scholarly journals Mapping Functional Associations in the Entire Genome ofDrosophila melanogasterUsing Fusion Analysis

2003 ◽  
Vol 4 (3) ◽  
pp. 337-341 ◽  
Author(s):  
Ioannis Iliopoulos ◽  
Anton J. Enright ◽  
Patrick Poullet ◽  
Christos A. Ouzounis
Keyword(s):  
Gene Fusion ◽  
Sequence Similarity ◽  
Developmental Pathways ◽  
Fusion Event ◽  
Entire Genome ◽  
Additional Information ◽  
Low Degree ◽  
Associated Proteins ◽  
Fusion Analysis ◽  
Additional Constraints

We have previously shown that the detection of gene fusion events can contribute towards the elucidation of functional associations of proteins within entire genomes. Here we have analysed the entire genome ofDrosophila melanogasterusing fusion analysis and two additional constraints that improve the reliability of the predictions, viz. low sequence similarity and low degree of paralogy of the component proteins involved in a fusion event. Imposing these constraints, the total number of unique component pairs is reduced from 18 654 to a mere 220 cases, which are expected to represent some of the most reliably detected functionally associated proteins. Using additional information from sequence databases, we have been able to detect pairs of functionally associated proteins with important functions in cellular and developmental pathways, such as spermatogenesis and programmed cell death.

scholarly journals A New Type of Fusion Analysis Applicable to Many Organisms: Protein Fusions to the URA3 Gene of Yeast

Genetics ◽  
1987 ◽  
Vol 117 (1) ◽  
pp. 5-12
Author(s):  
Eric Alani ◽  
Nancy Kleckner
Keyword(s):  
Gene Fusion ◽  
Enzyme Assay ◽  
Decarboxylase Activity ◽  
Lacz Gene ◽  
Coding Region ◽  
Ura3 Gene ◽  
Promoter Sequences ◽  
E Coli ◽  
New Type ◽  
Fusion Analysis

ABSTRACT We have made constructs that join the promoter sequences and a portion of the coding region of the Saccharomyces cerevisiae HIS4 and GAL1 genes and the E. coli lacZ gene to the sixth codon of the S. cerevisiae URA3 gene (encodes orotidine-5′-phosphate (OMP) decarboxylase) to form three in frame protein fusions. In each case the fusion protein has OMP decarboxylase activity as assayed by complementation tests and this activity is properly regulated. A convenient cassette consisting of the URA3 segment plus some immediately proximal amino acids of HIS4C is available for making URA3 fusions to other proteins of interest. URA3 fusions offer several advantages over other systems for gene fusion analysis: the URA3 specified protein is small and cytosolic; genetic selections exist to identify mutants with either increased or decreased URA3 function in both yeast (S. cerevisiae and Schizosaccharomyces pombe) and bacteria (Escherichia coli and Salmonella typhimurium); and a sensitive OMP decarboxylase enzyme assay is available. Also, OMP decarboxylase activity is present in mammals, Drosophila and plants, so URA3 fusions may eventually be applicable in these other organisms as well.

scholarly journals Protein functional links in Trypanosoma brucei, identified by gene fusion analysis

2011 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitris Dimitriadis ◽  
V Lila Koumandou ◽  
Philip Trimpalis ◽  
Sophia Kossida
Keyword(s):  
Trypanosoma Brucei ◽  
Gene Fusion ◽  
Fusion Analysis

scholarly journals Architecture of the Bacterial Flagellar Distal Rod and Hook of Salmonella

Biomolecules ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 260 ◽  
Author(s):  
Yumiko Saijo-Hamano ◽  
Hideyuki Matsunami ◽  
Keiichi Namba ◽  
Katsumi Imada
Keyword(s):  
Mechanical Properties ◽  
Structural Model ◽  
Sequence Similarity ◽  
Significant Sequence Similarity ◽  
Protein Subunits ◽  
Bacterial Flagellum ◽  
Curved Tube ◽  
Single Protein ◽  
Associated Proteins ◽  
Density Map

The bacterial flagellum is a large molecular complex composed of thousands of protein subunits for motility. The filamentous part of the flagellum, which is called the axial structure, consists of the filament, the hook, and the rods, with other minor components—the cap protein and the hook associated proteins. They share a common basic architecture of subunit arrangement, but each part shows quite distinct mechanical properties to achieve its specific function. The distal rod and the hook are helical assemblies of a single protein, FlgG and FlgE, respectively. They show a significant sequence similarity but have distinct mechanical characteristics. The rod is a rigid, straight cylinder, whereas the hook is a curved tube with high bending flexibility. Here, we report a structural model of the rod constructed by using the crystal structure of a core fragment of FlgG with a density map obtained previously by electron cryomicroscopy. Our structural model suggests that a segment called L-stretch plays a key role in achieving the distinct mechanical properties of the rod using a structurally similar component protein to that of the hook.

scholarly journals Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain

2017 ◽  
Vol 2017 ◽  
pp. 1-9
Author(s):  
Fuyi Xu ◽  
Tianzhu Chao ◽  
Yiyin Zhang ◽  
Shixian Hu ◽  
Yuxun Zhou ◽  
...  
Keyword(s):  
Mouse Strain ◽  
Sequence Similarity ◽  
Chromosome 1 ◽  
Nucleotide Polymorphisms ◽  
Mus Musculus Domesticus ◽  
Entire Genome ◽  
Functional Variants ◽  
Outbred Mouse ◽  
Km Mouse ◽  
New Perspective

The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms (SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. Moreover, 46,590 of them were classified as novel mutations. Further functional annotation identified 155 genes harboring potentially functional variants, among which 27 genes have been associated with human diseases. We then performed sequence similarity and Bayesian concordance analysis using the SNPs identified on Chr 1 and their counterparts in three subspecies, Mus musculus domesticus, M. m. musculus, and M. m. castaneus. Both analyses suggested that the Chr 1 sequence of B6-Chr1KM was predominantly derived from M. m. domesticus while 9.7% of the sequence was found to be from M. m. musculus. In conclusion, our analysis provided a detailed description of the genetic variations on Chr 1 of B6-Chr1KM and a new perspective on the subspecies origin of KM mouse which can be used to guide further genetic studies with this mouse strain.

scholarly journals Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review

Diagnostics ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 521
Author(s):  
Rossella Bruno ◽  
Gabriella Fontanini
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Gene Fusion ◽  
Repetitive Sequences ◽  
Clinical Samples ◽  
Gene Fusions ◽  
Next Generation ◽  
Hybrid Capture ◽  
Fusion Analysis ◽  
Generation Sequencing

Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.

A case of cutaneous syncytial myoepithelioma with extensive adipocytic metaplasia: Usefulness of EWSR1‐PBX3 gene fusion analysis

2021 ◽  
Author(s):  
Kanade Shimada ◽  
Osamu Ansai ◽  
Tatsuya Katsumi ◽  
Tokiko Deguchi ◽  
Ryota Hayashi ◽  
...  
Keyword(s):  
Gene Fusion ◽  
Fusion Analysis

scholarly journals mini spindles

1999 ◽  
Vol 146 (5) ◽  
pp. 1005-1018 ◽  
Author(s):  
C. Fiona Cullen ◽  
Peter Deák ◽  
David M. Glover ◽  
Hiroyuki Ohkura
Keyword(s):  
Cell Cycle ◽  
Mitotic Spindle ◽  
Structural Integrity ◽  
Sequence Similarity ◽  
High Similarity ◽  
Microtubule Associated Proteins ◽  
Spindle Poles ◽  
Associated Proteins ◽  
Diploid Cells

We describe a new Drosophila gene, mini spindles (msps) identified in a cytological screen for mitotic mutant. Mutation in msps disrupts the structural integrity of the mitotic spindle, resulting in the formation of one or more small additional spindles in diploid cells. Nucleation of microtubules from centrosomes, metaphase alignment of chromosomes, or the focusing of spindle poles appears much less affected. The msps gene encodes a 227-kD protein with high similarity to the vertebrate microtubule-associated proteins (MAPs), human TOGp and Xenopus XMAP215, and with limited similarity to the Dis1 and STU2 proteins from fission yeast and budding yeast. Consistent with their sequence similarity, Msps protein also associates with microtubules in vitro. In the embryonic division cycles, Msps protein localizes to centrosomal regions at all mitotic stages, and spreads over the spindles during metaphase and anaphase. The absence of centrosomal staining in interphase of the cellularized embryos suggests that the interactions between Msps protein and microtubules or centrosomes may be regulated during the cell cycle.

scholarly journals Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human

2019 ◽  
Vol 11 (9) ◽  
pp. 2678-2690 ◽  
Author(s):  
Ann M McCartney ◽  
Edel M Hyland ◽  
Paul Cormican ◽  
Raymond J Moran ◽  
Andrew E Webb ◽  
...  
Keyword(s):  
Segmental Duplication ◽  
Gene Fusion ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Gene Fusions ◽  
Putative Gene ◽  
Reading Frame ◽  
New Genes ◽  
Fused Gene ◽  
Sequence Similarity Networks

Abstract Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.

scholarly journals Aerococcus vaginalis sp. nov., isolated from the vaginal mucosa of a beef cow, and emended descriptions of Aerococcus suis, Aerococcus viridans, Aerococcus urinaeequi, Aerococcus urinaehominis, Aerococcus urinae, Aerococcus christensenii and Aerococcus sanguinicola

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1229-1236 ◽  
Author(s):  
Masanori Tohno ◽  
Maki Kitahara ◽  
Shuichi Matsuyama ◽  
Koji Kimura ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Vaginal Mucosa ◽  
Beef Cow ◽  
Link Type ◽  
Aerococcus Viridans ◽  
Low Degree ◽  
Aerococcus Urinae ◽  
Type Strains

A gram-stain-positive, facultatively anaerobic, non-spore-forming, catalase-negative, coccoid-shaped bacterial strain, designated BV2T, was isolated from the vaginal mucosa of a beef cow in Japan. Phylogenetic analysis showed that the isolate shared high 16S rRNA gene sequence similarity (92.9 %) with Aerococcus suis 1821/02T and low similarity (<92.7 %) with any other recognized species of the genus Aerococcus . The DNA G+C content was 44.7 mol%, which is within the range observed among species of the genus Aerococcus (37.5–48.4 mol%). The major cellular fatty acid was C18 : 1ω9c, similar to other type strains of species of the genus Aerococcus . The results of genotypic, phenotypic and chemotaxonomic analyses as well as the low degree of DNA–DNA relatedness with all recognized members of the genus Aerococcus indicate that strain BV2T represents a novel species of the genus Aerococcus , for which the name Aerococcus vaginalis sp. nov. is proposed. The type strain is BV2T ( = JCM 19163T = DSM 27293T). Emended descriptions of Aerococcus suis , Aerococcus viridans , Aerococcus urinaeequi , Aerococcus urinaehominis , Aerococcus urinae , Aerococcus christensenii and Aerococcus sanguinicola are also presented.

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