Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2013/Group 82H

Group 82H

This is the Wikipedia page for 410.602 Molecular Biology, Spring, 2013, group 82H. This group will be working on the article XRCC4.

Use the talk page here to collaborate as a group, when learning to use and navigate Wikipedia, assessing articles, or for any other topic.

Use this page (not the talk page) for article assessments; rationale for selecting an article; etc.

Please create a new section here for each of those assignments.

Initial article assessments from jgould1400

Article Assessment for "Missense Mutation"

This article will need a lot of work in order to achieve “GA” status. In the first place, this article is useful to very few readers and has obvious problems. There are few citations to reliable sources and there is a need for good in-line citations. More research is needed; the content is not complete enough to satisfy serious researchers. The article also needs a lot of work in terms of grammar and good writing style. In addition, I think an illustration or figure or two would be very helpful. Roth JR, Andersson DI (June 2004). "Amplification-mutagenesis--how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation". Res. Microbiol. 155 (5): 342–51. doi:10.1016/j.resmic.2004.01.016. PMID 15207866. Sigal A, Rotter V (December 2000). "Oncogenic mutations of the p53 tumor suppressor: the demons of the guardian of the genome". Cancer Res. 60 (24): 6788–93. PMID 11156366. Yang Z, Nie S, Zhu H, et al. (January 2013). "Association of p53 Arg72Pro polymorphism with bladder cancer: a meta-analysis". Gene. 512 (2): 408–13. doi:10.1016/j.gene.2012.09.085. PMID 23073555.

Article Assessment for "Point Mutation"

This article is already very good in many respects, but could still use some improvement to achieve “GA” status. I think it could use some additional discussion of diseases caused by a point mutation (including of course citations to reliable sources and good in-line citations). More research is still needed; the content is still not complete enough to satisfy serious researchers. In addition, the writing style could be improved and additional illustrations or figures could be added. Quiñones-Soto S, Roth JR (September 2011). "Effect of growth under selection on appearance of chromosomal mutations in Salmonella enterica". Genetics. 189 (1): 37–53. doi:10.1534/genetics.111.130187. PMC 3176110. PMID 21705757. Roth JR, Andersson DI (June 2004). "Amplification-mutagenesis--how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation". Res. Microbiol. 155 (5): 342–51. doi:10.1016/j.resmic.2004.01.016. PMID 15207866. Sigal A, Rotter V (December 2000). "Oncogenic mutations of the p53 tumor suppressor: the demons of the guardian of the genome". Cancer Res. 60 (24): 6788–93. PMID 11156366. Yang Z, Nie S, Zhu H, et al. (January 2013). "Association of p53 Arg72Pro polymorphism with bladder cancer: a meta-analysis". Gene. 512 (2): 408–13. doi:10.1016/j.gene.2012.09.085. PMID 23073555.

Article Assessment for "XRCC4"

This topic looks very interesting and could be a very good article to work on. Jgould1400 (talk) 07:08, 5 March 2013 (UTC)[reply]

Initial Article Assessments from Cdunca12

Article Assessment for XRCC4

The Wikipedia article for XRCC4 is still only a stub article. It contains a very simple lead section and a few other main sections including the function, pathology, interactions, and mechanism. Each section only covers the most basic scientific background with much of the most important content missing. It has two images of the protein but an image of the mechanism for non-homologous end joining with other proteins involved should also be included. The information from section to section is not cohesive and the article was most likely written as a starting off point and a way to encourage other editors to contribute. Based on Unit 5's "Style Guide and for Gene and Protein Articles", it should include more background information in the lead section instead of just one sentence. It should include a Gene and Protein section with fundamental information such as the chromosomal location of the gene, exons, protein splice variants and structure and domains (images), the specific mechanism of the protein and other proteins involved in the pathway with a clear schematic, its location in the organelles in the cell and how it may be visualized, known mutations and diseases they cause, experimental techniques currently being used to study the protein, and to make it really complete, a history section on who discovered the protein. So far, there are no contributions in the "Talk" tab of the article. Taking the above parameters into consideration combining with citing excellent peer-reviewed references in an accurate and original way should bring this article into a GA level article. This topic would be an excellent choice for our article because it is something that is covered in the textbook for our course and is very relevant to the DNA repair pathway, essential in molecular biology. A few sources that can be used to develop XRCC4 article include the following:

1. Cottarel, J; et al. (2013). "A non-catalytic function of the ligation complex during non homologous end joining". Journal of Cell Biology 200 (2): 173 - 186. http://www.ncbi.nlm.nih.gov/pubmed/23345432 2. Watson, James D., et al. (2008). Molecular Biology of the Gene. 6th Edition. New York: Cold Spring Harbor Laboratory Press. pp. 275 - 278. 3. Yurchenko, Vyacheslav, et al. (2006). "SUMO Modification of Human XRCC4 Regulates Its Localization and Function in DNA Double-Strand Break Repair". Molecular Cell Biology 26(5): 1786 - 1794. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1430232/

Article Assessment for Nick (DNA)

The Wikipedia article for Nick (DNA) is just the beginning of a stub article and contains only a lead section with no contributions. If I were to develop this article, I would include background information on what the structure of a nick looks like within the DNA backbone, how nicks are introduced through cleavage by topoisomerases to aid in the relaxation of DNA for replication by changing its invariant linking number, how free radicals damage DNA by creating nicks and the accumulation of these DNA lesions can result in the addition of mutations which over time can lead to cancer. A description of the base excision repair (BER) pathway and how it repairs nicks including descriptions of other proteins involved. I would also include how the generation of nicks in DNA can be a very useful experimental technique in molecular biology. For example, a nick can be introduced between two separate dsDNA molecules by ligating one dsDNA that contains a 5'-phophate on one end to another dsDNA molecule that does not have the 5'-phosphate. The first DNA molecule that has the 5'-phosphate can create a phosphodiester bond with the 3'-OH group of the second molecule but because there is no 5'-phosphate in the second molecule, a nick is generated. Nick translation can subsequently be performed to "move" the nick downstream of its original site using E. coli DNA polymerase I. This can be useful for creating different length DNA for further manipulation depending on the purpose. Here are a couple of sources for this topic:

1. Adey, Andrew, et al. (2010). "Rapid, low input, low bias, construction of shotgun fragment libraries by high-density in vitro transposition". Genome Biology 11:R119. http://genomebiology.com/2010/11/12/R119 2. Bohr, Vilhelm A. (2002). "Repair of oxidative DNA damage in nuclear and mitochondrial DNA, and some changes with aging in mammalian cells". Laboratory of Molecular Gerontology. 32(9): 804 - 812. http://www.sciencedirect.com/science/article/pii/S0891584902007876 Cdunca12 06:08, 7 March 2013 (UTC)

Article Selection Rationale

Group 82H has decided to improve the article for XRCC4. As indicated in the current Wikipedia stub, as well as in our Watson text book, XRCC4 is a DNA repair protein encoded by the XRCC4 gene in humans; and in particular, the XRCC4 protein functions in conjunction with DNA ligase IV and the DNA-dependent protein kinase in the repair of DNA double-strand break by non-homologous end joining and the completion of V(D)J recombination events. In addition to the fact that XRCC4 is covered in our textbook, a review of the scientific literature reveals an abundance of very recent articles discussing the importance of XRCC4 and reporting on current research in this area. This is in fact, a very exciting time for XRCC4, as a relatively recent study by Hammel, et al., 2011, revealed the crystal structure of the XLF-XRCC4 complex. Specifically, a "key lock" interaction and hydrogen bonds that holds both proteins together to maintain the complex required for ligation of the DSB, characterization of the C-terminal domain shows the key structures responsible for DNA binding in a concentration-dependent way, and another DNA binding region at the XLF-XRCC4 interface. These findings are extremely critical in the development of new therapeutics as they can serve as target sites to ensure that the "proper alignment of damaged DNA for ligation by DNA Ligase IV is successfully completed. Other recent research topics also include examination of the potential linkage between XRCC4 and cancers such as bladder cancer and hepatitis B-associated hepatocellular carcinoma.

With regard to specific ideas for improving the XRCC4 Wikipedia article, the current stub has minimal text (less than 280 words), and despite the abundance of recent scientific publications that we found (many with publication dates within the past several months), all of the references listed in the current stub — except for two― are over a decade old; and the two “newer” articles are from 2007 and 2008. With regard to specific topics for us to research and include in the improved XRCC4 article, we note that current stub has no background section, no explanation as to how double-stranded breaks can occur, and limited explanation of the pathway for DNA repair for this type of damage. We could also cover topics such as the XRCC4 gene, XRCC4 protein structure, other proteins working in concert with XRCC4, schematics of the mechanism, and descriptions as to how mutations occurring in different splice variants of this protein (and DNA sequences associated with these mutations) are the basis of specific diseases. We could also cover experimental techniques used to determine mutations, protein homology, and we could include substantial coverage on the recent publications on XRCC4.

Potential References

1. Andres, Sara N., et al. (2012). "A human XRCC4-XLF complex bridges DNA". Nucleic Acids Research 40(4): 1868 - 1878. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287209/ 2. Cottarel, J; et al. (2013). "A non-catalytic function of the ligation complex during non homologous end joining". Journal of Cell Biology 200 (2): 173 - 186. http://www.ncbi.nlm.nih.gov/pubmed/23345432 3. Hamel, Michal, et al. (2011). "Crystal Structure of XLF-XRCC4 Complex Provides Model for Double-Strand Break Repair". Journal of Biological Chemistry 286: 32638 - 32650. http://www.jbc.org/content/286/37/e99966.full 4. Watson, James D., et al. (2008). Molecular Biology of the Gene. 6th Edition. New York: Cold Spring Harbor Laboratory Press. pp. 275 - 278. 5. Yurchenko, Vyacheslav, et al. (2006). "SUMO Modification of Human XRCC4 Regulates Its Localization and Function in DNA Double-Strand Break Repair". Molecular Cell Biology 26(5): 1786 - 1794. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1430232/

• Wu CN, Liang SY, Tsai CW, Bau DT, The role of XRCC4 in carcinogenesis and anticancer drug discovery, Recent Pat Anticancer Drug Discov. 2008 Nov;3(3):209-19. Review. PMID 18991789.

•• Important Review for role of XRCC4 in cancer

• Dahm K, Role and regulation of human XRCC4-like factor/cernunnos, J Cell Biochem. 2008 Aug 1;104(5):1534-40. doi: 10.1002/jcb.21726. Review. PMID 18335491

•• Important Review for role of XLF

• Li Z, Alt FW, Identification of the XRCC4 gene: complementation of the DSBR and V(D)J recombination defects of XR-1 cells, Curr Top Microbiol Immunol. 1996;217:143-50. Review. PMID 8787623

•• Important Review for the XRCC4 gene

• Wu et al., Non-homologous end-joining partners in a helical dance: structural studies of XLF-XRCC4 interactions, Biochem Soc Trans. 2011 Oct;39(5):1387-92, suppl 2 p following 1392. doi: 10.1042/BST0391387 PMID 21936820.

•• Individual crystal structures show that the dimeric proteins XRCC4 and XLF are homologues with protomers containing head domains and helical coiled-coil tails related by approximate two-fold symmetry

•• Biochemical, mutagenesis, biophysical and structural studies have identified the regions of interaction between the two proteins and suggested models for the XLF-XRCC4 complex.

• Jung et al., Polymorphisms of DNA repair genes in Korean hepatocellular carcinoma patients with chronic hepatitis B: possible implications on survival, J Hepatol. 2012 Sep;57(3):621-7. doi: 10.1016/j. jhep.2012.04.039. Epub 2012 May 29, PMID 22659345

•• Conclusion: Polymorphisms of DNA repair genes play a potential role in the development, progression, and survival of Korean HCC patients with chronic HBV infection.

• Mahaney et al., XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair, Biochem Cell Biol. 2013 Feb;91(1):31-41. doi: 10.1139/bcb-2012-0058. Epub 2013 Feb 5. PMID 23442139.

• Zhang et al., Effects of expression level of DNA repair-related genes involved in the NHEJ pathway on radiation-induced cognitive impairment, J Radiat Res. 2013 Mar 1;54(2):235-42. doi: 10.1093/jrr/rrs095. Epub 2012 Nov 7. PMID 23135157

• Zhou LP, Luan H, Dong XH, Jin GJ, Ma DL, Shang H, Association of functional polymorphisms of the XRCC4 gene with the risk of breast cancer: a meta-analysis, Asian Pac J Cancer Prev. 2012;13(7):3431-6. PMID 22994773

• Zheng Z, Ng WL, Zhang X, Olson JJ, Hao C, Curran WJ, Wang Y., RNAi-mediated targeting of noncoding and coding sequences in DNA repair gene messages efficiently radiosensitizes human tumor cells, Cancer Res. 2012 Mar 1;72(5):1221-8. doi: 10.1158/0008-5472.CAN-11-2785. Epub 2012 Jan 11. PMID 22237628.

• Mandal RK, Singh V, Kapoor R, Mittal RD, Do polymorphisms in XRCC4 influence prostate cancer susceptibility in North Indian population?, Biomarkers. 2011 May;16(3):236-42. doi: 10.3109/1354750X.2010.547599. PMID 21506695.

•• XRCC4 and bladder cancer.

• Mittal RD, Gangwar R, Mandal RK, Srivastava P, Ahirwar DK, Gene variants of XRCC4 and XRCC3 and their association with risk for urothelial bladder cancer, Mol Biol Rep. 2012 Feb;39(2):1667-75. doi: 10.1007/s11033-011-0906-z. Epub 2011 May 27. PMID 21617942

•• linking XRCC4 to bladder cancer. Jgould1400 (talk) 06:16, 12 March 2013 (UTC)[reply]

Q13426 (XRCC4_Human). UniProt. Last modified 3/6/13.

-Contains gene and protein names, protein composition and subunits (motif domains), amino acid modifications, isoforms. http://www.uniprot.org/uniprot/Q13426

Junop, Murray S., et al., (2000), “Crystal structure of the Xrcc4 DNA repair protein and implications for end joining”, The EMBO Journal 19: 5962 – 5970. PMID 11080143.

http://www.nature.com/emboj/journal/v19/n22/abs/7593410a.html -Findings of crystal structure of functional fragment of protein composing of a dumb-bell-like tetramer, N-terminal domain are globular and is a potential DNA binding domain, its C-terminal stalk may serve a role in interacting with ligase IV; all required for effective DNA repair in NHEJ.

Hammel, M., et al., (2011), “XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair”, J Biol Chem 286(37): 32638-50. PMID 21775435. http://www.ncbi.nlm.nih.gov/pubmed/21775435

Li, Y., et al., (2008), “Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ”, EMBO J 27(1):290-300. PMID 18046455.

http://www.ncbi.nlm.nih.gov/pubmed/18046455 -Authors use various biochemical and biophysical techniques to elucidate the functional motif of Cer-XLF as a short, four helical bundle and a C-terminal helical structure inserted between its coiled-coil and head domain. They also predict the stoichiometric ratios of the XRCC4:XLF:Ligase IV complex.

Wu, Pei-Yu, et al., (2009), “Structural and Functional Interaction between the Human DNA Repair Proteins DNA Ligase IV and XRCC4”, Molecular and Cellular Biology 29(11):3163. PMID 19332554.

http://mcb.asm.org/content/29/11/3163.full.pdf+html -Authors characterized specific protein domains and the structural and functional interactions between XRCC4, LigIV and Cernunnos XRCC4-like Factor (Cer-XLF) in the complex required for ligation of DSB during NHEJ. Found the central domain of XRCC4 contains a helix-loop-helix motif that is the binding interface for the inter-BRCT linker at the C-terminus of LigIV.

Mari, PO, et al., (2006), “Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4”, Proc Natl Acad Sci USA 103(49):18597-602. PMID 17124166.

http://www.pnas.org/content/103/49/18597.full.pdf+html -Generation of DSB using near IR laser pulses demonstrate accumulation of NHEJ proteins, XRCC4/ligase IV in the presence of Ku70/80 in irradiated regions in vivo. Authors elucidate the function and assembly of the complex involving these proteins. Cdunca12 18:22, 17 March 2013 (UTC)

Unit 9 Progress Report

Added six new subsections under the "Pathology" Section: (1) Association of XRCC4 Polymorphisms with Risk of Cancer Susceptibility, (2) Possible Association of XRCC4 Polymorphisms with Pathologies Outside of Oncology, (3) Role of XRCC4 in V(D)J Rearrangement, (4) Potential Use of XRCC4 as a Biomarker for Cancer Screening and Diagnosis, (5) Radiosensitization of Tumor Cells, (6) Potential Role of XRCC4 in the Future Development of Therapeutics. At the moment, the subsection on cancer susceptibility is the most developed. Within the pathology section, I think that the subsections on the "role of XRCC4 in V(D)J rearrangement" and "radiosensitization" have the most potential in terms of further enrichment over the next couple of weeks. Jgould1400 (talk) 03:32, 5 April 2013 (UTC)[reply]

Additions and insertions from last night spanned 10 subsections. Numerous references were added to the footnotes, and some of the "old content" (pre-JHU) was corrected or deleted. Jgould1400 (talk) 10:55, 5 April 2013 (UTC)[reply]

Added a new lead section that includes the following: 1) Introduction to DNA damage and causes; 2) Background on DSB and why they are deleterious if not repaired; 3) Two methods for DSB repair for homologous recombination and NHEJ; 4) Mechanism for NHEJ including all proteins involved, especially importance of XRCC4 in role for NHEJ. Included all references cited from journal articles from Pubmed and textbooks. Created links for all important and relevant words related to molecular biology. Created a new section, "Structure". Uploaded image for the mechanism of NHEJ. Will be adding section on "Mechanism" for Unit 11. Cdunca12 07:59, 8 April 2013 (UTC)

Progress Report for Units 11-12

A very substantial amount of new material was added since our last progress report, including the new section on "History and Identification of the XRCC4 Gene", the new section on "Anti-XRCC4 Antibodies", and the new subsection on "Endometriosis Susceptibility" that was added to the Pathology section; and in addition, information and content was consolidated in several locations and many references were added. We have also considered the various comments we received and have made revisions and additions where appropriate. Jgould1400 (talk) 03:40, 26 April 2013 (UTC)[reply]

Progress Report for Units 13-14 (Final Project Report)

Revised/supplemented several sections/subsections; added text and several references; searched for more information and to see if we’ve missed anything significant; and corresponded with reviewers.Jgould1400 (talk) 09:39, 9 May 2013 (UTC). Substantial additions and revisions, as well as the addition of some subsections and an image, were carried out by my teammate. OA Keilana told me the article looks great. Jgould1400 (talk) 02:13, 10 May 2013 (UTC)[reply]