scholarly journals Effect of nucleotide polymorphism in cis-regulatory and coding regions on amylase activity and fitness in Drosophila melanogaster

Heredity ◽  
2005 ◽  
Vol 95 (5) ◽  
pp. 369-376 ◽  
Author(s):  
H Goto ◽  
A E Szmidt ◽  
T Yamazaki ◽  
N Inomata
Keyword(s):  
Drosophila Melanogaster ◽  
Amylase Activity ◽  
Nucleotide Polymorphism ◽  
Coding Regions ◽  
In Cis

scholarly journals Reduced variation at concertina, a heterochromatic locus in Drosophila

1996 ◽  
Vol 68 (2) ◽  
pp. 101-108 ◽  
Author(s):  
Marta L. Wayne ◽  
Martin Kreitman
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Neutral Theory ◽  
Background Selection ◽  
Nucleotide Polymorphism ◽  
Fourth Chromosome ◽  
Closely Related Species ◽  
Genetic Hitchhiking ◽  
Coding Regions ◽  
Polymorphism Level

SummaryIn Drosophila melanogaster and closely related species, polymorphism has been shown to be reduced at loci located in regions of low recombination on the X chromosome and on the fourth chromosome, which does not normally recombine. Thispositive correlation between nucleotide polymorphism level and recombination rate is not predicted by standard neutral theory and therefore must result from natural selection and genetic hitchhiking along the chromosomes. We report here the near-complete absence of variation at concertina (cta), a locus located in the β-heterochromatic base ofchromosome 2L, a region of strongly reduced recombination. A 1.2 kilobase region containing coding regions and introns was sequenced from each of nine lines of D. melanogaster and nine lines of D. simulans representingworldwide collections. Variation is significantly reduced in cta in both species compared with other available loci on the same chromosome. Two analyses of background selection demonstrate that the reduction in variation at cta, considered in combination with other loci on chromosome 2L or alone, is consistent with the background selection model.

scholarly journals A Cluster of Cuticle Protein Genes of Drosophila melanogaster at 65A: Sequence, Structure and Evolution

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1213-1224
Author(s):  
Jean-Philippe Charles ◽  
Carol Chihara ◽  
Shamim Nejad ◽  
Lynn M Riddiford
Keyword(s):  
Drosophila Melanogaster ◽  
Genomic Dna ◽  
Multiple Copy ◽  
Sequence Structure ◽  
Coding Regions ◽  
The Third ◽  
Genetic Complexity ◽  
Genes Encoding ◽  
Cuticle Protein ◽  
Cuticle Proteins

A 36-kb genomic DNA segment of the Drosophila melanogaster genome containing 12 clustered cuticle genes has been mapped and partially sequenced. The cluster maps at 65A 5-6 on the left arm of the third chromosome, in agreement with the previously determined location of a putative cluster encompassing the genes for the third instar larval cuticle proteins LCP5, LCP6 and LCP8. This cluster is the largest cuticle gene cluster discovered to date and shows a number of surprising features that explain in part the genetic complexity of the LCP5, LCP6 and LCP8 loci. The genes encoding LCP5 and LCP8 are multiple copy genes and the presence of extensive similarity in their coding regions gives the first evidence for gene conversion in cuticle genes. In addition, five genes in the cluster are intronless. Four of these five have arisen by retroposition. The other genes in the cluster have a single intron located at an unusual location for insect cuticle genes.

scholarly journals A novel transvection phenomenon affecting the white gene of Drosophila melanogaster.

Genetics ◽  
1990 ◽  
Vol 126 (1) ◽  
pp. 167-176
Author(s):  
D Gubb ◽  
M Ashburner ◽  
J Roote ◽  
T Davis
Keyword(s):  
Drosophila Melanogaster ◽  
Homologous Chromosome ◽  
Tandem Duplication ◽  
Gamma Ray ◽  
Insertion Site ◽  
Hairpin Loop ◽  
Homologous Chromosomes ◽  
Inverted Order ◽  
In Trans ◽  
In Cis

Abstract The zeste mutation of Drosophila melanogaster suppresses the expression of white genes in the eye. This suppression is normally dependent on there being two copies of w+ located close to each other in the genome--they may either be in cis (as in a tandem duplication of w+) or in trans, i.e. on homologous chromosomes. Duplicated w+ genes carried by a giant transposing element, TE146(Z), are suppressed by z whether they are in direct (tandem) or inverted order. The tandem form of the TE is very sensitive to a rearrangement on the homologous chromosome--many rearrangements with breakpoints "opposite" the TE's insertion site prevent the interaction between the white genes on a z background. These aberrations act as dominant suppressors of zeste that are specific to the tandemly duplicated form of TE146(Z). The inverted form of the TE146(Z) presumably pairs as a hairpin loop; this is more stable than the tandem form by the criterion that its zeste phenotype is unaffected by any of the aberrations. This effect of rearrangements has been used as the basis for a screen, gamma-ray induced aberrations with at least one breakpoint opposite the TE site were recovered by their suppression of the zeste phenotype.

Transvection and Silencing of the Scr Homeotic Gene of Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 733-746
Author(s):  
Jeffrey W Southworth ◽  
James A Kennison
Keyword(s):  
Drosophila Melanogaster ◽  
Chromosomal Aberrations ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Anomalous Behavior ◽  
Polycomb Group ◽  
Homeotic Gene ◽  
Polycomb Group Proteins ◽  
Sex Combs Reduced ◽  
In Cis

Abstract The Sex combs reduced (Scr) gene specifies the identities of the labial and first thoracic segments in Drosophila melanogaster. In imaginal cells, some Scr mutations allow cis-regulatory elements on one chromosome to stimulate expression of the promoter on the homolog, a phenomenon that was named transvection by Ed Lewis in 1954. Transvection at the Scr gene is blocked by rearrangements that disrupt pairing, but is zeste independent. Silencing of the Scr gene in the second and third thoracic segments, which requires the Polycomb group proteins, is disrupted by most chromosomal aberrations within the Scr gene. Some chromosomal aberrations completely derepress Scr even in the presence of normal levels of all Polycomb group proteins. On the basis of the pattern of chromosomal aberrations that disrupt Scr gene silencing, we propose a model in which two cis-regulatory elements interact to stabilize silencing of any promoter or cis-regulatory element physically between them. This model also explains the anomalous behavior of the Scx allele of the flanking homeotic gene, Antennapedia. This allele, which is associated with an insertion near the Antennapedia P1 promoter, inactivates the Antennapedia P1 and P2 promoters in cis and derepresses the Scr promoters both in cis and on the homologous chromosome.

scholarly journals Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 667-677
Author(s):  
Hitoshi Araki ◽  
Nobuyuki Inomata ◽  
Tsuneyuki Yamazaki
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Natural Populations ◽  
Sliding Window ◽  
Selective Constraint ◽  
Proximal Region ◽  
Coding Regions ◽  
Asian Populations ◽  
Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

The Effect of Heterologous Insertions on Gene Conversion in Mitotically Dividing Cells in Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 249-258
Author(s):  
Angela M Coveny ◽  
Tammy Dray ◽  
Gregory B Gloor
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Conversion ◽  
Strand Break ◽  
Double Strand Break ◽  
P Element ◽  
Double Strand Break Repair ◽  
Break Site ◽  
In Trans ◽  
Break Repair ◽  
In Cis

Abstract We examined the influence that heterologous sequences of different sizes have on the frequency of double-strand-break repair by gene conversion in Drosophila melanogaster. We induced a double-strand break on one X chromosome in female flies by P-element excision. These flies contained heterologous insertions of various sizes located 238 bp from the break site in cis or in trans to the break, or both. We observed a significant decrease in double-strand-break repair with large heterologous insertions located either in cis or in trans to the break. Reestablishing the homology by including the same heterologous sequence in cis and in trans to the double-strand break restored the frequency of gene conversion to wild-type levels. In one instance, an allelic nonhomologous insertion completely abolished repair by homologous recombination. The results show that the repair of a double-strand break by gene conversion requires chromosome pairing in the local region of the double-strand break.

scholarly journals “Abnormal vertebral patterns in genetically heterogeneous deceased fetuses and neonates: evidence of selection against variations”

2019 ◽  
Author(s):  
Pauline C. Schut ◽  
Erwin Brosens ◽  
Frietson Galis ◽  
Clara M. A. Ten Broek ◽  
Inge M.M. Baijens ◽  
...  
Keyword(s):  
Copy Number ◽  
Single Nucleotide Polymorphism Array ◽  
Copy Number Variations ◽  
Cervical Region ◽  
Nucleotide Polymorphism ◽  
Rare Cnvs ◽  
Single Nucleotide ◽  
Neonatal Deaths ◽  
Coding Regions ◽  
Cervical Ribs

AbstractObjectiveTo assess the vertebral pattern in a cohort of deceased fetuses and neonates, and to study the possible impact of DNA Copy Number Variations (CNVs) in coding regions and/or disturbing enhancers on the development of the vertebral pattern.MethodRadiographs of 445 fetuses and infants, deceased between 2009 and 2015, were assessed. Terminations of pregnancies, stillbirths and neonatal deaths were included. Patients were excluded if the vertebral pattern could not be determined. Copy number profiles of 265 patients were determined using single nucleotide polymorphism array.Results274/374 patients (73.3%) had an abnormal vertebral pattern. Cervical ribs were present in 188/374 (50.3%) and were significantly more common in stillbirths (69/128 (53.9%)) and terminations of pregnancies (101/188 (53.7%)), compared to live births (18/58, 31.0%, p = 0.006). None of the rare CNVs were recurrent or overlapped candidate genes for vertebral patterning.ConclusionThe presence of an abnormal vertebral pattern, particularly in the cervical region, could be a sign of disruption at critical, highly interactive and conserved stages of embryogenesis. The vertebral pattern might provide valuable information regarding fetal and neonatal outcome. CNV analyses did not identify a mutual genetic cause for the occurrence of vertebral patterning abnormalities, indicating genetic heterogeneity.

scholarly journals Non-Coding RNAs in Bacteria

2018 ◽  
Author(s):  
Amanda Carvalho Garcia ◽  
Vera Lúcia Pereira dos Santos ◽  
Teresa Cristina Santos Cavalcanti ◽  
Luiz Martins Collaço ◽  
Iara José Taborda de Messias ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Physiological Responses ◽  
Coding Regions ◽  
Short Rnas ◽  
Genes Encoding ◽  
Intergenic Regions ◽  
In Trans ◽  
Rna Interaction ◽  
In Cis ◽  
Target Rna

Genes encoding regulatory RNAs known as short RNAs (sRNAs) or non-coding sRNAs (ncRNAs), modulate physiological responses through different mechanisms, through RNA-RNA interaction or RNA-protein interaction. These molecules transcribed in trans and in cis relative to the target RNA. They are located between the coding regions of proteins, i.e., in the intergenic regions of the genome and show signals of promoters and termini sequences generally Rho-independent. The size of the ncRNAs genes ranges from ~ 50 to ~ 500 nucleotides and several transcripts are processed by RNase with smaller end products, which modulate physiological responses through different mechanisms, by RNA-RNA interaction or RNA-protein interactions and some interactions may be stabilized by the Hfq chaperone. The Riboswitches constitute another class of ncRNAs, located in the 5'UTR region of an mRNA that promote transcriptional regulation through their interaction with a linker molecule. Recently, in prokaryotes, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) regions have described, which repeats of sequences of palindromic bases are. Each replicate consists of short segments of "spacer DNA" from exposures prior to a bacteriophage virus or exogenous plasmid. The CRISPR system consists of an immune system of resistance to exogenous molecules.

Sign in / Sign up

Export Citation Format

Share Document