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Genetics. Feb 2004; 166(2): 807–822.
PMCID: PMC1470754

Genetic and bioinformatic analysis of 41C and the 2R heterochromatin of Drosophila melanogaster: a window on the heterochromatin-euchromatin junction.


Genomic sequences provide powerful new tools in genetic analysis, making it possible to combine classical genetics with genomics to characterize the genes in a particular chromosome region. These approaches have been applied successfully to the euchromatin, but analysis of the heterochromatin has lagged somewhat behind. We describe a combined genetic and bioinformatics approach to the base of the right arm of the Drosophila melanogaster second chromosome, at the boundary between pericentric heterochromatin and euchromatin. We used resources provided by the genome project to derive a physical map of the region, examine gene density, and estimate the number of potential genes. We also carried out a large-scale genetic screen for lethal mutations in the region. We identified new alleles of the known essential genes and also identified mutations in 21 novel loci. Fourteen complementation groups map proximal to the assembled sequence. We used PCR to map the endpoints of several deficiencies and used the same set of deficiencies to order the essential genes, correlating the genetic and physical map. This allowed us to assign two of the complementation groups to particular "computed/curated genes" (CGs), one of which is Nipped-A, which our evidence suggests encodes Drosophila Tra1/TRRAP.

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Selected References

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  • Casso D, Ramírez-Weber F, Kornberg TB. GFP-tagged balancer chromosomes for Drosophila melanogaster. Mech Dev. 2000 Mar 1;91(1-2):451–454. [PubMed]
  • Celniker Susan E, Wheeler David A, Kronmiller Brent, Carlson Joseph W, Halpern Aaron, Patel Sandeep, Adams Mark, Champe Mark, Dugan Shannon P, Frise Erwin, et al. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol. 2002;3(12):RESEARCH0079–RESEARCH0079. [PMC free article] [PubMed]
  • Cleveland Don W, Mao Yinghui, Sullivan Kevin F. Centromeres and kinetochores: from epigenetics to mitotic checkpoint signaling. Cell. 2003 Feb 21;112(4):407–421. [PubMed]
  • Corradini Nicoletta, Rossi Fabrizio, Vernì Fiammetta, Dimitri Patrizio. FISH analysis of Drosophila melanogaster heterochromatin using BACs and P elements. Chromosoma. 2003 Jul;112(1):26–37. [PubMed]
  • Dimitri P. Cytogenetic analysis of the second chromosome heterochromatin of Drosophila melanogaster. Genetics. 1991 Mar;127(3):553–564. [PMC free article] [PubMed]
  • Dimitri P, Junakovic N. Revising the selfish DNA hypothesis: new evidence on accumulation of transposable elements in heterochromatin. Trends Genet. 1999 Apr;15(4):123–124. [PubMed]
  • Dimitri P, Arcà B, Berghella L, Mei E. High genetic instability of heterochromatin after transposition of the LINE-like I factor in Drosophila melanogaster. Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):8052–8057. [PMC free article] [PubMed]
  • Gloor GB, Preston CR, Johnson-Schlitz DM, Nassif NA, Phillis RW, Benz WK, Robertson HM, Engels WR. Type I repressors of P element mobility. Genetics. 1993 Sep;135(1):81–95. [PMC free article] [PubMed]
  • Grant PA, Schieltz D, Pray-Grant MG, Yates JR, 3rd, Workman JL. The ATM-related cofactor Tra1 is a component of the purified SAGA complex. Mol Cell. 1998 Dec;2(6):863–867. [PubMed]
  • Gray M, Charpentier A, Walsh K, Wu P, Bender W. Mapping point mutations in the Drosophila rosy locus using denaturing gradient gel blots. Genetics. 1991 Jan;127(1):139–149. [PMC free article] [PubMed]
  • Grewal Shiv I S, Elgin Sarah C R. Heterochromatin: new possibilities for the inheritance of structure. Curr Opin Genet Dev. 2002 Apr;12(2):178–187. [PubMed]
  • Hilliker AJ. Genetic analysis of the centromeric heterochromatin of chromosome 2 of Drosophila melanogaster: deficiency mapping of EMS-induced lethal complementation groups. Genetics. 1976 Aug;83(4):765–782. [PMC free article] [PubMed]
  • Hoskins RA, Nelson CR, Berman BP, Laverty TR, George RA, Ciesiolka L, Naeemuddin M, Arenson AD, Durbin J, David RG, et al. A BAC-based physical map of the major autosomes of Drosophila melanogaster. Science. 2000 Mar 24;287(5461):2271–2274. [PubMed]
  • Hoskins Roger A, Smith Christopher D, Carlson Joseph W, Carvalho A Bernardo, Halpern Aaron, Kaminker Joshua S, Kennedy Cameron, Mungall Chris J, Sullivan Beth A, Sutton Granger G, et al. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 2002;3(12):RESEARCH0085–RESEARCH0085. [PMC free article] [PubMed]
  • Kaminker Joshua S, Bergman Casey M, Kronmiller Brent, Carlson Joseph, Svirskas Robert, Patel Sandeep, Frise Erwin, Wheeler David A, Lewis Suzanna E, Rubin Gerald M, et al. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 2002;3(12):RESEARCH0084–RESEARCH0084. [PMC free article] [PubMed]
  • Kholodilov NG, Bolshakov VN, Blinov VM, Solovyov VV, Zhimulev IF. Intercalary heterochromatin in Drosophila. III. Homology between DNA sequences from the Y chromosome, bases of polytene chromosome limbs, and chromosome 4 of D. melanogaster. Chromosoma. 1988 Nov;97(3):247–253. [PubMed]
  • Kusch Thomas, Guelman Sebastián, Abmayr Susan M, Workman Jerry L. Two Drosophila Ada2 homologues function in different multiprotein complexes. Mol Cell Biol. 2003 May;23(9):3305–3319. [PMC free article] [PubMed]
  • Locke J, Howard LT, Aippersbach N, Podemski L, Hodgetts RB. The characterization of DINE-1, a short, interspersed repetitive element present on chromosome and in the centric heterochromatin of Drosophila melanogaster. Chromosoma. 1999 Nov;108(6):356–366. [PubMed]
  • Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al. The genome sequence of Drosophila melanogaster. Science. 2000 Mar 24;287(5461):2185–2195. [PubMed]
  • Locke J, Podemski L, Roy K, Pilgrim D, Hodgetts R. Analysis of two cosmid clones from chromosome 4 of Drosophila melanogaster reveals two new genes amid an unusual arrangement of repeated sequences. Genome Res. 1999 Feb;9(2):137–149. [PMC free article] [PubMed]
  • Anastasiadis PZ, Reynolds AB. The p120 catenin family: complex roles in adhesion, signaling and cancer. J Cell Sci. 2000 Apr;113(Pt 8):1319–1334. [PubMed]
  • Miklos GL, Yamamoto MT, Davies J, Pirrotta V. Microcloning reveals a high frequency of repetitive sequences characteristic of chromosome 4 and the beta-heterochromatin of Drosophila melanogaster. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2051–2055. [PMC free article] [PubMed]
  • Shiloh Y. ATM: sounding the double-strand break alarm. Cold Spring Harb Symp Quant Biol. 2000;65:527–533. [PubMed]
  • Spradling AC, Stern D, Beaton A, Rhem EJ, Laverty T, Mozden N, Misra S, Rubin GM. The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. Genetics. 1999 Sep;153(1):135–177. [PMC free article] [PubMed]
  • Sullivan BA, Blower MD, Karpen GH. Determining centromere identity: cyclical stories and forking paths. Nat Rev Genet. 2001 Aug;2(8):584–596. [PubMed]
  • Mount SM, Burks C, Hertz G, Stormo GD, White O, Fields C. Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res. 1992 Aug 25;20(16):4255–4262. [PMC free article] [PubMed]
  • Sun X, Wahlstrom J, Karpen G. Molecular structure of a functional Drosophila centromere. Cell. 1997 Dec 26;91(7):1007–1019. [PMC free article] [PubMed]
  • Sun Xiaoping, Le Hiep D, Wahlstrom Janice M, Karpen Gary H. Sequence analysis of a functional Drosophila centromere. Genome Res. 2003 Feb;13(2):182–194. [PMC free article] [PubMed]
  • Myster Steven H, Cavallo Robert, Anderson Charles T, Fox Donald T, Peifer Mark. Drosophila p120catenin plays a supporting role in cell adhesion but is not an essential adherens junction component. J Cell Biol. 2003 Feb 3;160(3):433–449. [PMC free article] [PubMed]
  • Wallrath LL. Unfolding the mysteries of heterochromatin. Curr Opin Genet Dev. 1998 Apr;8(2):147–153. [PubMed]
  • Rollins RA, Morcillo P, Dorsett D. Nipped-B, a Drosophila homologue of chromosomal adherins, participates in activation by remote enhancers in the cut and Ultrabithorax genes. Genetics. 1999 Jun;152(2):577–593. [PMC free article] [PubMed]
  • Weiler KS, Wakimoto BT. Heterochromatin and gene expression in Drosophila. Annu Rev Genet. 1995;29:577–605. [PubMed]
  • Yan Christopher M, Dobie Kenneth W, Le Hiep D, Konev Alexander Y, Karpen Gary H. Efficient recovery of centric heterochromatin P-element insertions in Drosophila melanogaster. Genetics. 2002 May;161(1):217–229. [PMC free article] [PubMed]
  • Roseman RR, Johnson EA, Rodesch CK, Bjerke M, Nagoshi RN, Geyer PK. A P element containing suppressor of hairy-wing binding regions has novel properties for mutagenesis in Drosophila melanogaster. Genetics. 1995 Nov;141(3):1061–1074. [PMC free article] [PubMed]
  • Yap AS, Brieher WM, Gumbiner BM. Molecular and functional analysis of cadherin-based adherens junctions. Annu Rev Cell Dev Biol. 1997;13:119–146. [PubMed]
  • Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, et al. Comparative genomics of the eukaryotes. Science. 2000 Mar 24;287(5461):2204–2215. [PMC free article] [PubMed]

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