scholarly journals Efficient Recovery of Centric Heterochromatin P-Element Insertions in Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 217-229 ◽  
Author(s):  
Christopher M Yan ◽  
Kenneth W Dobie ◽  
Hiep D Le ◽  
Alexander Y Konev ◽  
Gary H Karpen
Keyword(s):  
Drosophila Melanogaster ◽  
Large Scale ◽  
Structure And Function ◽  
P Element ◽  
Inverse Pcr ◽  
Fish Analysis ◽  
Genomic Scaffold ◽  
Efficient Recovery ◽  
Resolution Banding ◽  
And Function

Abstract Approximately one-third of the human and Drosophila melanogaster genomes are heterochromatic, yet we know very little about the structure and function of this enigmatic component of eukaryotic genomes. To facilitate molecular and cytological analysis of heterochromatin we introduced a yellow+ (y+)-marked P element into centric heterochromatin by screening for variegated phenotypes, that is, mosaic gene inactivation. We recovered >110 P insertions with variegated yellow expression from ∼3500 total mobilization events. FISH analysis of 71 of these insertions showed that 69 (97%) were in the centric heterochromatin, rather than telomeres or euchromatin. High-resolution banding analysis showed a wide but nonuniform distribution of insertions within centric heterochromatin; variegated insertions were predominantly recovered near regions of satellite DNA. We successfully used inverse PCR to clone and sequence the flanking DNA for ∼63% of the insertions. BLAST analysis of the flanks demonstrated that either most of the variegated insertions could not be placed on the genomic scaffold, and thus may be inserted within novel DNA sequence, or that the flanking DNA hit multiple sites on the scaffold, due to insertions within different transposons. Taken together these data suggest that screening for yellow variegation is a very efficient method for recovering centric insertions and that a large-scale screen for variegated yellow P insertions will provide important tools for detailed analysis of centric heterochromatin structure and function.

scholarly journals An inverse PCR screen for the detection of P element insertions in cloned genomic intervals in Drosophila melanogaster.

Genetics ◽  
1995 ◽  
Vol 139 (2) ◽  
pp. 757-766 ◽  
Author(s):  
B Dalby ◽  
A J Pereira ◽  
L S Goldstein
Keyword(s):  
Drosophila Melanogaster ◽  
Large Scale ◽  
P Element ◽  
Inverse Pcr ◽  
Drosophila Genome ◽  
Screening Approach ◽  
Genes Encoding ◽  
Larval Serum Protein ◽  
Insertion Sites ◽  
Sib Selection

Abstract We developed a screening approach that utilizes an inverse polymerase chain reaction (PCR) to detect P element insertions in or near previously cloned genes in Drosophila melanogaster. We used this approach in a large scale genetic screen in which P elements were mobilized from sites on the X chromosome to new autosomal locations. Mutagenized flies were combined in pools, and our screening approach was used to generate probes corresponding to the sequences flanking each site of insertion. These probes then were used for hybridization to cloned genomic intervals, allowing individuals carrying insertions in them to be detected. We used the same approach to perform repeated rounds of sib-selection to generate stable insertion lines. We screened 16,100 insert bearing individuals and recovered 11 insertions in five intervals containing genes encoding members of the kinesin superfamily in Drosophila melanogaster. In addition, we recovered an insertion in the region including the Larval Serum Protein-2 gene. Examination by Southern hybridization confirms that the lines we recovered represent genuine insertions in the corresponding genomic intervals. Our data indicates that this approach will be very efficient both for P element mutagenesis of new genomic regions and for detection and recovery of "local" P element transposition events. In addition, our data constitutes a survey of preferred P element insertion sites in the Drosophila genome and suggests that insertion sites that are mutable at a rate of approximately 10(-4) are distributed every 40-50 kb.

Plant hormones, plant growth regulators

2014 ◽  
Vol 155 (26) ◽  
pp. 1011-1018 ◽  
Author(s):  
György Végvári ◽  
Edina Vidéki
Keyword(s):  
Nervous System ◽  
Growth And Development ◽  
Large Scale ◽  
Essential Role ◽  
Higher Plants ◽  
Structure And Function ◽  
Wide Sense ◽  
Large Scale Integration ◽  
Scale Integration ◽  
And Function

Plants seem to be rather defenceless, they are unable to do motion, have no nervous system or immune system unlike animals. Besides this, plants do have hormones, though these substances are produced not in glands. In view of their complexity they lagged behind animals, however, plant organisms show large scale integration in their structure and function. In higher plants, such as in animals, the intercellular communication is fulfilled through chemical messengers. These specific compounds in plants are called phytohormones, or in a wide sense, bioregulators. Even a small quantity of these endogenous organic compounds are able to regulate the operation, growth and development of higher plants, and keep the connection between cells, tissues and synergy beween organs. Since they do not have nervous and immume systems, phytohormones play essential role in plants’ life. Orv. Hetil., 2014, 155(26), 1011–1018.

Identification of Chromosome Inheritance Modifiers in Drosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1623-1637 ◽  
Author(s):  
Kenneth W Dobie ◽  
Cameron D Kennedy ◽  
Vivienne M Velasco ◽  
Tory L McGrath ◽  
Juliani Weko ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Biological Activity ◽  
Cancer Progression ◽  
Birth Defects ◽  
Mitotic Chromosome ◽  
P Element ◽  
Inverse Pcr ◽  
Gtpase Activating Protein ◽  
New Genes ◽  
Genomic Analyses

Abstract Faithful chromosome inheritance is a fundamental biological activity and errors contribute to birth defects and cancer progression. We have performed a P-element screen in Drosophila melanogaster with the aim of identifying novel candidate genes involved in inheritance. We used a “sensitized” minichromosome substrate (J21A) to screen ∼3,000 new P-element lines for dominant effects on chromosome inheritance and recovered 78 Sensitized chromosome inheritance modifiers (Scim). Of these, 69 decreased minichromosome inheritance while 9 increased minichromosome inheritance. Fourteen mutations are lethal or semilethal when homozygous and all exhibit dramatic mitotic defects. Inverse PCR combined with genomic analyses identified P insertions within or close to genes with previously described inheritance functions, including wings apart-like (wapl), centrosomin (cnn), and pavarotti (pav). Further, lethal insertions in replication factor complex 4 (rfc4) and GTPase-activating protein 1 (Gap1) exhibit specific mitotic chromosome defects, discovering previously unknown roles for these proteins in chromosome inheritance. The majority of the lines represent mutations in previously uncharacterized loci, many of which have human homologs, and we anticipate that this collection will provide a rich source of mutations in new genes required for chromosome inheritance in metazoans.

Neural system-enriched gene expression: relationship to biological pathways and neurological diseases

2004 ◽  
Vol 18 (2) ◽  
pp. 167-183 ◽  
Author(s):  
Jianhua Zhang ◽  
Amy Moseley ◽  
Anil G. Jegga ◽  
Ashima Gupta ◽  
David P. Witte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Intracellular Signaling ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene List ◽  
Structure And Function ◽  
System Structure ◽  
Psychiatric Disease ◽  
And Function

To understand the commitment of the genome to nervous system differentiation and function, we sought to compare nervous system gene expression to that of a wide variety of other tissues by gene expression database construction and mining. Gene expression profiles of 10 different adult nervous tissues were compared with that of 72 other tissues. Using ANOVA, we identified 1,361 genes whose expression was higher in the nervous system than other organs and, separately, 600 genes whose expression was at least threefold higher in one or more regions of the nervous system compared with their median expression across all organs. Of the 600 genes, 381 overlapped with the 1,361-gene list. Limited in situ gene expression analysis confirmed that identified genes did represent nervous system-enriched gene expression, and we therefore sought to evaluate the validity and significance of these top-ranked nervous system genes using known gene literature and gene ontology categorization criteria. Diverse functional categories were present in the 381 genes, including genes involved in intracellular signaling, cytoskeleton structure and function, enzymes, RNA metabolism and transcription, membrane proteins, as well as cell differentiation, death, proliferation, and division. We searched existing public sites and identified 110 known genes related to mental retardation, neurological disease, and neurodegeneration. Twenty-one of the 381 genes were within the 110-gene list, compared with a random expectation of 5. This suggests that the 381 genes provide a candidate set for further analyses in neurological and psychiatric disease studies and that as a field, we are as yet, far from a large-scale understanding of the genes that are critical for nervous system structure and function. Together, our data indicate the power of profiling an individual biologic system in a multisystem context to gain insight into the genomic basis of its structure and function.

scholarly journals Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function

2017 ◽  
Vol 127 (5) ◽  
pp. 1798-1812 ◽  
Author(s):  
Philipp S. Wild ◽  
Janine F. Felix ◽  
Arne Schillert ◽  
Alexander Teumer ◽  
Ming-Huei Chen ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Large Scale ◽  
Structure And Function ◽  
Cardiac Structure ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Cardiac Structure And Function ◽  
And Function

scholarly journals Comprehensively Surveying Structure and Function of RING Domains from Drosophila melanogaster

PLoS ONE ◽  
2011 ◽  
Vol 6 (9) ◽  
pp. e23863 ◽  
Author(s):  
Muying Ying ◽  
Xiaotian Huang ◽  
Haijun Zhao ◽  
Yuehao Wu ◽  
Fusheng Wan ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Structure And Function ◽  
Ring Domains ◽  
And Function

scholarly journals Large-scale mutagenesis of the mouse to understand the genetic bases of nervous system structure and function

2004 ◽  
Vol 132 (2) ◽  
pp. 105-115 ◽  
Author(s):  
Dan Goldowitz ◽  
Wayne N. Frankel ◽  
Joseph S. Takahashi ◽  
Martha Holtz-Vitaterna ◽  
Carol Bult ◽  
...  
Keyword(s):  
Nervous System ◽  
Large Scale ◽  
Structure And Function ◽  
System Structure ◽  
And Function ◽  
Genetic Bases

scholarly journals Construction, stable transformation, and function of an amber suppressor tRNA gene in Drosophila melanogaster

1989 ◽  
Vol 86 (17) ◽  
pp. 6696-6698 ◽  
Author(s):  
F A Laski ◽  
S Ganguly ◽  
P A Sharp ◽  
U L RajBhandary ◽  
G M Rubin
Keyword(s):  
Drosophila Melanogaster ◽  
Trna Gene ◽  
P Element ◽  
Female Sterility ◽  
Suppressor Trna ◽  
Amber Codon ◽  
Amber Suppressor ◽  
Chloramphenicol Acetyltransferase Gene ◽  
Male And Female Sterility ◽  
And Function

Drosophila melanogaster strains with a stably incorporated amber suppressor tRNA gene have been generated. A tRNATyr gene was site specifically mutated to produce an anticodon sequence that recognizes the amber codon and then introduced into Drosophila by using P-element-mediated transformation. Transformants from four integration events were recovered. Two integrations resulted in both male and female sterility, whereas the other two resulted in male sterility but female fertility. Strains derived from the two female-fertile integration events were shown to have a low level of amber-suppressing activity by their ability to suppress an amber mutation in a chloramphenicol acetyltransferase gene.

Changes in large-scale chromatin structure and function during oogenesis: A journey in company with follicular cells

2014 ◽  
Vol 149 (1-2) ◽  
pp. 3-10 ◽  
Author(s):  
Alberto M. Luciano ◽  
Federica Franciosi ◽  
Cecilia Dieci ◽  
Valentina Lodde
Keyword(s):  
Chromatin Structure ◽  
Large Scale ◽  
Structure And Function ◽  
Follicular Cells ◽  
And Function

scholarly journals Biochemical and genetic analysis of Ecm14, a conserved fungal pseudopeptidase

2020 ◽  
Author(s):  
R Christian McDonald ◽  
Matthew J Schott ◽  
Temitope A Idowu ◽  
Peter J Lyons
Keyword(s):  
Enzyme Activity ◽  
Large Scale ◽  
Structure And Function ◽  
Activation Mechanism ◽  
Marker Genes ◽  
Synthetic Lethal ◽  
Fungal Process ◽  
And Function

Abstract Background. Like most major enzyme families, the M14 family of metallocarboxypeptidases (MCPs) contains a number of pseudoenzymes predicted to lack enzyme activity and with poorly characterized molecular function. The genome of the yeast Saccharomyces cerevisiae encodes one member of the M14 MCP family, a pseudoenzyme named Ecm14 proposed to function in the extracellular matrix. In order to better understand the function of such pseudoenzymes, we studied the structure and function of Ecm14 in S. cerevisiae. Results. A phylogenetic analysis of Ecm14 in fungi found it to be conserved throughout the ascomycete phylum, with a group of related pseudoenzymes found in basidiomycetes. To investigate the structure and function of this conserved protein, His6-tagged Ecm14 was overexpressed in Sf9 cells and purified. The prodomain of Ecm14 was cleaved in vivo and in vitro by endopeptidases, suggesting an activation mechanism; however, no activity was detectable using standard carboxypeptidase substrates. In order to determine the function of Ecm14 using an unbiased screen, we undertook a synthetic lethal assay. Upon screening approximately 27,000 yeast colonies, twenty-two putative synthetic lethal clones were identified. Further analysis showed many to be synthetic lethal with auxotrophic marker genes and requiring multiple mutations, suggesting that there are few, if any, single S. cerevisiae genes that present synthetic lethal interactions with ecm14Δ. Conclusions. We show in this study that Ecm14, although lacking detectable enzyme activity, is a conserved carboxypeptidase-like protein that is secreted from cells and is processed to a mature form by the action of an endopeptidase. Our study and datasets from other recent large-scale screens suggest a role for Ecm14 in processes such as vesicle-mediated transport and aggregate invasion, a fungal process that has been selected against in modern laboratory strains of S. cerevisiae.

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