A P1-based physical map of the Drosophila euchromatic genome.

Kimmerly, W J; Stultz, K; Lewis, Suzanna; Lewis, Kathleen; Lustre, Veronica M.; Romero, Rodrigo Efrén Vásquez; Benke, J; Sun, Daxi; Shirley, G; Martin, Christopher H.; Palazzolo, Michael J.

doi:10.1101/gr.6.5.414

Cited by 63 publications

(42 citation statements)

References 35 publications

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“…To isolate the entire gene, we used the 2-90 cDNA insert to probe a macroarray of D. melanogaster genomic P1 clones; we found two (overlapping) P1 clones that hybridized to 2-90 cDNA. These clones, DS00857 and DS00968, previously had been mapped to a contig containing tra2 (28). Restriction maps of the smaller (DS00857) suggested that the HP2 gene was located near the P element insertion site l(2)07214.…”

Section: Resultsmentioning

confidence: 99%

Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin

Shaffer

Stephens²,

Thompson³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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Heterochromatin protein 1 (HP1), first discovered in Drosophila melanogaster, is a highly conserved chromosomal protein implicated in both heterochromatin formation and gene silencing. We report here characterization of an HP1-interacting protein, heterochromatin protein 2 (HP2), which codistributes with HP1 in the pericentric heterochromatin. HP2 is a large protein with two major isoforms of approximately 356 and 176 kDa. The smaller isoform is produced from an alternative splicing pattern in which two exons are skipped. Both isoforms contain the domain that interacts with HP1; the larger isoform contains two AT-hook motifs. Mutations recovered in HP2 act as dominant suppressors of position effect variegation, confirming a role in heterochromatin spreading and gene silencing.

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Section: Resultsmentioning

confidence: 99%

Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin

Shaffer

Stephens²,

Thompson³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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“…We used mapped STSs as a source of genomic sequences (Kimmerly et al 1996). At the time this project was initiated, these STSs were the only mapped sequence elements with a genome-wide distribution of the required density.…”

Section: Genome-wide Snp Discoverymentioning

confidence: 99%

“…Using genomic DNA from six wild-type strains (Barcelona, Capetown, Hikone, Pyrenees, w;iso2;iso3, and a P-element containing strain) as templates, we compared sequences from 24 third chromosome sequence tagged sites (STSs) from the P1-based physical map of the genome (Kimmerly et al 1996). The results shown in Table 1 indicate that the rate of sequence variation between any two strains ranges from 2.1 per kilobase (1 polymorphism/476 bp) to 5.2 per kilobase (1 polymorphism/192 bp, Table 1A), in agreement with previous studies.…”

mentioning

confidence: 99%

Single Nucleotide Polymorphism Markers for Genetic Mapping in Drosophila melanogaster

Hoskins

Phan²,

Naeemuddin³

et al. 2001

Genome Research

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For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that recently have revolutionized human, mouse, and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila by using a sequence tagged site-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that span the genome. Most of these markers are single nucleotide polymorphisms and sequences for these variants are provided in an accessible format. The average density of the new markers is one per 225 kb on the autosomes and one per megabase on the X chromosome. We include in this survey a set of P-element strains that provide additional use for high-resolution mapping. We show one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community.

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“…A genomic fragment covering the 2.2-kb upstream region of the D. melanogaster rho gene was generated by PCR using the D. melanogaster genomic P1 clone DS02734 (GenBank accession number AC004343) as a template (Kimmerly et al, 1996), and subcloned into the BamHI site of pCaSpeR-NLSlacZ (gift of C. Thummel, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT …”

Section: Transgene Construction For Rho Enhancer Analysismentioning

confidence: 99%

Soma-dependent modulations contribute to divergence ofrhomboidexpression during evolution ofDrosophilaeggshell morphology

et al. 2007

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*Patterning of the respiratory dorsal appendages (DAs) on the Drosophila melanogaster eggshell is tightly regulated by epidermal growth factor receptor (EGFR) signaling. Variation in the DA number is observed among Drosophila species; D. melanogaster has two DAs and D. virilis has four. Diversification in the expression pattern of rhomboid (rho), which activates EGFR signaling in somatic follicle cells, could cause the evolutionary divergence of DA numbers. Here we identified a cis-regulatory element of D. virilis rho. A comparison with D. melanogaster rho enhancer and activity studies in homologous and heterologous species suggested that these rho enhancers did not functionally diverge significantly during the evolution of these species. Experiments using chimeric eggs composed of a D. virilis oocyte and D. melanogaster follicle cells showed the evolution of DA number was not attributable to germline Gurken (Grk) signaling, but to divergence in events downstream of Grk signaling affecting the rho enhancer activity in somatic follicle cells. We found that a transcription factor, Mirror, which activates rho, could be one of these downstream factors. Thus, evolution of the trans-regulatory environment that controls rho expression in somatic follicle cells could be a major contributor to the evolutionary changes in DA number.

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A P1-based physical map of the Drosophila euchromatic genome.

Cited by 63 publications

References 35 publications

Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin

Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin

Single Nucleotide Polymorphism Markers for Genetic Mapping in Drosophila melanogaster

Soma-dependent modulations contribute to divergence ofrhomboidexpression during evolution ofDrosophilaeggshell morphology

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