#Taylor: [http://www.nature.com/nature/journal/v464/n7288/pdf/nature08802.pdf Heteroplasmic mitochondrial DNA mutations in normal and tumour cells]
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##Second Oral Presentation
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## Final Draft: [[CH391L/S2013 Taylor Pursell April 10 2013]]
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# Tanya R: [http://www.sciencedirect.com/science/article/pii/S1097276512009781 eRNAs are required for p53-dependent enhancer activity and gene transcription]
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##First oral presentation
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##Wiki article [[CH391L/S2013 Tanya Raymond April 10 2013]]
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'''Be brief and consise.''' The PowerPoint presentation should contain no more than ten slides. You are encouranged to follow the outline of your written Wiki report. Other members of the class are expected to provide feedback by asking questions during your presentation and by editing the Talk pages for your written Wiki report after your presentation. Comments should be constructive, with proper citations were applicable. Your classmates will ask you interesting questions or bring up issues that you may not immediately answer, and that all of us will all learn from the feedback and revision cycle! You are encouraged (but not required) to bring a laptop / tablet / smart-phone to view Wiki pages and related scientific papers during in-class presentations.
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==Due April 17, 2013==
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# Alesha S: [http://www.nature.com/onc/journal/vaop/ncurrent/pdf/onc20136a.pdf p53 promotes repair of heterochromatin DNA by regulating JMJD2b and SUV39H1 expression]
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## Second oral presentation
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## Wiki article -- Final draft: [[CH391L/S2013 Alesha Stewart Apr 17 2013]]
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# Hala Ouzon: Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta [http://www.sciencemag.org/content/318/5852/967.long]
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## First oral presentation
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## Wiki article -- final draft: [[CH391L/S2013 Hala Ouzon April 17 2013]]
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# Tanya R:
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##Second oral presentation
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##Final wiki draft [[CH391L/S2013 Tanya Raymond April 17 2013]]
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== Second Section — Topic Updates. ==
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[[CH391L/S2013/Assignments|Class Assignments]]
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In the second half of the class period, students who presented new topics the previous time will present their answers to questions that were raised during the in-class discussion of their topic or on the Wiki talk pages since they presented. You may need to add additional citations to research papers to expand on the background.
 
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To keep a record of your changes, you should keep track of your point-by-point responses and the Wiki edits that you made to your written report on your topic's Talk page as if you were responding to reviewers of a scientific paper.
 
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== Topic Choice ==
 
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== Topics ==
 
[[CH391L/S2013/SuggestedTopics]]
[[CH391L/S2013/SuggestedTopics]]
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= Suggested Reading =
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== A Brief Overview of Cancer Biology ==
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# [http://www.ncbi.nlm.nih.gov/pubmed/10647931 The hallmarks of cancer.] Hanahan D, Weinberg RA. Cell. 2000 Jan 7;100(1):57-70.
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# [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1016%2Fj.cell.2011.02.013 Hallmarks of cancer: the next generation.] Hanahan D, Weinberg RA. Cell. 2011 Mar 4;144(5):646-74.
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=== Week 1 (Jan 16): Introduction ===
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== DNA Double Strand Break (DSB) Repair ==
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* [[CH391L/S2013/Introduction | Introduction]].
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# [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1038%2Fnature09318 Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae.] Niu H, Chung WH, Zhu Z, Kwon Y, Zhao W, Chi P, Prakash R, Seong C, Liu D, Lu L, Ira G, Sung P. Nature. 2010 Sep 2;467(7311):108-11.
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* Wiki editing tutorial.  
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# [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1038%2Fng2051 Spontaneous DNA breakage in single living Escherichia coli cells.] Pennington JM, Rosenberg SM. Nat Genet. 2007 Jun;39(6):797-802. Epub 2007 May 27.
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* Overview of course structure and topics.
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# [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1101%2Fgad.946401 Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells.] Pierce AJ, Hu P, Han M, Ellis N, Jasin M. Genes Dev. 2001 Dec 15;15(24):3237-42.
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# [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1038%2Fnature10522 Rad51 paralogues Rad55-Rad57 balance the antirecombinase Srs2 in Rad51 filament formation.] Liu J, Renault L, Veaute X, Fabre F, Stahlberg H, Heyer WD. Nature. 2011 Oct 23;479(7372):245-8.
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=== Week 2 (Jan 23): Double Strand Break (DSB) Repair ===
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# [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1038%2Fnature09399 Purified human BRCA2 stimulates RAD51-mediated recombination.] Jensen RB, Carreira A, Kowalczykowski SC. Nature. 2010 Oct 7;467(7316):678-83.
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==== Suggested Topics ====
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# [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1038%2Fnature11598 Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA.] Bell JC, Plank JL, Dombrowski CC, Kowalczykowski SC. Nature. 2012 Nov 8;491(7423):274-8.
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* DSB repair mechanisms in prokaryotes
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# [http://www.ncbi.nlm.nih.gov/pubmed?term=10.1126%2Fscience.1074584 Identification of a DNA nonhomologous end-joining complex in bacteria.] Weller GR, Kysela B, Roy R, Tonkin LM, Scanlan E, Della M, Devine SK, Day JP, Wilkinson A, d'Adda di Fagagna F, Devine KM, Bowater RP, Jeggo PA, Jackson SP, Doherty AJ. Science. 2002 Sep 6;297(5587):1686-9.
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** Homologous Recombination
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** SOS Response
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* DSB repair in eukaryotes
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** Homologous Recombination
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** Non-Homologous End Joining
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** Alternative End-Joining
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=== Week 3 (Jan 30): Double Strand Break (DSB) & Associated Diseases ===
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==== Suggested Topics ====
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* DSB Repair: Pathway Choice
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* DSB-related diseases:
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** Seckel & Jawad Syndromes
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** Nijmegen Breakage Syndrome
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** Ataxia - telangiectasia
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** Werner & Bloom Syndromes
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=== Week 4 (Feb 6): DNA Replication as a Source of Genomic Instability ===
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==== Suggested Topics ====
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* Replicating Aberrant Structures
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** DNA Hairpins
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** Z-DNA
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** G-Quadruplex DNA
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** Chromosome Fragile Sites
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* Replication-Transcription Conflicts
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* Replication-Collapse at Interstrand Cross Links
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== DNA Replication and Genome Maintenance ==
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# [http://www.ncbi.nlm.nih.gov/pubmed/21854980 Linking RNA polymerase backtracking to genome instability in E. coli.] Dutta D, Shatalin K, Epshtein V, Gottesman ME, Nudler E. Cell. 2011 Aug 19;146(4):533-43.
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# [http://www.ncbi.nlm.nih.gov/pubmed/23352430 Identification of Early Replicating Fragile Sites that Contribute to Genome Instability.] Barlow JH, Faryabi RB, Callén E, Wong N, Malhowski A, Chen HT, Gutierrez-Cruz G, Sun HW, McKinnon P, Wright G, Casellas R, Robbiani DF, Staudt L, Fernandez-Capetillo O, Nussenzweig A. Cell. 2013 Jan 22. pii: S0092-8674(13)00008-1.
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# [http://www.ncbi.nlm.nih.gov/pubmed?term=17934473 The structure-specific endonuclease Mus81 contributes to replication restart by generating double-strand DNA breaks.] Hanada K, Budzowska M, Davies SL, van Drunen E, Onizawa H, Beverloo HB, Maas A, Essers J, Hickson ID, Kanaar R. Nat Struct Mol Biol. 2007 Nov;14(11):1096-104. Epub 2007 Oct 14.
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# [http://www.ncbi.nlm.nih.gov/pubmed/19560424 Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae.] Azvolinsky A, Giresi PG, Lieb JD, Zakian VA. Mol Cell. 2009 Jun 26;34(6):722-34.
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# [http://www.ncbi.nlm.nih.gov/pubmed/19941825 Rep provides a second motor at the replisome to promote duplication of protein-bound DNA.] Guy CP, Atkinson J, Gupta MK, Mahdi AA, Gwynn EJ, Rudolph CJ, Moon PB, van Knippenberg IC, Cadman CJ, Dillingham MS, Lloyd RG, McGlynn P. Mol Cell. 2009 Nov 25;36(4):654-66.
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=== Week 5 (Feb 13): Mechanisms of DNA Mismatch Repair===
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== Replication and DNA Damage ==
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==== Suggested Topics ====
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# [http://www.ncbi.nlm.nih.gov/pubmed/19560424 Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae.] Azvolinsky A, Giresi PG, Lieb JD, Zakian VA. Mol Cell. 2009 Jun 26;34(6):722-34.
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* Mismatch Repair in Prokaryotes
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# [http://www.ncbi.nlm.nih.gov/pubmed/23352430 Identification of Early Replicating Fragile Sites that Contribute to Genome Instability.] Barlow JH, Faryabi RB, Callén E, Wong N, Malhowski A, Chen HT, Gutierrez-Cruz G, Sun HW, McKinnon P, Wright G, Casellas R, Robbiani DF, Staudt L, Fernandez-Capetillo O, Nussenzweig A. Cell. 2013 Jan 31;152(3):620-32.
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# [http://www.ncbi.nlm.nih.gov/pubmed/23178807 Coordinated control of replication and transcription by a SAPK protects genomic integrity.] Duch A, Felipe-Abrio I, Barroso S, Yaakov G, García-Rubio M, Aguilera A, de Nadal E, Posas F. Nature. 2013 Jan 3;493(7430):116-9.
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# [http://www.ncbi.nlm.nih.gov/pubmed/22607975 Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions.] Roberts SA, Sterling J, Thompson C, Harris S, Mav D, Shah R, Klimczak LJ, Kryukov GV, Malc E, Mieczkowski PA, Resnick MA, Gordenin DA. Mol Cell. 2012 May 25;46(4):424-35.
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# [http://www.ncbi.nlm.nih.gov/pubmed/22388737 Topoisomerase I poisoning results in PARP-mediated replication fork reversal.] Ray Chaudhuri A, Hashimoto Y, Herrador R, Neelsen KJ, Fachinetti D, Bermejo R, Cocito A, Costanzo V, Lopes M. Nat Struct Mol Biol. 2012 Mar 4;19(4):417-23.
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* Very short patch repair
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== DNA Mismatch Repair ==
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# [http://www.ncbi.nlm.nih.gov/pubmed/22139012 Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H.] Shen Y, Koh KD, Weiss B, Storici F. Nat Struct Mol Biol. 2011 Dec 4;19(1):98-104.
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# [http://www.ncbi.nlm.nih.gov/pubmed/22194578 Mismatch repair, but not heteroduplex rejection, is temporally coupled to DNA replication.] Hombauer H, Srivatsan A, Putnam CD, Kolodner RD. Science. 2011 Dec 23;334(6063):1713-6.
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# [http://www.ncbi.nlm.nih.gov/pubmed/23012240 Single-molecule imaging reveals target-search mechanisms during DNA mismatch repair.] Gorman J, Wang F, Redding S, Plys AJ, Fazio T, Wind S, Alani EE, Greene EC. Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):E3074-83.
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# [http://www.ncbi.nlm.nih.gov/pubmed/22118461 Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates.] Hombauer H, Campbell CS, Smith CE, Desai A, Kolodner RD. Cell. 2011 Nov 23;147(5):1040-53.
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# [http://www.ncbi.nlm.nih.gov/pubmed/21855803 The hMsh2-hMsh6 complex acts in concert with monoubiquitinated PCNA and Pol η in response to oxidative DNA damage in human cells.] Zlatanou A, Despras E, Braz-Petta T, Boubakour-Azzouz I, Pouvelle C, Stewart GS, Nakajima S, Yasui A, Ishchenko AA, Kannouche PL. Mol Cell. 2011 Aug 19;43(4):649-62.
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* Mismatch Repair in Eukaryotes
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== DNA Inter-strand Crosslink Repair ==
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** How is a Mismatch Recognized?
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# [http://www.ncbi.nlm.nih.gov/pubmed/22445484 BRCA1 functions independently of homologous recombination in DNA interstrand crosslink repair.] Bunting SF, Callén E, Kozak ML, Kim JM, Wong N, López-Contreras AJ, Ludwig T, Baer R, Faryabi RB, Malhowski A, Chen HT, Fernandez-Capetillo O, D'Andrea A, Nussenzweig A. Mol Cell. 2012 Apr 27;46(2):125-35.
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** How is a Mismatch Removed?
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# [http://www.ncbi.nlm.nih.gov/pubmed/19748364 Recruitment of fanconi anemia and breast cancer proteins to DNA damage sites is differentially governed by replication.] Shen X, Do H, Li Y, Chung WH, Tomasz M, de Winter JP, Xia B, Elledge SJ, Wang W, Li L. Mol Cell. 2009 Sep 11;35(5):716-23.
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=== Week 6 (Feb 20): Mismatch Repair, Adaptation & Diseases===
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== DNA Nucleotide Excision Repair ==
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==== Suggested Topics ====
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# [http://www.ncbi.nlm.nih.gov/pubmed/16497933 Structure of a DNA glycosylase searching for lesions.] Banerjee A, Santos WL, Verdine GL. Science. 2006 Feb 24;311(5764):1153-7.
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*Mismatch repair and adaptation
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** Mutagenesis in Bacteria
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** Mutagenesis in Eukaryotes
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* Meiotic-specific Roles of Mismatch Repair Proteins
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= Class Participants =
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[[User:Ilya J. Finkelstein]]
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*Diseases
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[[User:Alesha Stewart]]
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** Lynch Syndrome
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=== Week 7 (Feb 27): Mitochondrial DNA Damage ===
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[[User:Tanya_E_Raymond]]
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==== Suggested Topics ====
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* Structure of Mitochondrial DNA
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* Mechanisms of DNA Repair
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* Mitochondrial DNA repair and aging
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* Diseases Associated with Mitochondrial DNA Damage
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=== Week 8 (Mar 6): Special Topics Lecture ===
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[[User:Hala Ouzon-Shubeita]]
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=== Week 9 (Mar 20): Nucleotide Excision Repair ===
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=== Week 10 (Mar 27): Base Excision Repair ===
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[[User:Logan_R._Myler]]
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=== Week 11 (Apr 3): Damage Tolerance and Mutagenesis  — Prokaryotes ===
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=== Week 12 (Apr 10): Damage Tolerance and Mutagenesis — Eukaryotes ===
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=== Week 13 (Apr 17): Cell-cycle response to DNA damage ===
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=== Week 14 (Apr 24): p53 -- The Guardian of the Genome===
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=== Week 15 (May 1): Student-selected topic ===
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The above schedule and topics may be modified at the instructor's discretion. The class will be notified of any changes in class and on the OpenWetWare [http://openwetware.org/wiki/CH391L/2013 course web site].
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[[User:Taylor Pursell]]

Current revision


Contents

Molecular Mechanisms of Genome Maintenance

CH 391L (Spring 2013)

Unique # 52955

Wednesdays 2–5 PM, WEL 3.422, Professor: Finkelstein

Instructor: Dr. Ilya Finkelstein

Office Hours: by appointment only

Office: MBB 3.422AA

Syllabus

Index of All CH391/S2013 Pages

View Recent Changes to CH391/S2013 Pages

Introduction

Topics: This course will focus on current developments in understanding the molecular mechanisms of genome maintenance and cancerogenesis. A strong emphasis of the course will be to understand the methods and techniques that have enabled modern breakthroughs in understanding genome stability. The course will rely heavily on primary literature and class presentations.

Prerequisite: Biochemistry (CH339K and CH339L) or equivalent. Undergraduate students must have the instructor's permission to register for this course.

Course web page: The course web site on the OpenWetWare (OWW) Wiki will be used to complete assignments. Participants will be required to register an account on OWW and learn to edit this Wiki.

Assignments

A Wiki Editing Tutorial borrowed from (The Other) CH391L

Due January 23, 2013

  1. Alesha S: Spontaneous DNA breakage in single living Escherichia coli cells.
    1. First oral presentation
    2. Wiki article -- first draft
  2. Tanya R: Activation of DSB Processing Requires Phosphorylation of CtIP by ATR.
    1. First oral presentation
    2. Wiki article -- first draft
      1. CH391L/S2013 Tanya Raymond Jan 23 2013
  3. Hala Ouzon: Purified human BRCA2 stimulates RAD51-mediated recombination.
    1. First oral presentation
    2. Wiki article -- first draft
      1. CH391L/S2013 Hala Ouzon Jan 23 2013

Due January 30, 2013

  1. Alesha S: Spontaneous DNA breakage in single living Escherichia coli cells.
    1. Second oral presentation
    2. Wiki article -- final draft
     *CH391L/S2013 Alesha Stewart Jan 30 2013
  1. Tanya R: Activation of DSB Processing Requires Phosphorylation of CtIP by ATR.
    1. Second oral presentation
    2. Wiki article -- final draft
      1. CH391L/S2013 Tanya Raymond Jan 30 2013
  2. Hala Ouzon: Purified human BRCA2 stimulates RAD51-mediated recombination.
    1. Second oral presentation
    2. Wiki article -- final draft
      1. CH391L/S2013 Hala Ouzon Jan 30 2013
  3. Logan M: Activation of the cellular DNA damage Response in the Absence of DNA Lesions.
    1. First oral presentation
    2. Wiki article -- first draft
      1. CH391L/S2013 Logan R Myler Jan 30 2013

Due February 6, 2013

  1. Tanya R: Recombination-restarted replication makes inverted chromosome fusions at inverted repeats
    1. First Oral Presentation
    2. Wiki article -- first draft
      1. CH391L/S2013 Tanya Raymond Feb 6 2013
  2. Taylor Pursell: [1]
    1. First Oral Presentation
    2. Wiki Article First Draft: CH391L/S2013 Taylor Pursell Feb 6/Feb 13 2013

Due February 13, 2013

  1. Alesha S: Regulation of DNA repair by parkin
    1. First oral presentation
    2. Wiki article -- first draft: CH391L/S2013 Alesha Stewart Feb 13 2013
  2. Hala Ouzon: Linking RNA Polymerase Backtracking to Genome Instability in E. coli
    1. First oral presentation
    2. Wiki article -- first draft: Hala_Ouzon_Feb_13_2013
  3. Taylor Pursell: Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA.
    1. Second Oral Presentation
    2. Final Wiki Article: CH391L/S2013 Taylor Pursell Feb 13 2013
  4. Tanya R: Recombination-restarted replication makes inverted chromosome fusions at inverted repeats
    1. Second Oral Presentation
    2. Final Wiki Article CH391L/S2013 Tanya Raymond Feb 13 2013

Due February 20, 2013

  1. Logan M: The Fanconi anemia pathway promotes replication-dependent DNA interstrand cross-link repair.
    1. Wiki article -- first draft
  2. Alesha S: Regulation of DNA repair by parkin
    1. Second oral presentation
    2. Wiki article -- final draft: CH391L/S2013 Alesha Stewart Feb 13 2013

Due February 27, 2013

  1. Taylor P: Identification of Early Replicating Fragile Sites that Contribute to Genome Instability.
    1. Article:CH391L/S2013 Taylor Pursell Feb 27 2013
  2. Tanya R: Atl1 regulates choice between global genome repair and transcription-coupled repair of O(6)-alkylguanines
    1. First Oral presentation
    2. CH391L/S2013 Tanya Raymond February 27 2013
  3. Logan M: The Fanconi anemia pathway promotes replication-dependent DNA interstrand cross-link repair.
    1. Final Oral presentation
    2. CH391L/S2013 Logan Myler February 27 2013

Due March 20, 2013

  1. Hala Ouzon: Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair [2]
    1. First oral presentation
    2. Wiki article -- first draft: CH391L/S2013 Hala Ouzon March 20 2013
  2. Alesha S: Structure of a DNA glycosylase searching for lesions.
    1. First oral presentation
    2. Wiki article -- first draft: CH391L/S2013 Alesha Stewart Mar 20 2013
  3. Taylor P: Identification of Early Replicating Fragile Sites that Contribute to Genome Instability.
    1. Final Article:CH391L/S2013 Taylor Pursell March 20 2013
  4. Tanya R: Atl1 regulates choice between global genome repair and transcription-coupled repair of O(6)-alkylguanines
    1. Wiki article -- final draft: CH391L/S2013 Tanya Raymond Mar 20 2013

Due March 27, 2013

  1. Logan M: Single-molecule imaging reveals target-search mechanisms during DNA mismatch repair.
    1. First Oral presentation
    2. First Draft -- CH391L/S2013 Logan Myler March 27 2013
  2. Alesha S: Structure of a DNA glycosylase searching for lesions.
    1. Second oral presentation
    2. Wiki article -- Final draft: CH391L/S2013 Alesha Stewart Mar 27 2013
  3. Hala Ouzon: Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair [3]
    1. First oral presentation
    2. Wiki article -- final draft: CH391L/S2013 Hala Ouzon March 20 2013

Due April 3, 2013

  1. Taylor: Heteroplasmic mitochondrial DNA mutations in normal and tumour cells
    1. First Oral Presentation
    2. First Draft: CH391L/S2013 Taylor Pursell April 3 2013

Due April 10, 2013

  1. Alesha S: p53 promotes repair of heterochromatin DNA by regulating JMJD2b and SUV39H1 expression
    1. First oral presentation
    2. Wiki article -- first draft: CH391L/S2013 Alesha Stewart Apr 10 2013
  2. Hala Ouzon: Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta [4]
    1. First oral presentation
    2. Wiki article -- first draft: CH391L/S2013 Hala Ouzon April 10 2013
  3. Taylor: Heteroplasmic mitochondrial DNA mutations in normal and tumour cells
    1. Second Oral Presentation
    2. Final Draft: CH391L/S2013 Taylor Pursell April 10 2013
  4. Tanya R: eRNAs are required for p53-dependent enhancer activity and gene transcription
    1. First oral presentation
    2. Wiki article CH391L/S2013 Tanya Raymond April 10 2013

Due April 17, 2013

  1. Alesha S: p53 promotes repair of heterochromatin DNA by regulating JMJD2b and SUV39H1 expression
    1. Second oral presentation
    2. Wiki article -- Final draft: CH391L/S2013 Alesha Stewart Apr 17 2013
  2. Hala Ouzon: Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta [5]
    1. First oral presentation
    2. Wiki article -- final draft: CH391L/S2013 Hala Ouzon April 17 2013
  3. Tanya R:
    1. Second oral presentation
    2. Final wiki draft CH391L/S2013 Tanya Raymond April 17 2013

Class Assignments

CH391L/S2013/SuggestedTopics

Suggested Reading

A Brief Overview of Cancer Biology

  1. The hallmarks of cancer. Hanahan D, Weinberg RA. Cell. 2000 Jan 7;100(1):57-70.
  2. Hallmarks of cancer: the next generation. Hanahan D, Weinberg RA. Cell. 2011 Mar 4;144(5):646-74.

DNA Double Strand Break (DSB) Repair

  1. Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae. Niu H, Chung WH, Zhu Z, Kwon Y, Zhao W, Chi P, Prakash R, Seong C, Liu D, Lu L, Ira G, Sung P. Nature. 2010 Sep 2;467(7311):108-11.
  2. Spontaneous DNA breakage in single living Escherichia coli cells. Pennington JM, Rosenberg SM. Nat Genet. 2007 Jun;39(6):797-802. Epub 2007 May 27.
  3. Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells. Pierce AJ, Hu P, Han M, Ellis N, Jasin M. Genes Dev. 2001 Dec 15;15(24):3237-42.
  4. Rad51 paralogues Rad55-Rad57 balance the antirecombinase Srs2 in Rad51 filament formation. Liu J, Renault L, Veaute X, Fabre F, Stahlberg H, Heyer WD. Nature. 2011 Oct 23;479(7372):245-8.
  5. Purified human BRCA2 stimulates RAD51-mediated recombination. Jensen RB, Carreira A, Kowalczykowski SC. Nature. 2010 Oct 7;467(7316):678-83.
  6. Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA. Bell JC, Plank JL, Dombrowski CC, Kowalczykowski SC. Nature. 2012 Nov 8;491(7423):274-8.
  7. Identification of a DNA nonhomologous end-joining complex in bacteria. Weller GR, Kysela B, Roy R, Tonkin LM, Scanlan E, Della M, Devine SK, Day JP, Wilkinson A, d'Adda di Fagagna F, Devine KM, Bowater RP, Jeggo PA, Jackson SP, Doherty AJ. Science. 2002 Sep 6;297(5587):1686-9.

DNA Replication and Genome Maintenance

  1. Linking RNA polymerase backtracking to genome instability in E. coli. Dutta D, Shatalin K, Epshtein V, Gottesman ME, Nudler E. Cell. 2011 Aug 19;146(4):533-43.
  2. Identification of Early Replicating Fragile Sites that Contribute to Genome Instability. Barlow JH, Faryabi RB, Callén E, Wong N, Malhowski A, Chen HT, Gutierrez-Cruz G, Sun HW, McKinnon P, Wright G, Casellas R, Robbiani DF, Staudt L, Fernandez-Capetillo O, Nussenzweig A. Cell. 2013 Jan 22. pii: S0092-8674(13)00008-1.
  3. The structure-specific endonuclease Mus81 contributes to replication restart by generating double-strand DNA breaks. Hanada K, Budzowska M, Davies SL, van Drunen E, Onizawa H, Beverloo HB, Maas A, Essers J, Hickson ID, Kanaar R. Nat Struct Mol Biol. 2007 Nov;14(11):1096-104. Epub 2007 Oct 14.
  4. Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Azvolinsky A, Giresi PG, Lieb JD, Zakian VA. Mol Cell. 2009 Jun 26;34(6):722-34.
  5. Rep provides a second motor at the replisome to promote duplication of protein-bound DNA. Guy CP, Atkinson J, Gupta MK, Mahdi AA, Gwynn EJ, Rudolph CJ, Moon PB, van Knippenberg IC, Cadman CJ, Dillingham MS, Lloyd RG, McGlynn P. Mol Cell. 2009 Nov 25;36(4):654-66.

Replication and DNA Damage

  1. Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Azvolinsky A, Giresi PG, Lieb JD, Zakian VA. Mol Cell. 2009 Jun 26;34(6):722-34.
  2. Identification of Early Replicating Fragile Sites that Contribute to Genome Instability. Barlow JH, Faryabi RB, Callén E, Wong N, Malhowski A, Chen HT, Gutierrez-Cruz G, Sun HW, McKinnon P, Wright G, Casellas R, Robbiani DF, Staudt L, Fernandez-Capetillo O, Nussenzweig A. Cell. 2013 Jan 31;152(3):620-32.
  3. Coordinated control of replication and transcription by a SAPK protects genomic integrity. Duch A, Felipe-Abrio I, Barroso S, Yaakov G, García-Rubio M, Aguilera A, de Nadal E, Posas F. Nature. 2013 Jan 3;493(7430):116-9.
  4. Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. Roberts SA, Sterling J, Thompson C, Harris S, Mav D, Shah R, Klimczak LJ, Kryukov GV, Malc E, Mieczkowski PA, Resnick MA, Gordenin DA. Mol Cell. 2012 May 25;46(4):424-35.
  5. Topoisomerase I poisoning results in PARP-mediated replication fork reversal. Ray Chaudhuri A, Hashimoto Y, Herrador R, Neelsen KJ, Fachinetti D, Bermejo R, Cocito A, Costanzo V, Lopes M. Nat Struct Mol Biol. 2012 Mar 4;19(4):417-23.

DNA Mismatch Repair

  1. Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H. Shen Y, Koh KD, Weiss B, Storici F. Nat Struct Mol Biol. 2011 Dec 4;19(1):98-104.
  2. Mismatch repair, but not heteroduplex rejection, is temporally coupled to DNA replication. Hombauer H, Srivatsan A, Putnam CD, Kolodner RD. Science. 2011 Dec 23;334(6063):1713-6.
  3. Single-molecule imaging reveals target-search mechanisms during DNA mismatch repair. Gorman J, Wang F, Redding S, Plys AJ, Fazio T, Wind S, Alani EE, Greene EC. Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):E3074-83.
  4. Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates. Hombauer H, Campbell CS, Smith CE, Desai A, Kolodner RD. Cell. 2011 Nov 23;147(5):1040-53.
  5. The hMsh2-hMsh6 complex acts in concert with monoubiquitinated PCNA and Pol η in response to oxidative DNA damage in human cells. Zlatanou A, Despras E, Braz-Petta T, Boubakour-Azzouz I, Pouvelle C, Stewart GS, Nakajima S, Yasui A, Ishchenko AA, Kannouche PL. Mol Cell. 2011 Aug 19;43(4):649-62.

DNA Inter-strand Crosslink Repair

  1. BRCA1 functions independently of homologous recombination in DNA interstrand crosslink repair. Bunting SF, Callén E, Kozak ML, Kim JM, Wong N, López-Contreras AJ, Ludwig T, Baer R, Faryabi RB, Malhowski A, Chen HT, Fernandez-Capetillo O, D'Andrea A, Nussenzweig A. Mol Cell. 2012 Apr 27;46(2):125-35.
  2. Recruitment of fanconi anemia and breast cancer proteins to DNA damage sites is differentially governed by replication. Shen X, Do H, Li Y, Chung WH, Tomasz M, de Winter JP, Xia B, Elledge SJ, Wang W, Li L. Mol Cell. 2009 Sep 11;35(5):716-23.

DNA Nucleotide Excision Repair

  1. Structure of a DNA glycosylase searching for lesions. Banerjee A, Santos WL, Verdine GL. Science. 2006 Feb 24;311(5764):1153-7.

Class Participants

User:Ilya J. Finkelstein

User:Alesha Stewart

User:Tanya_E_Raymond

User:Hala Ouzon-Shubeita

User:Logan_R._Myler

User:Taylor Pursell

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