Sarah Elgin - Washington University in St. Louis
- 1 Bio 4342/434W: General Course Information (Spring 2016)
- 2 Bio 4342: Schedule (Spring 2016)
- 3 Reading
- 3.1 Required Reading (paper copies provided; reading reflections due):
- 3.2 Additional References
- 3.2.1 Sequencing Technology
- 3.2.2 Chromatin Structure / Epigenetics
- 3.2.3 Human Genomics
- 3.2.4 Finding Genes in Drosophila
- 3.2.5 The following papers may be helpful during the second half of the course
Bio 4342/434W: General Course Information (Spring 2016)
|Sarah C R Elgin||131 McDonnell Hallemail@example.com|
|Elaine Mardis||The Genome Institutefirstname.lastname@example.org|
|Jeremy Buhler||Jolley Hall email@example.com|
|Chris Shaffer||McDonnell 112 (Danforth)||firstname.lastname@example.org|
|Wilson Leung||McDonnell 112 (Danforth)||email@example.com|
|Lee Trani||Genome Institute|
|Daniel Cui Zhoufirstname.lastname@example.org|
Lecture and lab will function together. The class will meet from 1:30 to 5:00 PM on Monday and Wednesday, and from 1:30 to 2:30 PM on Friday; occasionally the Friday session will extend to 3:30 or 4:30 (see schedule). Students who elect the writing-intensive option (Bio 434W) will have ca. 5 additional hour-long meetings to focus on writing, scheduled for Friday 2:30-3:30 PM. Attendance is required. Because this is a laboratory course, true make-up sessions are often not possible. Students who must miss a class due to ill health, a death in the family, or a med school/grad school interview should inform Dr. Elgin prior to the class session to obtain a bye. If you miss a class, you are responsible for obtaining notes and information from the instructor; consulting with the instructor and/or a TA as necessary to gain an understanding of the material covered; and catching up on your work as needed.
Class will meet in the Biology Department, Life Sciences 311, on the Danforth Campus. On Friday January 22 we will meet at the WU Genome Institute, Fourth Floor Lobby, 4444 Forest Park Parkway, for a tour. The Institute is ca. 2 blocks from the West End Metro stop (catch the 1:14 pm train at Skinker).
There are no required texts. The texts used in Bio 2960/2970 (or any molecular genetics course) will cover the basic biology knowledge needed. The following books in bioinformatics may be useful, depending on your background. These books will be on reserve in Olin Library.
- "Bioinformatics and Functional Genomics" by R. Pevsner, 2015 (3nd ed.), J. Wiley & Sons, NJ, (ISBN: 978-0-470-08585-1; WU QH441.2 .P48). Recommended for Bio majors if you would like more introduction to the computer tools we use.
- "BLAST" by I. Korf, M. Yandell, J. Bedell, 2003, O'Reilly (ISBN 0596002998) (recommended for in-depth use of BLAST and interpretation of results). Available on-line from Olin Library.
All course information, announcements, reading assignments, etc. will be posted on BlackBoard. Basic information and reading will also be posted on the Bio 4342 web site http://www.nslc.wustl.edu/courses/Bio4342/bio4342.html maintained by the Biology Department through the NSLC. The latter portion of the web site is password protected. This has copies of all of the recommended and required reading. Most of the teaching materials used in the course can be found at the Genomics Education Partnership web page (http://gep.wustl.edu) under Curriculum. Examples of student papers from previous years are also found on the GEP site.
Student Responsibilities, Grading
Grades will be assigned based on the following components: participation in discussions, four summary papers on reading, 12%; six graded computer-based problem sets, 18%; final report on finishing a ~100 kb Drosophila project (written 15% and oral 5%); report on genes/pseudogenes, (written 10% and oral 5%); TSS oral report 5%; final report on individual Drosophila fosmid (analysis and annotation) (written 25% and oral 5%). (Note homeworks and reading summaries are graded with a check = 8 pts, check plus = 10 pts, or check minus = 6 pt.) Students who elect the Writing Intensive version of the course will have an introductory writing assignment; quality of all critiques and revisions will constitute 5% of the final grade.
Lab Overview: Sequencing / Finishing
During the first 2 ½ weeks of the semester, we will be engaged in sequence improvement and genome assembly, covering the following:
- Direct sequencing techniques for DNA—both manual and automated (videos);
- Use of Phred/Phrap/Consed to assemble and evaluate sequence reads;
- Finishing process — scanning for errors in mononucleotide runs, sorting reads, searching for additional project data in the original data set, calling sequencing primers from the genomic DNA template, adding additional data; methods for assessing quality of finished sequence.
Lab Overview: Analysis / Annotation
We anticipate that students will become familiar with commonly used DNA databases; model organism websites; genome browsers; RepeatMasker; Genscan and other gene prediction tools; BLAST, BLAT searches for similarity; Clustal for comparative analysis; techniques for annotating transcription start sites; techniques for motif searching. As time permits and the research dictates, we may explore other databases and comparative tools.
We will have large-screen Macs available for your work in class, and/or we can provide Mac laptops for your use during the course. If you check out a laptop, you will be responsible for returning it in good condition at the end of the semester. If you prefer, you can use your own portable computer. However, we recommend that only Macs be used during our work on sequence improvement (first 2 ½ weeks of the course), as Consed (the key software) is available only in a Mac version. (It can only be used on a PC in a virtual machine.) Either a Mac or a PC can be used when we are working on annotation (remaining weeks of the course). We will provide a portable hard-drive for the class, but you are responsible for backing up your work at the end of each session!
Bio 4342: Schedule (Spring 2016)
M, W 1:30-5:00; F 1:30-2:30 (occasionally 3:30), Writing Intensive group F 2:30-3:30 when scheduled. Meet in LS 311, Danforth Campus; on Friday 1/22 there will be a visit to the Washington University McDonnell Genome Institute. Please review our research problem (on the course website at http://www.nslc.wustl.edu/courses/Bio4342/bio4342.html) and read "A Guide to Consed" on the GEP website) prior to the first class.
|3/14 - 3/18||Washington University Spring Break|
|5/2 Mon||Final written and oral annotation reports: Submit final paper on your project, with a map of genes (including estimates of transcription start sites), repetitious elements, and alignment to D. melanogaster, including a discussion of synteny. Complete annotation of all exons, all isoforms. Include results of searches for TSS candidate sites and regulatory elements. As time permits, exploration of one gene on FlyBase, expanding on gene features, regulation, and function. Use Clustal at least once. 10' presentations (1 pm 3 pm OR 3 pm - 5 pm in LS 311).|
|5/3 Tue||Course Assessment: Follow-up session on course evaluation, submission of final files, return of computers, etc. (12 noon lunch - 2 pm, LS 311) (http://evals.wustl.edu; GEP web site; and Bio 4342 surveys/suggestions).|
We will read and discuss four papers over the course of the semester, centered on the theme of genome organization and evolution in Drosophila, with an emphasis on the role of repetitious elements. [If you have not read scientific papers before, look at "How to Read a Scientific Paper" by Mary Williams, pp 1-5 (on the Bio 4342 website) before starting.] These papers are listed below; for each paper you will turn in a "reading reflection" (~2 pages, double-spaced, typed) that summarizes the big idea and proposes the next experiment. In addition, we have assembled a list of papers that are pertinent to the material we will be discussing, including papers recommended by our guest lecturers. Among these, papers marked "R" are highly recommended background reading. Background material on BLAST and other computer programs can be found in the recommended texts, and on-line through our subscription to "Current Protocols in Bioinformatics," available at http://onlinelibrary.wiley.com/book/10.1002/0471250953 . Background information on many scientific terms is available through the Genomics Education Partnership Glossary (http://gep.wustl.edu ) and information on terms and techniques is available through Wikipedia (generally a good source, but be cautious!).
Required Reading (paper copies provided; reading reflections due):
1. Ellison CE, Bachtrog D. (2013) Dosage compensation via transposable element mediated rewiring of a regulatory network. Science 342: 846-50. (See also Chuong EB & Feschotte C (2013) Evolution: Transposons up the dosage. Science 342: 812-13.)
2. Haynes KA, Caudy AA, Collins L, Elgin SCR (2007) Element 1360 and RNAi components contribute to HP1-dependent silencing of a pericentric reporter. Curr Biol 16: 2222-7. (See also Grewal & Elgin (2002) for background on concepts tested in this paper.)
3. Leung W et al. (2015) Muller F elements maintain a distinct set of genomic properties over 40 million years of evolution. G3 Genes|Genomes|Genetics 5: 719-40. Focus your review and experiment either on genome organization (figures 1-4, 9) OR on properties of genes (figures 5-8).
4. Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MI (2008) A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134: 599-609.
Before class starts
- "Sequencing a Genome" (view on line, including review of chemistry if needed): http://gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/tour/html/gsc.htm R
- "Next generation Sequencing: Genome Center Video Tour" (view all four segments online): http://gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/nextgen_video_tour R
- Heather JM, Chain B. (2015) The sequence of sequencers: The history of sequencing DNA. Genomics. 2015 Nov 10. pii: S0888-7543(15)30041-0. doi: 10.1016/j.ygeno.2015.11.003.
- Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. (2013) The nextgeneration sequencing revolution and its impact on genomics. Cell 155: 27-38. doi: 10.1016/j.cell.2013.09.006.
- Miyamoto M, Motooka D, Gotoh K, Imai T, Yoshitake K, Goto N, Iida T, Yasunaga T, Horii T, Arakawa K, Kasahara M, Nakamura S. (2014) Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes. BMC Genomics 15:699. doi: 10.1186/1471-2164-15-699.
- Christensen KD, Dukhovny D, Siebert U, Green RC. (2015) Assessing the Costs and Cost-Effectiveness of Genomic Sequencing. J Pers Med. 5:470-86. doi: 10.3390/jpm5040470.
- Gordon D, Green P. (2013) Consed: a graphical editor for next-generation sequencing. Bioinformatics. 29: 2936-7. doi: 10.1093/bioinformatics/btt515
- Nielsen, CB, Cantor, C, Dubchak, I, Gordon, D & Wang, T. (2010) Visualizing genomes: techniques and challenges. Nature Methods 7, S5 - S15. [Covers Consed, UCSC Genome Browser and Vist.]
- Pavlopoulos GA, Malliarakis D, Papanikolaou N, Thiodosiou T, Enright AJ, Iliopoulos I. (2015) Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. GigaScience 4: 38. doi: 10.1186/s13742-015-0077-2 [Recent comprehensive list.]
- Treangen, TJ, and Salzberg, SL (2011) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Rev. Genet. 13: 36-46. [Nice visualization of assembly problems associated with repeats.]
Chromatin Structure / Epigenetics
- modENCODE Consortium (2014) Chromatin, plus Vignette: Fly Chromatin. R http://modencode.sciencemag.org/chromatin/introduction
- Cot curve packet with HW2. From "Biochemistry: A Problems Approach," 2nd ed., by WB Wood, JH Wilson, RM Benbow, LE Hood; Benjamin/Cummings, CA. 1981.
- Eddy, S R (2012) The C-value paradox, junk DNA and ENCODE. Curr Biol 22: R898-9. R
- Palazzo AF, Gregory TR. (2014) The case for junk DNA. PLoS Genet. 10: e1004351. doi: 10.1371/journal.pgen.1004351.
- Felsenfeld G, Groudine M (2003) Controlling the double helix, Nature 421: 448-453.
- Li G, Reinberg D. (2011) Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev. 21: 175-86. doi: 10.1016/j.gde.2011.01.022.
- Grewal SIS, Elgin, SCR. (2002) Heterochromatin: new possibilities for the inheritance of structure, Curr Opin Genetics & Develop. 12: 178-187. (R if needed; overlaps with reading #2.)
- Elgin SCR, Reuter G (2013) Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila. Cold Spring Harb Perspect Biol 5: a017780. doi: 10.1101/cshperspect.a017780.
- Yandim C, Natisvili T, Festenstein R. (2013) Gene regulation and epigenetics in Friedreich's ataxia. J Neurochem.126 Suppl 1: 21-42. (This paper includes a review of background information as well as recent results in a mammalian system.)
- Kharchenko, PV,... M Kellis, SCR Elgin, MI Kuroda, V Pirrotta, G Karpen, PJ Park. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471: 480-5.
- Riddle NC ... Karpen GH, Park PJ, Elgin, SCR (2012) Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 8:e1002954.
- Sentmanat MF, Elgin SCR (2012) Ectopic assembly of heterochromatin in Drosophila melanogaster triggered by transposable elements. Proc Natl Acad Sci USA 109: 14104-9.
- Dumesic PA, Madhani HD (2014) Recognizing the enemy within: licensing RNA-guided genome defense. Trds Biochem Sci 39: 25-34.
- Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D (2007) Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A 104: 18613-18618.
- Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Madden PA, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, Costello JF, Wang T. (2013) DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet. 45: 836-41. doi: 10.1038/ng.2649.
- Maunakea AK, Nagarajan RP, Bilenkyh M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielson C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SSJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466: 253-257. Variation 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison
- 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. (2015) A global reference for human genetic variation. Nature 526: 68-74. doi: 10.1038/nature15393.
- Sudmant PH, et al. (2015) An integrated map of structural variation in 2,504 human genomes. Nature 526: 75-81. doi: 10.1038/nature15394.
- Chen, R. et al. (2012) Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148: 1293 - 1307.
- Wartman, LD (2015) A case of me: clinical cancer sequencing and the future of precision medicine. Cold Spring Harb Mol Case Stud 1: a000349. Doi: 10:1101/mcs.a000349.
- Kico, JM. et al. (2015). Association between mutation clearance after induction therapy and outcomes in acute myeloid leukemia. J Amer Med Asso 314: 811-22.
- White BS, DiPersio JF. (2014) Genomic tools in acute myeloid leukemia: From the bench to the bedside. Cancer 120: 1134-44. doi: 10.1002/cncr.28552
- The Cancer Genome Atlas Network (2012) Comprehensive molecular portraits of human breast tumors. Nature 490: 61 - 70.
- Mardis ER (2014) Sequencing the AML genome, transcriptome, and epigenome. Sem Hematology 51: 250-58.
- Carreno, BM et al. (2015) Cancer immunotherapy: A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells. Science 348: 803-8.
- Griffith M. et al. (2015) Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 11: e1004274. doi: 10.1371/journal.pcbi.1004274.
- Edwards JR, O'Donnell AH, Rollins RA, Peckham HE, Lee C, Milekic MH, Chanrion B, Fu Y, Su T, Hibshoosh H, Gingrich JA, Haghighi F, Nutter R, Bestor TH. (2010) Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. Genome Res 20: 972-80.
Finding Genes in Drosophila
- Hardison RC. (2003) Primer: Comparative Genomics. PloS Biology 1: 156-160.
- Webber C, Ponting CP. (2004) Genes and homology. Curr Biol 14: R332-R333. R
- Peter McQuilton, Susan E. St. Pierre, Jim Thurmond, and the FlyBase Consortium. (2011) FlyBase 101 - the basics of navigating FlyBase. Nuc Acids Res 39: 21.
- St Pierre SE, Ponting L, Stefancsik R, McQuilton P; FlyBase Consortium (2014) FlyBase 102--advanced approaches to interrogating FlyBase. Nucleic Acids Res. 42:D780-8.
- dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015). FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res. 43(Database issue):D690-7. doi: 10.1093/nar/gku1099.
- Kondrashov AS. (2005) Evolutionary biology: fruit fly genome is not junk. Nature 437:1106. R
- Birney E. (2007) Come fly with us. Nature 450: 5-6. (Synopsis of 12 genomes paper; R)
- Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
- Eddy, S. (2004a) What is a hidden Markov model? Nature Biotech. 22: 1315-16. R
- Eddy, S. (2004b) What is dynamic programming? Nature Biotech. 22: 909-910. R
- Brent MR (2008). Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet. 9: 62-73.
- Shiryev SA, Papadopoulos JS, Schäffer AA, Agarwala R. (2007). Improved BLAST searches using longer words for protein seeding. Bioinformatics. 23(21):2949-51.
- W. James Kent, Charles W. Sugnet, Terrence S. Furey, Krishna M. Roskin, Tom H. Pringle, Alan M. Zahler, and David Haussler. (2002) The Human Genome Browser at UCSC. Genome Res. 12: 996-1006.
- Rosenbloom KR, et al. (2015) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 43 (Database issue):D670-81. doi: 10.1093/nar/gku1177.
- Chen ZX, ..., Celniker SE, Oliver B, Richards S. (2014). Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 24(7):1209-23.
- Hoskins, R. A., Landolin, J. M., Brown, J. B., Sandler, J. E., Takahashi, H., Lassmann, T., ... Celniker, S. E. (2011). Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Research, 21: 182-192. doi:10.1101/gr.112466.110
- Brown JB, ..., Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE. (2014). Diversity and dynamics of the Drosophila transcriptome. Nature. 512(7515):393-399.
- Lenhard B, Sandelin A, Carninci P. (2012) Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet. Mar 6;13(4):233-45. doi: 10.1038/nrg3163.
- Palmieri N, Nolte V, Suvorov A, Kosiol C, Schlötterer C. (2012). Evaluation of different reference based annotation strategies using RNA-Seq - A case study in Drosophila pseudoobscura. PLoS One. 7(10): e46415
- Irwin Jungreis, Michael F. Lin, Rebecca Spokony, Clara S. Chan, Nicolas Negre, Alec Victorsen, Kevin P. White, and Manolis Kellis. (2011) Evidence of abundant stop codon read-through in Drosophila and other metazoa. Genome Res. 21:2096-2113.
- Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D. (2005) Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol. 1:166-75.
- Bergman CM, Quesneville H. (2007). Discovering and detecting transposable elements in genome sequences. Brief Bioinform. 8:382-92
- Leung, W, CD Shaffer, T Cordonnier, J Wong, MS Itano, EE Slawson-Tempel, E Kellmann, DM Desruisseau, C Cain, R Carrasquillo, TM Chusak, K Falkowska, KD Grim, R Guan, J Honeybourne, S Khan, L Lo, R McGaha, J Plunkett, JM Richner, R Richt, L Sabin, A Shah, A Sharma, S Singhal, F Song, C Swope, CB Wilen, J Buhler, ER Mardis, SCR Elgin (2010) "Evolution of a distinct genomic domain in Drosophila: Comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis." Genetics 185: 1519-1534.
- Kadonaga JT. (2012). Perspectives on the RNA polymerase II core promoter. Wiley Interdiscip Rev Dev Biol. 1(1):40-51.
- Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS (2011) REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res. 39: D118-23.
- Zhu LJ, Christensen RG, Kazemian M, Hull CJ, Enuameh MS, Basciotta MD, Brasefield JA, Zhu C, Asriyan Y, Lapointe DS, Sinha S, Wolfe SA, Brodsky MH. (2011) FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res. 39: D111-7.
- Bailey TL, Johnson J, Grant CE, Noble WS. (2015) The MEME Suite. Nucleic Acids Res. 2015 Jul 1;43(W1):W39-49. doi: 10.1093/nar/gkv416.
- Ihuegbu NE, Stormo GD, Buhler J (2012) Fast, sensitive discovery of conserved genome-wide motifs. J Comput Biol 19: 139 - 47.
The following papers may be helpful during the second half of the course
- Celniker SE, Rubin GM. (2003) The Drosophila melanogaster genome. Annu Rev Genomics Hum Genet. 4: 89-117.
- Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE. (2002) The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3:RESEARCH0084. PMID: 1253757
- Bartolome C, Maside X, Charlesworth B. (2002) On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol Biol Evol. 19: 926-37.
- Yang H-P, Hung T-L, You T-L, Yang T-H. (2006) Genome-wide comparative analysis of the highly abundant transposable element DINE-1 suggests a recent transpositional burst in Drosophila yakuba. Genetics, 173: 189-96.
- Thomas J, Vadnagara K, Pritham EJ. (2014) DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons). Mob DNA 5:18. doi: 10.1186/1759-8753-5-18.
- Smith CD, Shu S, Mungall CJ, Karpen GH. (2007) The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science 316: 1586-91.
- Hoskins RA, Carlson JW, Kennedy C, Acevedo D, Evans-Holm M, Frise E, Wan KH, Park S, Mendez-Lago M, Rossi F, Villasante A, Dimitri P, Karpen GH, Celniker SE. (2007) Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science 316: 1625-8.