title: Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster.
abstract: Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes ("H-probes") for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin.
authors: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.
authors: Bing
authors: B
authors: He
authors: Amy
authors: A
authors: Caudy
authors: Lance
authors: L
authors: Parsons
authors: Adam
authors: A
authors: Rosebrock
authors: Attilio
authors: A
authors: Pane
authors: Sandeep
authors: S
authors: Raj
authors: Eric
authors: E
authors: Wieschaus
mesh_terms: D000818:Animals; D002872:Chromosome Deletion; D002874:Chromosome Mapping / Q000379:methods*; D059006:Chromosomes, Insect / Q000235:genetics; D055028:Comparative Genomic Hybridization / Q000379:methods*; D056915:DNA Copy Number Variations; D004331:Drosophila melanogaster / Q000235:genetics*; D047108:Embryonic Development / Q000235:genetics; D005260:Female; D005786:Gene Expression Regulation; D015321:Gene Rearrangement; D006570:Heterochromatin / Q000737:chemistry / Q000235:genetics*; D008297:Male; D046228:Microarray Analysis; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
chemical_list: D006570:Heterochromatin