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BU Bioinformatics Program Newsletter BU Bioinformatics Program Newsletter Issue #21 November 30th, 2009 Quotes of the week: “If terminally differentiated cells that lack non‐CpG methylation are engineered to become pluripotent stem cells, they regain this unusual modification...,”– Schübeler, D. (2009), “Methylation Matters,” News & Views, Nature 462, 296‐297 (19 November 2009). See the paper by Lister, R., et al. reviewed below (under “NOTEWORTHY NEW PAPERS AND BOOKS.”) “I have found articles like these to be a nice source of advising in my graduate career.” – Eric Franzosa, who suggested that bioInfoBeat describe the “Ten Simple Rules” collection at PLoS Biology’s website (see “NOTEWORTHY NEW PAPERS AND BOOKS” below.) N.B. (note well): Back issues of bioInfoBeat are now on the web. Go to http://www.bu.edu/bioinformatics/news/newsletter‐archives/ to view them. ********** CALENDAR OF EVENTS This Week and Next . Monday, November 30, 2009 Classes Resume Chemistry Colloquia Seminar Series ‐ Professor Robert Doyle, Syracuse University Title: ʺProteins for metal transport and metals for Protein transport: Oral insulin delivery and Iron uptake in pathogenic bacteriaʺ, 4:00 p.m., LSE B01, 24 Cummington Street Wednesday, December 2, 2009 Bioinformatics Student Seminar – 4:00 John Farrell, Title: “Unraveling HLA Disease Associations from Genome Scan Data,” 4:45 Andy McMurry, Title: TBA. LSE 103, 24 Cummington Street Thursday, December 3, 2009 Systems Biology Free Lunch Seminar – Professor Ron Weiss, MIT, Title: “Synthetic Biology: from Modules to Systems.” Lunch 12:15 LSE lobby, talk 12:45 p.m. 103 LSE, 24 Cummington Street Monday, December 7, 2009 Biology Department Darwin Bicentennial Lecture – Pardis Sabeti, Harvard FAS Center for Systems Biology. Host: Chris Schneider. Title: TBA. LSE B01, 24 Cummington Street 12:00 p.m. Chemistry Colloquia Seminar Series ‐ Professor Katherine J. Franz, Duke University Host: Professor Sean Elliott,. Title: ʺManipulating Metal‐Catalyzed Oxidative Stress with Triggerable Chelating Agentsʺ, 4:00 p.m., LSE B01, 24 Cummington Street Wednesday, December 9, 2009 BIOINFORMATICS PROGRAM HOLIDAY PARTY! – “The Castle” (225 Bay State Road), 3‐5 p.m. Friday, December 11, 2009 Last Day of Classes For information about additional seminars, colloquia, etc. in the Boston area of interest to molecular life scientists, consult http://www.whitehead.mit.edu/cgi‐bin/view/webevent.cgi?calID=918&cmd=startup RECENT PUBLICATIONS BY BIOINFORMATICS PROGRAM STUDENTS AND FACULTY Please send full bibliographic citations for any papers you have published so far in 2009! Send these to [email protected] AND [email protected]. NOTEWORTHY NEW PAPERS AND BOOKS Lister, R., Pelizzola, M., Dowen, R.H., Hawkins, R.D., Hon, G., Tonti‐Filippini, J., Nery, J.R., Lee, L., Ye, Z., Ngo, Q‐M., Edsall, L., Antosiewicz‐Bourget, J., Stewart, R., Ruotti, V. Millar, A.H., Thomson, J.A., Ren, B. & Ecker, J.R. (2009) “Human DNA Methylomes at Base Resolution Show Widespreat Epigenomic Differences,” Nature 462, 315‐322. Relying on the chemical treatment of DNA with bisulfite – which converts non‐ methylated C bases to Us, but has no effect on 5‐methylcytosine (5‐MeC) – followed by massive, high‐throughput sequencing, Lister et al. compared the positions and extent of C‐methylation in two human cell lines, differentiated fetal lung fibroblasts and human embryonic stem cells. This tour‐de‐force involved approximately 90 gigabases of sequence from each cell line with an average read depth of 14‐15 per strand. The sequencing covered 86% of both strands of the reference human genome with at least one sequence read and accounted for 94% of all the cytosines in the genome. The stem cells had 62 million methyl‐C residues and the fibroblasts approximately 45 million. Note that demethylation corresponds to the differentiation process rather than the (naïvely expected) other way around. Remarkably, when the fibroblasts were engineered to become induced pluripotent stem cells, they regained their initial methylation state (insofar as limited data analyzed by these authors goes). Most methyl groups in DNA occur in the dinucleotide sequence CpG, and that was nicely confirmed in this study. However, in the stem cells 25% of the MeC residues occurred outside the CpG sequences. The detailed analysis in this paper reveals many previously unsuspected features of methylation, and the correlation with state of differentiation makes it seem likely that there is some truth to a previous suggestion that methylation functions as a genomic “memory module” that indicates the cell’s identity and state of differentiation. If so, we have much reason to get serious about sorting out the properties of different “methylomes.” It also seems like a good idea for methylomologists (genomics seems to have unlimited potential for ever‐more unaesthetic neologisms!) to consider working on a model organism with a reasonably small genome in order to sort out the nuances of this additional genetic code. Obviously the stakes are high in this game since it’s clear both gene therapy and successful synthetic biology on higher eukaryotes will depend upon understanding and controlling the positions of millions of tiny –CH3 groups... Ten Simple Rules Collection. (Suggested by Eric Franzosa.) (http://collections.plos.org/ploscompbiol/tensimplerules.php) Conceived and organized by Philip E. Bourne, Editor‐in‐Chief of PLoS Computational Biology, this very pragmatic set of essays – with engaging titles like “Ten Simple Rules for Graduate Students,” “Ten Simple Rules for Getting Grants,” and “Ten Simple Rules for Choosing between Industry and Academia” – has a down‐to‐earth appeal that should cross over the lines from graduate student to post‐doc to faculty member/group leader. If nothing else, they will assure the reader that he/she is not alone in some of the challenges he/she faces – and the solutions proposed may work out to have definite utility! These are definitely worth browsing. Every issue of the newsletter will highlight one or more new papers (or books) that should be of general interest and provide awareness of significant new developments in the broad field of bioinformatics and integrative/systems biology. Please send suggestions for such items to [email protected]. USEFUL BBMB WEBSITES (BBMB = Bioinformatics, Biochemistry & Molecular Biology) http://f1000.com – To quote from the introduction to this website, “Faculty of 1000 Biology and Medicine are authoritative online services in which over 4,500 leading researchers and clinicians share their expert opinions by highlighting and evaluating the most important articles in biology and medicine.” So if bioInfoBeat hasn’t given you enough hot articles relevant to your interests, try Faculty of 1000. Two members of our Bioinformatics faculty, by the way, are also members of the Faculty of 1000: Professor Tom Tullius and Professor Karen Allen. Bookmark this site! Every issue of the newsletter will highlight one or more high‐quality websites that should be of general interest and provide awareness of significant new developments in the broad field of bioinformatics and integrative/systems biology. Please send suggestions for such items to [email protected]. MEETING REPORTS? Have you attended a meeting (or more than one) in 2009, or do you have plans to do so? bioInfoBeat can publish a brief summary of interesting new results and ideas. Just send the highlights in a paragraph or two to Johanna Squillacioti Janatsch ([email protected]). Note that students who have received travel support for attending a meeting and presenting a talk or poster must submit a brief report on the scientific highlights they encountered. ALUMNI CORNER Have you just published a paper? Gotten a new job? Gotten a grant? Started a company? Are you raising one or more children in your spare time...? Moved to Europe, China...? Judging from the conversations during coffee breaks, in the elevator, at lunch and dinner during the 10th Anniversary Symposium, your fellow alumni would love to know “what’s up” with you. Please send your information along to [email protected] AND [email protected]. Photos are also welcome! Oh, and one more thing, if you meet promising candidates for admission to the Program, please send them our way! As a suggestion from Adrian Heilbut thereʹs a Facebook group for connecting people in the Bioinformatics program, so for all who have not joined yet and would like to here is the link: http://www.facebook.com/home.php/group.php?gid=2363206546 BIOINFORMATICS BRAIN‐TEASER (#1) What is the difference between epistatic and epigenomic? Define each term carefully as it is currently used in genomics and bioinformatics. How do your definitions affect the subtlety required when we seek to define “gene?” Do you have any penetrating, stimulating or just‐plain‐useful questions, riddles or challenging problems that might interest your colleagues? If so, send it to Professor Mohr ([email protected]) for consideration as a newsletter item. ******************************************************************************************** FEEDBACK: Thanks to those of you who have sent comments and suggestions for bioInfoBeat. More are welcome! We would like to make this newsletter as useful as possible to the BU Bioinformatics community! ******************************************************************************************** .
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