The division of chromosomes into euchromatic and heterochromatic regions is an enigmatic aspect of genome organization in multicellular eukaryotes. Heterochromatin is a major component of genomes as diverse as humans and fruit flies, and plays critical roles in chromosome inheritance and metabolism. In the absence of a detailed analysis of heterochromatin organization and sequence, our ability to investigate chromosome function, heterochromatic genes, and genome evolution remains limited. In the previous granting period, the Drosophila Heterochromatin Genome Project (DHGP) used genomic resources available in Drosophila melanogaster to generate basic information about the structure and sequence composition of the heterochromatin, specifically focusing on gene- and transposable element- rich regions that do not contain long arrays of highly-repeated satellite DNAs. We have assembled 12.5Mb of finished or nearly finished sequence and a BAC-based physical map that spans 16.5Mb of the heterochromatin, and linked sequences and clones to specific locations in the cytological maps. Annotation of 49Mb of sequence identified 700 gene models and other genetic elements, as well as orthologs in other Drosophilids, and demonstrated that >85% of the target sequences contains repetitive DNA. Here, we propose to extend the D. melanogaster heterochromatin sequence and physical maps to encompass most or all of the non-satellite regions, and to initiate studies of satellite regions. We will also to improve annotations and public data displays, examine evolution of heterochromatin through comparative analysis with other Drosophila species, and develop tools to facilitate heterochromatin assemblies and analysis. Achieving these aims will provide information and tools that will further our understanding of higher eukaryotic genome structure, and will lay the groundwork for more complete analysis of heterochromatin structure and function in Drosophila and other eukaryotes, including humans. ? ? ?
| Hoskins, Roger A; Carlson, Joseph W; Wan, Kenneth H et al. (2015) The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res 25:445-58 |
| Werren, John H; Richards, Stephen; Desjardins, Christopher A et al. (2010) Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327:343-8 |
| Sharakhova, Maria V; George, Phillip; Brusentsova, Irina V et al. (2010) Genome mapping and characterization of the Anopheles gambiae heterochromatin. BMC Genomics 11:459 |
| Xia, Ai; Sharakhova, Maria V; Leman, Scotland C et al. (2010) Genome landscape and evolutionary plasticity of chromosomes in malaria mosquitoes. PLoS One 5:e10592 |
| Hoang, Margaret L; Tan, Frederick J; Lai, David C et al. (2010) Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination. PLoS Genet 6:e1001228 |
| Karpen, Gary H (2009) Preparation of high-molecular-weight DNA from Drosophila embryos. Cold Spring Harb Protoc 2009:pdb.prot5254 |
| Peng, Jamy C; Karpen, Gary H (2008) Epigenetic regulation of heterochromatic DNA stability. Curr Opin Genet Dev 18:204-11 |
| Smith, Christopher D; Edgar, Robert C; Yandell, Mark D et al. (2007) Improved repeat identification and masking in Dipterans. Gene 389:1-9 |
| Hoskins, Roger A; Carlson, Joseph W; Kennedy, Cameron et al. (2007) Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science 316:1625-8 |
| (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-18 |
Showing the most recent 10 out of 19 publications
