1
|
Three-Dimensional Genome Organization and Function in Drosophila. Genetics 2017; 205:5-24. [PMID: 28049701 PMCID: PMC5223523 DOI: 10.1534/genetics.115.185132] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/15/2016] [Indexed: 12/18/2022] Open
Abstract
Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques.
Collapse
|
2
|
Wu R. Development of enzyme-based methods for DNA sequence analysis and their applications in the genome projects. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 67:431-68. [PMID: 8322619 DOI: 10.1002/9780470123133.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R Wu
- Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY
| |
Collapse
|
3
|
Michellod MA, Forquignon F, Santamaria P, Randsholt NB. Differential requirements for the neurogenic gene almondex during Drosophila melanogaster development. Genesis 2004; 37:113-22. [PMID: 14595834 DOI: 10.1002/gene.10233] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
During early development, the neurogenic genes of Drosophila melanogaster are involved in the control of cell fates in the neurectoderm; almondex (amx) belongs to this category of genes. We have identified the amx locus and rescued the amx embryonic neurogenic phenotype with a 1.5 kb DNA fragment. Using a small deficiency, we generated a new amx mutant background called amx(m), which is a null allele. Besides the characteristic neurogenic maternal effect caused by loss of amx, amx(m) flies display a new imaginal phenotype resembling loss of function of Notch. We describe amx-induced misregulation of the Notch pathway target E(spl) m7 in embryos and genetic interactions between amx and Notch pathway mutants in adult flies. These data show that wildtype amx acts as a novel positive regulator of the Notch pathway and is required at different levels during development.
Collapse
Affiliation(s)
- Marie-Agnès Michellod
- Centre de Génétique Moléculaire du C.N.R.S., UPR 2167 CNRS, associée à l'Université de Paris 6, Gif-sur-Yvette, France
| | | | | | | |
Collapse
|
4
|
Saura AO, Heino TI, Sorsa V. Electron microscopic analysis of the banding pattern in the salivary gland chromosomes of Drosophila melanogaster. Divisions 11 through 20 of X. Hereditas 2004; 119:123-41. [PMID: 8106260 DOI: 10.1111/j.1601-5223.1993.00123.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The banding pattern of the proximal half of the polytene salivary gland X chromosome of Drosophila melanogaster was studied using thin section electron microscopy. The bands were identified according to Bridges' revised light microscopic map. On Bridges' map, the divisions 11 to 20 contain 112 single bands and as many as 181 double bands. A majority of Bridges' single bands were identified in the thin sections. A total of 23 Bridges' single bands (and 4 bands of division 20) could not be found; in particular, bands were missing from the difficult regions 11DE, 15A, 15C and 16A. Electron microscopy showed the existence of 18 additional faint bands, 4 at the region 18D and 7 at 19EF. Bridges' faintest single bands and the new bands were best seen in formaldehyde fixed material. About 1/4 of Bridges' double bands were found to be made up of two separate bands each. The remaining Bridges' doublets include all kinds of bands: broad, narrow, dark, faint, puffed. Many of them look single in thin sections.
Collapse
Affiliation(s)
- A O Saura
- Department of Genetics, University of Helsinki, Finland
| | | | | |
Collapse
|
5
|
Saura AO, Heino TI, Sorsa V. Electron micrograph map of the Drosophila melanogaster polytene chromosome 3R divisions 91 through 100. Hereditas 2004; 124:71-90. [PMID: 8690616 DOI: 10.1111/j.1601-5223.1996.00071.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The banding pattern of the distal half of the polytene salivary gland 3R chromosome of Drosophila melanogaster was studied by means of the thin section electron microscopy. Bands were identified according to the revised light microscopic map of Bridges. Bridges' map contains 332 single bands and 137 double bands within the region 91 through 100. This makes a total of 606 bands when the doublets are counted as two bands each, but 469 bands when the doublets are counted as one band. In the electron micrographs we found a total of 443 bands within this region. 109 Bridges' singlets were easily detected in almost all thin sections, while 144 mainly faint bands could be seen only in some micrographs. 79 Bridges' single bands and one doublet (94D7-8) could not be found. 42 Bridges' doublets were made up of two separate bands each, 87 Bridges' doublets looked single, and three pairs of Bridges' doublets formed dark complexes in the thin sections. The telomere region with the most distal band 100F4-5 was gray. A total of 15 new bands, which are not drawn on Bridges' map, were detected. Most of the new bands were in the divisions 96 and 99.
Collapse
Affiliation(s)
- A O Saura
- Department of Biosciences, University of Helsinki, Finland
| | | | | |
Collapse
|
6
|
Yezerski A, Stevens L, Ametrano J. A genetic linkage map for Tribolium confusum based on random amplified polymorphic DNAs and recombinant inbred lines. INSECT MOLECULAR BIOLOGY 2003; 12:517-526. [PMID: 12974957 DOI: 10.1046/j.1365-2583.2003.00438.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Tribolium beetles provide an excellent and easily manipulated model system for the study of genetics. However, despite significant increases in the availability of molecular markers for the study of genetics in recent years, a significant genetic linkage map for these beetles remains undeveloped. We present the first molecular genetic linkage map for Tribolium confusum using random amplified polymorphic DNA markers. The linkage map contains 137 loci mapped on to eight linkage groups totaling 968.5 cM.
Collapse
Affiliation(s)
- A Yezerski
- King's College, Biology Department, 133 North River Street, Wilkes-Barre, PA 18711, USA.
| | | | | |
Collapse
|
7
|
Volpe AM, Horowitz H, Grafer CM, Jackson SM, Berg CA. Drosophila rhino encodes a female-specific chromo-domain protein that affects chromosome structure and egg polarity. Genetics 2001; 159:1117-34. [PMID: 11729157 PMCID: PMC1461866 DOI: 10.1093/genetics/159.3.1117] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Here we describe our analyses of Rhino, a novel member of the Heterochromatin Protein 1(HP1) subfamily of chromo box proteins. rhino (rhi) is expressed only in females and chiefly in the germline, thus providing a new tool to dissect the role of chromo-domain proteins in development. Mutations in rhi disrupt eggshell and embryonic patterning and arrest nurse cell nuclei during a stage-specific reorganization of their polyploid chromosomes, a mitotic-like state called the "five-blob" stage. These visible alterations in chromosome structure do not affect polarity by altering transcription of key patterning genes. Expression levels of gurken (grk), oskar (osk), bicoid (bcd), and decapentaplegic (dpp) transcripts are normal, with a slight delay in the appearance of bcd and dpp mRNAs. Mislocalization of grk and osk transcripts, however, suggests a defect in the microtubule reorganization that occurs during the middle stages of oogenesis and determines axial polarity. This defect likely results from aberrant Grk/Egfr signaling at earlier stages, since rhi mutations delay synthesis of Grk protein in germaria and early egg chambers. In addition, Grk protein accumulates in large, actin-caged vesicles near the endoplasmic reticulum of stages 6-10 egg chambers. We propose two hypotheses to explain these results. First, Rhi may play dual roles in oogenesis, independently regulating chromosome compaction in nurse cells at the end of the unique endoreplication cycle 5 and repressing transcription of genes that inhibit Grk synthesis. Thus, loss-of-function mutations arrest nurse cell chromosome reorganization at the five-blob stage and delay production or processing of Grk protein, leading to axial patterning defects. Second, Rhi may regulate chromosome compaction in both nurse cells and oocyte. Loss-of-function mutations block nurse cell nuclear transitions at the five-blob stage and activate checkpoint controls in the oocyte that arrest Grk synthesis and/or inhibit cytoskeletal functions. These functions may involve direct binding of Rhi to chromosomes or may involve indirect effects on pathways controlling these processes.
Collapse
Affiliation(s)
- A M Volpe
- Department of Genetics, University of Washington, Seattle, Washington 98195-7360, USA
| | | | | | | | | |
Collapse
|
8
|
Benos PV, Gatt MK, Murphy L, Harris D, Barrell B, Ferraz C, Vidal S, Brun C, Demaille J, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Borkova D, Miñana B, Kafatos FC, Bolshakov S, Sidén-Kiamos I, Papagiannakis G, Spanos L, Louis C, Madueño E, de Pablos B, Modolell J, Peter A, Schöttler P, Werner M, Mourkioti F, Beinert N, Dowe G, Schäfer U, Jäckle H, Bucheton A, Callister D, Campbell L, Henderson NS, McMillan PJ, Salles C, Tait E, Valenti P, Saunders RD, Billaud A, Pachter L, Glover DM, Ashburner M. From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies. Genome Res 2001; 11:710-30. [PMID: 11337470 PMCID: PMC311117 DOI: 10.1101/gr.173801] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2000] [Accepted: 02/16/2001] [Indexed: 11/24/2022]
Abstract
We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through "shotgun" sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation.
Collapse
Affiliation(s)
- P V Benos
- EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Lukacsovich T, Asztalos Z, Juni N, Awano W, Yamamoto D. The Drosophila melanogaster 60A chromosomal division is extremely dense with functional genes: their sequences, genomic organization, and expression. Genomics 1999; 57:43-56. [PMID: 10191082 DOI: 10.1006/geno.1999.5746] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We cloned and sequenced genomic DNA contigs spanning over 45 kb, surrounding the insertion site of the P-element that is responsible for the developmental defects in the ken and barbie (ken) mutant of Drosophila. This region harbors 10 functional transcription units, in addition to the already well-characterized TGFbeta-60A gene. These include the genes, undefined 1 (UD1), UD2, and UD3, each coding for proteins of unknown function, the ken gene encoding a new Krüppel-like putative transcription factor, the fly homologues of the mammalian mitochondrial trifunctional enzyme (thiolase), and the TAR DNA-binding protein-43 (TBPH), the first nonvertebrate member of the transmembrane 4 superfamily (TM4SF) gene, a new homeodomain gene, and a gene coding for a putative nuclear binding protein (PNBP) that is homologous to maleless, and a Copia-like element. UD3 exists in an intron of the maleless homologue, yet is expressed independent of it. The UD1 and TM4SF genes orient in a tail-to-tail manner with their 3' untranslated region sequences overlapping over 44 nucleotides. Thus the partial overlap and intraintronic organization permitted dense packing of the functional genes within a short segment of the genome.
Collapse
Affiliation(s)
- T Lukacsovich
- ERATO Yamamoto Behavior Genes Project, Mitsubishi Kasei Institute of Life Sciences, Machida, 194-8511, Japan
| | | | | | | | | |
Collapse
|
10
|
Alphey L, Jimenez J, Glover D. A Drosophila homologue of oxysterol binding protein (OSBP)--implications for the role of OSBP. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1395:159-64. [PMID: 9473651 DOI: 10.1016/s0167-4781(97)00159-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The identification of a Drosophila homologue (OSBP-Dm) of mammalian oxysterol binding protein (OSBP) is reported. OSBP-Dm was identified by its ability to overcome the cell cycle arrest induced by over-expression of Wee1p in fission yeast. OSBP-Dm has an overall sequence identity of 52% with mammalian OSBP, and shows a number of highly conserved regions of functional significance. Insects are unable to biosynthesize the steroid core, relying instead on dietary sterols to satisfy their requirements. It is therefore unlikely that OSBP-Dm is involved in feedback inhibition of the mevalonate pathway, as has previously been suggested for its mammalian homologues.
Collapse
Affiliation(s)
- L Alphey
- School of Biological Sciences, University of Manchester, UK.
| | | | | |
Collapse
|
11
|
Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
12
|
Louis C, Madueño E, Modolell J, Omar MM, Papagiannakis G, Saunders RD, Savakis C, Sidén-Kiamos I, Spanos L, Topalis P, Zhang YQ, Ashburner M, Benos P, Bolshakov VN, Deak P, Glover DM, Herrmann S, Kafatos FC. One-hundred and five new potential Drosophila melanogaster genes revealed through STS analysis. Gene 1997; 195:187-93. [PMID: 9305763 DOI: 10.1016/s0378-1119(97)00138-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Complementation analysis had suggested that the Drosophila melanogaster genome contains approximately 5000 genes, but it is now generally accepted that the actual number is several times as high. We report here an analysis of 1788 anonymous sequence tagged sites (STSs) from the European Drosophila Genome Project (EDGP), totalling 463 kb. The data reveal a substantial number of previously undescribed potential genes, amounting to 6.1% of the number of Drosophila genes already in the sequence databases.
Collapse
Affiliation(s)
- C Louis
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Alphey L, Parker L, Hawcroft G, Guo Y, Kaiser K, Morgan G. KLP38B: a mitotic kinesin-related protein that binds PP1. J Cell Biol 1997; 138:395-409. [PMID: 9230081 PMCID: PMC2138191 DOI: 10.1083/jcb.138.2.395] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/1996] [Revised: 04/14/1997] [Indexed: 02/04/2023] Open
Abstract
We have identified a new member of the kinesin superfamily in Drosophila, KLP38B (kinesin-like protein at 38B). KLP38B was isolated through its two-hybrid interaction with the catalytic subunit of type 1 serine/threonine phosphoprotein phosphatase (PP1). We demonstrate that recombinant KLP38B and PP1 associate in vitro. This is the first demonstration of direct binding of a kinesin-related protein to a regulatory enzyme. Though most closely related to the Unc-104 subfamily of kinesin-related proteins, KLP38B is expressed only in proliferating cells. KLP38B mutants show cell proliferation defects in many tissues. KLP38B is required for normal chromatin condensation as embryos from KLP38B mutant mothers have undercondensed chromatin at metaphase and anaphase. This is the first time that a kinesin-related protein has been shown to have such a role. Incomplete lethality of a strong KLP38B allele suggests partial redundancy with one or more additional kinesin-related proteins.
Collapse
Affiliation(s)
- L Alphey
- School of Biological Sciences, University of Manchester, Manchester M13 9PT, UK.
| | | | | | | | | | | |
Collapse
|
14
|
Segarra C, Lozovskaya ER, Ribó G, Aguadé M, Hartl DL. P1 clones from Drosophila melanogaster as markers to study the chromosomal evolution of Muller's A element in two species of the obscura group of Drosophila. Chromosoma 1995; 104:129-36. [PMID: 8585990 DOI: 10.1007/bf00347695] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Thirty P1 clones from the X chromosome (Muller's A element) of Drosophila melanogaster were cross-hybridized in situ to Drosophila subobscura and Drosophila pseudoobscura polytene chromosomes. An additional recombinant phage lambda Dsuby was also used as a marker. Twenty-three (77%) of the P1 clones gave positive hybridization on D. pseudoobscura chromosomes but only 16 (53%) did so with those of D. subobscura. Eight P1 clones gave more than one hybridization signal on D. pseudoobscura and/or D. subobscura chromosomes. All P1 clones and lambda Dsuby hybridized on Muller's A element (X chromosome) of D. subobscura. In contrast, only 18 P1 clones and lambda Dsuby hybridized on Muller's A element (XL chromosomal arm) of D. pseudoobscura; 4 additional P1 clones hybridized on Muller's D element (XR chromosomal arm) of this species and the remaining P1 clone gave one hybridization signal on each arm of the X chromosome. This latter clone may contain one breakpoint of a pericentric inversion that may account for the interchange of genetic material between Muller's A and D elements in D. pseudoobscura. In contrast to the rare interchange of genetic material between chromosomal elements, profound differences in the order and spacing of markers were detected between D. melanogaster, D. pseudoobscura and D. subobscura. In fact, the number of chromosomal segments delimited by identical markers and conserved between pairwise comparisons is small. Therefore, extensive reorganization within Muller's A element has been produced during the divergence of the three species. Rough estimates of the number of cytologically detectable inversions contributing to differentiation of Muller's A element were obtained. The most reliable of these estimates is that obtained from the D. pseudoobscura and D. melanogaster comparison since a greater number of markers have been mapped in both species. Tentatively, one inversion breakpoint about every 200 kb has been produced and fixed during the divergence of D. pseudoobscura and D. melanogaster.
Collapse
Affiliation(s)
- C Segarra
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, E-08071 Barcelona, Spain
| | | | | | | | | |
Collapse
|
15
|
Brown SE, Menninger J, Difillipantonio M, Beaty BJ, Ward DC, Knudson DL. Toward a physical map of Aedes aegypti. INSECT MOLECULAR BIOLOGY 1995; 4:161-167. [PMID: 8589842 DOI: 10.1111/j.1365-2583.1995.tb00021.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Labelled recombinant cosmids were used as in situ hybridization probes to Aedes aegypti metaphase chromosomes. The cosmid probes yielded paired signals, one on each arm of sister chromatids, and they were ordered along the three chromosomes. In total, thirty-seven different probes were mapped to the three chromosomes of Ae. aegypti (2n = 6): twenty-eight to chromosome 1, six to chromosome 2, and six to chromosome 3. These results represent an initial stage in the generation of a physical map of the Ae. aegypti genome.
Collapse
Affiliation(s)
- S E Brown
- Department of Entomology, College of Agricultural Sciences, Colorado State University, Fort Collins 80523, USA
| | | | | | | | | | | |
Collapse
|
16
|
Hartl DL, Nurminsky DI, Jones RW, Lozovskaya ER. Genome structure and evolution in Drosophila: applications of the framework P1 map. Proc Natl Acad Sci U S A 1994; 91:6824-9. [PMID: 8041703 PMCID: PMC44290 DOI: 10.1073/pnas.91.15.6824] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Physical maps showing the relative locations of cloned DNA fragments in the genome are important resources for research in molecular genetics, genome analysis, and evolutionary biology. In addition to affording a common frame of reference for organizing diverse types of genetic data, physical maps also provide ready access to clones containing DNA sequences from any defined region of the genome. In this paper, we present a physical map of the genome of Drosophila melanogaster based on in situ hybridization with 2461 DNA fragments, averaging approximately 80 kilobase pairs each, cloned in bacteriophage P1. The map is a framework map in the sense that most putative overlaps between clones have not yet been demonstrated at the molecular level. Nevertheless, the framework map includes approximately 85% of all genes in the euchromatic genome. A continuous physical map composed of sets of overlapping P1 clones (contigs), which together span most of the euchromatic genome, is currently being assembled by screening a library of 9216 P1 clones with single-copy genetic markers as well as with the ends of the P1 clones already assigned positions in the framework map. Because most P1 clones from D. melanogaster hybridize in situ with chromosomes from related species, the framework map also makes it possible to determine the genome maps of D. pseudoobscura and other species in the subgenus Sophophora. Likewise, a P1 framework map of D. virilis affords potential access to genome organization and evolution in the subgenus Drosophila.
Collapse
Affiliation(s)
- D L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | | | | | | |
Collapse
|
17
|
Heino TI. Polytene chromosomes from ovarian pseudonurse cells of the Drosophila melanogaster otu mutant. II. Photographic map of the X chromosome. Chromosoma 1994; 103:4-15. [PMID: 8013253 DOI: 10.1007/bf00364721] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The banding pattern of the polytene chromosomes of the ovarian pseudonurse cells (PNC) of the Drosophila melanogaster otu mutant were compared with larval salivary gland (SG) polytene chromosomes. The X chromosome was studied and no significant differences were found in the banding pattern between these functionally very different tissues. Most of the differences result from differential puffing activity. In situ hybridisation with five different DNA probes located along the X chromosome was used to cross-check the results obtained by morphological mapping. The constrictions present in the SG chromosomes were found to be absent in the germ line derived PNC chromosomes. There are prominent puffs in the PNC chromosomes at certain locations where genes known to be transcriptionally active in the germ line reside. This suggests that at least some of the genes active in the wild-type nurse cells may also be active in the PNC cells.
Collapse
Affiliation(s)
- T I Heino
- Department of Genetics, University of Helsinki, Finland
| |
Collapse
|
18
|
Affiliation(s)
- M F Wolfner
- Section of Genetics and Development, Cornell University, Ithaca, New York 14853
| | | |
Collapse
|
19
|
Dombrádi V, Mann DJ, Saunders RD, Cohen PT. Cloning of the fourth functional gene for protein phosphatase 1 in Drosophila melanogaster from its chromosomal location. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 212:177-83. [PMID: 8383037 DOI: 10.1111/j.1432-1033.1993.tb17648.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Complementary DNA encoding a catalytic subunit of protein phosphatase 1, PP1 87B, hybridises at four positions (87B, 9C, 13C and 96A) to Drosophila melanogaster polytene chromosomes, three of which are known to be expressed [Dombrádi, V., Axton, J.M., Brewis, N.D., Da Cruz e Silva, E.F., Alphey, L. & Cohen, P.T.W. (1990) Eur. J. Biochem. 194, 739-745]. The fourth gene has been isolated by screening a genomic library of cosmid clones, representing division 13 of the X-chromosome of D. melanogaster, with a PP1 87B probe. This library was constructed as part of the Drosophila genome mapping project [Sidén-Kiamos, I., Saunders, R.D.C., Spanos, L., Majerus, T., Trenear, J., Savakis, C., Louis, C., Glover, D.M., Ashburner, M. & Kafatos, F.C. (1990) Nucleic Acids Res. 18, 6261-6270]. The 5' non-coding region of the isolated gene hybridised to cytological position 13C1-2. By combining reverse transcription and the polymerase chain reaction, the gene was shown to be expressed at a very low level. The PP1 13C gene encodes a protein of 302 amino acids with a predicted molecular mass of 34.5 kDa. It shows 85-94% amino acid identity to the other three protein phosphatase 1 catalytic subunits (PP1 87B, PP1 96A and PP1 9C) described previously, being most closely related to the isoform PP1 87B, which is involved in the control of chromosome separation at cell division and the regulation of chromosome condensation at interphase.
Collapse
Affiliation(s)
- V Dombrádi
- Department of Biochemistry, The University, Dundee, Scotland
| | | | | | | |
Collapse
|
20
|
Hartl DL, Lozovskaya ER. The Drosophila genome project: current status of the physical map. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1992; 103:1-8. [PMID: 1451426 DOI: 10.1016/0305-0491(92)90404-f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- D L Hartl
- Department of Genetics, Washington University, St Louis, MO 63110-1095
| | | |
Collapse
|
21
|
Hartl DL, Ajioka JW, Cai H, Lohe AR, Lozovskaya ER, Smoller DA, Duncan IW. Towards a Drosophila genome map. Trends Genet 1992; 8:70-5. [PMID: 1566375 DOI: 10.1016/0168-9525(92)90353-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A physical map of the genome of Drosophila melanogaster has been created using 965 yeast artificial chromosome (YAC) clones assigned to locations in the cytogenetic map by in situ hybridization with the polytene salivary gland chromosomes. Clones with insert sizes averaging about 200 kb, totaling 1.7 genome equivalents, have been mapped. More than 80% of the euchromatic genome is included in the mapped clones, and 75% of the euchromatic genome is included in 161 cytological contigs ranging in size up to 2.5 Mb (average size 510 kb). On the other hand, YAC coverage of the one-third of the genome constituting the heterochromatin is incomplete, and clones containing long tracts of highly repetitive simple satellite DNA sequences have not been recovered.
Collapse
Affiliation(s)
- D L Hartl
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110
| | | | | | | | | | | | | |
Collapse
|