scholarly journals The Berkeley Drosophila Genome Project Gene Disruption Project: Single P-Element Insertions Mutating 25% of Vital Drosophila Genes

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 135-177 ◽  
Author(s):  
Allan C Spradling ◽  
Dianne Stern ◽  
Amy Beaton ◽  
E Jay Rhem ◽  
Todd Laverty ◽  
...  
Keyword(s):  
Gene Disruption ◽  
Genome Project ◽  
Open Reading Frames ◽  
P Element ◽  
Model Organisms ◽  
Berkeley Drosophila Genome Project ◽  
Drosophila Genome ◽  
P Elements ◽  
Wide Range ◽  
Reading Frames

AbstractA fundamental goal of genetics and functional genomics is to identify and mutate every gene in model organisms such as Drosophila melanogaster. The Berkeley Drosophila Genome Project (BDGP) gene disruption project generates single P-element insertion strains that each mutate unique genomic open reading frames. Such strains strongly facilitate further genetic and molecular studies of the disrupted loci, but it has remained unclear if P elements can be used to mutate all Drosophila genes. We now report that the primary collection has grown to contain 1045 strains that disrupt more than 25% of the estimated 3600 Drosophila genes that are essential for adult viability. Of these P insertions, 67% have been verified by genetic tests to cause the associated recessive mutant phenotypes, and the validity of most of the remaining lines is predicted on statistical grounds. Sequences flanking >920 insertions have been determined to exactly position them in the genome and to identify 376 potentially affected transcripts from collections of EST sequences. Strains in the BDGP collection are available from the Bloomington Stock Center and have already assisted the research community in characterizing >250 Drosophila genes. The likely identity of 131 additional genes in the collection is reported here. Our results show that Drosophila genes have a wide range of sensitivity to inactivation by P elements, and provide a rationale for greatly expanding the BDGP primary collection based entirely on insertion site sequencing. We predict that this approach can bring >85% of all Drosophila open reading frames under experimental control.

scholarly journals Zygotic Lethal Mutations With Maternal Effect Phenotypes in Drosophila melanogaster. II. Loci on the Second and Third Chromosomes Identified by P-Element-Induced Mutations

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1681-1692 ◽  
Author(s):  
Norbert Perrimon ◽  
Anne Lanjuin ◽  
Charles Arnold ◽  
Elizabeth Noll
Keyword(s):  
Maternal Effect ◽  
Genome Project ◽  
P Element ◽  
Berkeley Drosophila Genome Project ◽  
Drosophila Genome ◽  
Gene Products ◽  
Induced Mutations ◽  
Lethal Mutations ◽  
Egg Formation ◽  
Normal Embryonic Development

Screens for zygotic lethal mutations that are associated with specific maternal effect lethal phenotypes have only been conducted for the X chromosome. To identify loci on the autosomes, which represent four-fifths of the Drosophila genome, we have used the autosomal “FLP-DFS” technique to screen a collection of 496 P element-induced mutations established by the Berkeley Drosophila Genome Project. We have identified 64 new loci whose gene products are required for proper egg formation or normal embryonic development.

scholarly journals Ras1 Interacts With Multiple New Signaling and Cytoskeletal Loci in Drosophila Eggshell Patterning and Morphogenesis

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 609-622
Author(s):  
Jon D Schnorr ◽  
Robert Holdcraft ◽  
Brett Chevalier ◽  
Celeste A Berg
Keyword(s):  
Cell Signaling ◽  
Egf Receptor ◽  
Genome Project ◽  
Dominant Negative ◽  
P Element ◽  
Follicle Cells ◽  
Berkeley Drosophila Genome Project ◽  
Ras Signaling ◽  
Drosophila Genome ◽  
Epithelial Sheet

Abstract Little is known about the genes that interact with Ras signaling pathways to regulate morphogenesis. The synthesis of dorsal eggshell structures in Drosophila melanogaster requires multiple rounds of Ras signaling followed by dramatic epithelial sheet movements. We took advantage of this process to identify genes that link patterning and morphogenesis; we screened lethal mutations on the second chromosome for those that could enhance a weak Ras1 eggshell phenotype. Of 1618 lethal P-element mutations tested, 13 showed significant enhancement, resulting in forked and fused dorsal appendages. Our genetic and molecular analyses together with information from the Berkeley Drosophila Genome Project reveal that 11 of these lines carry mutations in previously characterized genes. Three mutations disrupt the known Ras1 cell signaling components Star, Egfr, and Blistered, while one mutation disrupts Sec61β, implicated in ligand secretion. Seven lines represent cell signaling and cytoskeletal components that are new to the Ras1 pathway; these are Chickadee (Profilin), Tec29, Dreadlocks, POSH, Peanut, Smt3, and MESK2, a suppressor of dominant-negative Ksr. A twelfth insertion disrupts two genes, Nrk, a “neurospecific” receptor tyrosine kinase, and Tpp, which encodes a neuropeptidase. These results suggest that Ras1 signaling during oogenesis involves novel components that may be intimately associated with additional signaling processes and with the reorganization of the cytoskeleton. To determine whether these Ras1 Enhancers function upstream or downstream of the Egf receptor, four mutations were tested for their ability to suppress an activated Egfr construct (λtop) expressed in oogenesis exclusively in the follicle cells. Mutations in Star and l(2)43Bb had no significant effect upon the λtop eggshell defect whereas smt3 and dock alleles significantly suppressed the λtop phenotype.

scholarly journals Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1103-1115 ◽  
Author(s):  
Hongguang Shao ◽  
Zhijian Tu
Keyword(s):  
Phylogenetic Analyses ◽  
Mosquito Species ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Sequence Comparisons ◽  
Wide Range ◽  
Multiple Copies ◽  
Catalytic Motif ◽  
Open The Doors ◽  
Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

scholarly journals Genome of Staphylococcal Phage K: a New Lineage of Myoviridae Infecting Gram-Positive Bacteria with a Low G+C Content

2004 ◽  
Vol 186 (9) ◽  
pp. 2862-2871 ◽  
Author(s):  
S. O'Flaherty ◽  
A. Coffey ◽  
R. Edwards ◽  
W. Meaney ◽  
G. F. Fitzgerald ◽  
...  
Keyword(s):  
Restriction Enzymes ◽  
Rnase H ◽  
Open Reading Frames ◽  
The Other ◽  
Gram Positive Bacteria ◽  
Acid Protein ◽  
Wide Range ◽  
Highly Virulent ◽  
Reading Frames ◽  
Amino Acid Protein

ABSTRACT Phage K is a polyvalent phage of the Myoviridae family which is active against a wide range of staphylococci. Phage genome sequencing revealed a linear DNA genome of 127,395 bp, which carries 118 putative open reading frames. The genome is organized in a modular form, encoding modules for lysis, structural proteins, DNA replication, and transcription. Interestingly, the structural module shows high homology to the structural module from Listeria phage A511, suggesting intergenus horizontal transfer. In addition, phage K exhibits the potential to encode proteins necessary for its own replisome, including DNA ligase, primase, helicase, polymerase, RNase H, and DNA binding proteins. Phage K has a complete absence of GATC sites, making it insensitive to restriction enzymes which cleave this sequence. Three introns (lys-I1, pol-I2, and pol-I3) encoding putative endonucleases were located in the genome. Two of these (pol-I2 and pol-I3) were found to interrupt the DNA polymerase gene, while the other (lys-I1) interrupts the lysin gene. Two of the introns encode putative proteins with homology to HNH endonucleases, whereas the other encodes a 270-amino-acid protein which contains two zinc fingers (CX2CX22CX2C and CX2CX23CX2C). The availability of the genome of this highly virulent phage, which is active against infective staphylococci, should provide new insights into the biology and evolution of large broad-spectrum polyvalent phages.

scholarly journals Reconstructing the invasion route of DNA transposons using extant population samples

2019 ◽  
Author(s):  
Lukas Weilguny ◽  
Christos Vlachos ◽  
Divya Selvaraju ◽  
Robert Kofler
Keyword(s):  
P Element ◽  
Model Organisms ◽  
Migration Patterns ◽  
Dna Transposons ◽  
Time Points ◽  
Wide Range ◽  
Invasion Routes ◽  
Geographic Regions ◽  
Extant Population ◽  
Shed Light

AbstractReconstructing invasion routes of transposable elements (TEs), so far, required capturing an ongoing invasion with population samples from different geographic regions and time points. Here, we propose a more accessible approach. Abundantly occurring internal deletions of DNA transposons allow to trace the direction as well as the path of an invasion, even hundreds of generations after the spread of a TE. We validated this hypothesis with computer simulations and by accurately reproducing the route of the P-element invasion in Drosophila melanogaster. Finally, we used our method to shed light on the controversial hobo invasion in D. melanogaster. Our approach solely requires sequenced samples from extant populations and sequences of TEs of interest. Hence, DNA transposons in a wide range of model and non-model organisms may be analyzed. Our approach will further our understanding of TE dynamics, migration patterns, and the ecology of species.

scholarly journals HYBRID DYSGENESIS IN DROSOPHILA MELANOGASTER: NATURE AND INHERITANCE OF P ELEMENT REGULATION

Genetics ◽  
1985 ◽  
Vol 111 (2) ◽  
pp. 337-350
Author(s):  
Margaret G Kidwell
Keyword(s):  
Gonadal Dysgenesis ◽  
Continuous Distribution ◽  
Hybrid Dysgenesis ◽  
P Element ◽  
Variable Degree ◽  
Genetic Determination ◽  
Strain Characteristic ◽  
P Elements ◽  
Wide Range ◽  
P Element Regulation

ABSTRACT The genetic determination of the control of resistance or susceptibility to germ line changes mediated by P elements was studied in two strains and in derivatives of crosses between them. One strain, characterized as true M, completely lacked P elements. The second strain, pseudo-M (M'), carried a number of P elements, but these did not have the potential to induce the gonadal sterility that is associated with P-M hybrid dysgenesis. Individuals from the true M strain were invariably unable to suppress P factor activity (i.e., all daughters of outcrosses of M females and P males were sterile). In contrast, individuals from the M' strain showed variable degrees of suppression that were manifested in a wide range of gonadal sterility frequencies in standard tests. This continuous distribution pattern was reproducible for more than 25 generations.—The results of the genetic analysis indicate that a strain with a variable degree of suppression of gonadal dysgenesis is not necessarily in a transient state between the extreme conditions of P and M cytotype. A large variance in the ability to suppress gonadal dysgenesis with a mean value intermediate between the extremes of P and M cytotype may be a relatively stable strain characteristic. No reciprocal cross effect was observed in the suppression of sterility of F1 females from M × M' matings. Thus, the existence of M' strains indicates a Mendelian component in P element regulation and suggests that cytotype, which has an extrachromosomal aspect, may be only one of perhaps several mechanisms involved in regulation. Analysis of the effects of individual chromosomes from the M' strain showed that each chromosome contributed to the reduction of gonadal dysgenesis in the progeny of test matings. The results are consistent with a one-component titration model for P element regulation.

A new P element subfamily from Drosophila tristis, D. ambigua, and D. obscura

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 978-985 ◽  
Author(s):  
S. Hagemann ◽  
E. Haring ◽  
W. Pinsker
Keyword(s):  
Drosophila Melanogaster ◽  
Genomic Sequence ◽  
P Element ◽  
Inverted Repeats ◽  
Sequence Comparisons ◽  
Closely Related Species ◽  
Dna Phylogeny ◽  
P Elements ◽  
Obscura Group ◽  
Reading Frames

A new P element subfamily, designated T-type, was found in the genomes of the three closely related species Drosophila ambigua, Drosophila obscura, and Drosophila tristis. The subfamily comprises both full-sized and internally deleted P elements. The T-type element of D. ambigua is longer than the canonical P elements owing to a 300-bp insertion in the 3′ noncoding region. Tandemly arranged T-type elements were detected in D. ambigua and D. tristis. The overall structure of T-type elements resembles that of the Drosophila melanogaster P element and the termini are formed by perfect inverted repeats of 33 bp. However, none of the elements studied so far have intact reading frames. Sequence comparisons with other P element subfamilies from the obscura group indicate that the T-type elements are most closely related to the terminally truncated P homologues of Drosophila guanche and Drosophila subobscura. Therefore they can be considered as the lineage-specific P transposons of the obscura group. Furthermore, this finding indicates that the clustered P homologues of D. guanche and D. subobscura must be derived from transpositionally active P elements rather than from an immobile genomic sequence. Key words : Drosophila, obscura group, P element, transposon, DNA phylogeny.

AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model

2019 ◽  
Vol 35 (16) ◽  
pp. 2834-2842 ◽  
Author(s):  
Yang Yang ◽  
Mingyu Zhou ◽  
Qingwei Fang ◽  
Hong-Bin Shen
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Image Annotation ◽  
Fruit Fly ◽  
Genome Project ◽  
Supplementary Information ◽  
Berkeley Drosophila Genome Project ◽  
Drosophila Genome ◽  
Single Instance ◽  
Temporal Expression Pattern

Abstract Motivation In the post-genomic era, image-based transcriptomics have received huge attention, because the visualization of gene expression distribution is able to reveal spatial and temporal expression pattern, which is significantly important for understanding biological mechanisms. The Berkeley Drosophila Genome Project has collected a large-scale spatial gene expression database for studying Drosophila embryogenesis. Given the expression images, how to annotate them for the study of Drosophila embryonic development is the next urgent task. In order to speed up the labor-intensive labeling work, automatic tools are highly desired. However, conventional image annotation tools are not applicable here, because the labeling is at the gene-level rather than the image-level, where each gene is represented by a bag of multiple related images, showing a multi-instance phenomenon, and the image quality varies by image orientations and experiment batches. Moreover, different local regions of an image correspond to different CV annotation terms, i.e. an image has multiple labels. Designing an accurate annotation tool in such a multi-instance multi-label scenario is a very challenging task. Results To address these challenges, we develop a new annotator for the fruit fly embryonic images, called AnnoFly. Driven by an attention-enhanced RNN model, it can weight images of different qualities, so as to focus on the most informative image patterns. We assess the new model on three standard datasets. The experimental results reveal that the attention-based model provides a transparent approach for identifying the important images for labeling, and it substantially enhances the accuracy compared with the existing annotation methods, including both single-instance and multi-instance learning methods. Availability and implementation http://www.csbio.sjtu.edu.cn/bioinf/annofly/ Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints

Life ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 701
Author(s):  
Bo Song ◽  
Mengyun Jiang ◽  
Lei Gao
Keyword(s):  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Model Organisms ◽  
Widespread Application ◽  
Optimized Protocol ◽  
Membrane Bound ◽  
Noise Tolerant ◽  
Diverse Plant Species ◽  
Small Orfs ◽  
Reading Frames

Ribo-seq, also known as ribosome profiling, refers to the sequencing of ribosome-protected mRNA fragments (RPFs). This technique has greatly advanced our understanding of translation and facilitated the identification of novel open reading frames (ORFs) within untranslated regions or non-coding sequences as well as the identification of non-canonical start codons. However, the widespread application of Ribo-seq has been hindered because obtaining periodic RPFs requires a highly optimized protocol, which may be difficult to achieve, particularly in non-model organisms. Furthermore, the periodic RPFs are too short (28 nt) for accurate mapping to polyploid genomes, but longer RPFs are usually produced with a compromise in periodicity. Here we present RiboNT, a noise-tolerant ORF predictor that can utilize RPFs with poor periodicity. It evaluates RPF periodicity and automatically weighs the support from RPFs and codon usage before combining their contributions to identify translated ORFs. The results demonstrate the utility of RiboNT for identifying both long and small ORFs using RPFs with either good or poor periodicity. We implemented the pipeline on a dataset of RPFs with poor periodicity derived from membrane-bound polysomes of Arabidopsis thaliana seedlings and identified several small ORFs (sORFs) evolutionarily conserved in diverse plant species. RiboNT should greatly broaden the application of Ribo-seq by minimizing the requirement of RPF quality and allowing the use of longer RPFs, which is critical for organisms with complex genomes because these RPFs can be more accurately mapped to the position from which they were derived.

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