A BAC-Based Physical Map of the Major Autosomes of
            <i>Drosophila melanogaster</i>

Hoskins, Roger A.; Nelson, Catherine R.; Berman, Benjamin P.; Laverty, Todd R.; George, Reed A.; Ciesiolka, Lisa; Naeemuddin, Mohammed; Arenson, Andrew D.; Durbin, James; Dávid, Róbert; Tabor, Paul E.; Bailey, Michael R.; DeShazo, Denise R.; Catanese, Joseph J.; Mammoser, Aaron; Osoegawa, Kazutoyo; de, Pieter J.; Jong,; Celniker, S; Gibbs, Richard A.; Rubin, Gerald M.; Scherer, Steven E.

doi:10.1126/science.287.5461.2271

Cited by 128 publications

(99 citation statements)

References 21 publications

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“…The orb2 gene structure and homology to CPEB The orb2 gene is located in the cytogenetic interval 66E4 on the left arm of the third chromosome (Hoskins et al 2000). According to FlyBase, the orb2 locus is predicted to produce two sets of transcripts and proteins ( Figure 1A).…”

Section: Resultsmentioning

confidence: 99%

The Drosophila CPEB Protein Orb2 Has a Novel Expression Pattern and Is Important for Asymmetric Cell Division and Nervous System Function

Hafer

Bhat

et al. 2011

Genetics

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Cytoplasmic polyadenylation element binding (CPEB) proteins bind mRNAs to regulate their localization and translation. While the first CPEBs discovered were germline specific, subsequent studies indicate that CPEBs also function in many somatic tissues including the nervous system. Drosophila has two CPEB family members. One of these, orb, plays a key role in the establishment of polarity axes in the developing egg and early embryo, but has no known somatic functions or expression outside of the germline. Here we characterize the other Drosophila CPEB, orb2. Unlike orb, orb2 mRNA and protein are found throughout development in many different somatic tissues. While orb2 mRNA and protein of maternal origin are distributed uniformly in early embryos, this pattern changes as development proceeds and by midembryogenesis the highest levels are found in the CNS and PNS. In the embryonic CNS, Orb2 appears to be concentrated in cell bodies and mostly absent from the longitudinal and commissural axon tracts. In contrast, in the adult brain, the protein is seen in axonal and dendritic terminals. Lethal effects are observed for both RNAi knockdowns and orb2 mutant alleles while surviving adults display locomotion and behavioral defects. We also show that orb2 funtions in asymmetric division of stem cells and precursor cells during the development of the embryonic nervous system and mesoderm. C YTOPLASMIC polyadenylation element binding (CPEB) family proteins bind to target sequences in the 39-UTR of mRNAs and control their localization and translation. CPEB proteins function in many different biologocial contexts including oogenesis in Xenopus and Drosophila (Lantz et al. 1992(Lantz et al. , 1994Christerson and McKearin 1994;Hake and Richter 1994), synaptic plasticity in the rat hippocampus (Wu et al. 1998), and long-term memory in Aplysia . In Xenopus oocytes, CPEB regulates oocyte maturation. Prior to progesterone stimulation, it functions to repress target mRNAs in conjunction with proteins such as Maskin. After hormone stimulation, CPEB is phosphorylated, and the phosphorylated isoform recruits factors that stimulate poly(A) addition and translational activation of mRNAs that mediate the maturation process. In Drosophila, the CPEB protein Orb is required for oocyte determination and the establishment of the anterior-posterior and dorsal-ventral axes of the developing egg chamber. It functions by promoting the on-site translation of mRNAs that are localized in the developing oocyte, and like the Xenopus oocyte CPEB, its activity is regulated by phosphorylation.Most animals have two or more CPEB genes. Completed genome sequences reveal that humans, mice, and Caenorhabditis elegans have four CPEB genes, but only two CPEBs in Drosophila. The homology between the CPEB proteins is limited to the C-terminal half of the protein, which has two RNA-recognition motif (RRM) domains and a zinc finger domain, while the N-terminal half is highly divergent. Phylogenetic trees indicate that the CPEB genes fall into two differen...

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Section: Resultsmentioning

confidence: 99%

The Drosophila CPEB Protein Orb2 Has a Novel Expression Pattern and Is Important for Asymmetric Cell Division and Nervous System Function

Hafer

Bhat

et al. 2011

Genetics

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“…Cao et al (1999) built a sequence ready map of chromosome 16p13.1-p11.2 by using BACs and previously mapped STSs. Zhu et al (1999) built a sequence ready map of chromosome 7 of the rice blast fungus Magnaporthe grisea by using BAC contigs assembled by hybridization and integrated with fingerprinted BAC contigs Hoskins et al (2000) integrated STS content, restriction fingerprinting, and polytene chromosome in situ hybridization to produce a Drosophila melanogaster map for 81% of the genome. Klein et al (2000) used amplified fragment length polymorphism (AFLP)-based markers integrated with fingerprints to map sorghum.…”

mentioning

confidence: 99%

Contigs Built with Fingerprints, Markers, and FPC V4.7

Soderlund

Humphray²,

French³

2000

Genome Research

304

299

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Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.

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“…UAS-dpld transgenes were prepared using the pUAST vector (Brand and Perrimon, 1993) and the genomic area containing the dpld gene, present in the BAC clone RP98-4G20 obtained from the Children's Hospital Oakland Research Institute (CHORI) (Hoskins et al, 2000). An 11.1-kb fragment generated by BglII restriction digest, which contained the dpld gene and surrounding genomic region up to the 3Ј region of the upstream gene (CG1624), was cloned into pUAST using the BglII site.…”

Section: Fly Strains and Geneticsmentioning

confidence: 99%

Regulation of the Drosophila lin‐41 homologue dappled by let‐7 reveals conservation of a regulatory mechanism within the LIN‐41 subclade

O’Farrell

Esfahani

Engström

et al. 2007

Developmental Dynamics

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Drosophila Dappled (DPLD) is a member of the RBCC/TRIM superfamily, a protein family involved in numerous diverse processes such as developmental timing and asymmetric cell divisions. DPLD belongs to the LIN-41 subclade, several members of which are micro RNA (miRNA) regulated. We re-examined the LIN-41 subclade members and their relation to other RBCC/TRIMs and dpld paralogs, and identified a new Drosophila muscle specific RBCC/TRIM: Another B-Box Affiliate, ABBA. In silico predictions of candidate miRNA regulators of dpld identified let-7 as the strongest candidate. Overexpression of dpld led to abnormal eye development, indicating that strict regulation of dpld mRNA levels is crucial for normal eye development. This phenotype was sensitive to let-7 dosage, suggesting let-7 regulation of dpld in the eye disc. A cell-based assay verified let-7 miRNA down-regulation of dpld expression by means of its 3 -untranslated region. Thus, dpld seems also to be miRNA regulated, suggesting that miRNAs represent an ancient mechanism of LIN-41 regulation. Developmental Dynamics 237:196 -208, 2008.

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A BAC-Based Physical Map of the Major Autosomes of Drosophila melanogaster

Cited by 128 publications

References 21 publications

The Drosophila CPEB Protein Orb2 Has a Novel Expression Pattern and Is Important for Asymmetric Cell Division and Nervous System Function

The Drosophila CPEB Protein Orb2 Has a Novel Expression Pattern and Is Important for Asymmetric Cell Division and Nervous System Function

Contigs Built with Fingerprints, Markers, and FPC V4.7

Regulation of the Drosophila lin‐41 homologue dappled by let‐7 reveals conservation of a regulatory mechanism within the LIN‐41 subclade

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