scholarly journals Oligogenic effects of 16p11.2 copy number variation on craniofacial development

2019 ◽  
Author(s):  
Yuqi Qiu ◽  
Thomas Arbogast ◽  
Sandra Martin Lorenzo ◽  
Honying Li ◽  
Shih C. Tang ◽  
...  
Keyword(s):  
Copy Number ◽  
Gene Dosage ◽  
Copy Number Variant ◽  
Craniofacial Development ◽  
Model Organisms ◽  
List Type ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Craniofacial Structure ◽  
Mirror Effects

AbstractA copy number variant (CNV) of 16p11.2, which encompasses 30 genes, is associated with developmental and psychiatric disorders, head size and body mass. The genetic mechanisms that underlie these associations are not understood. To elucidate the effects of genes on development, we exploited the quantitative effects of CNV on craniofacial structure in humans and model organisms. We show that reciprocal deletion and duplication of 16p11.2 have characteristic “mirror” effects on craniofacial features that are conserved in human, rat and mouse. By testing gene dosage effects on the shape of the mandible in zebrafish, we show that the distribution of effects for all individual genes is consistent with that of the CNV, and some combinations have non-additive effects. Our results suggest that, at minimum, one third of genes within the 16p11.2 region influence craniofacial development, and the facial gestalt of each CNV represents a product of 30 dosage effects.HighlightsReciprocal CNVs of 16p11.2 have mirror effects on craniofacial structure. Copy number is associated with a positive effect on nasal and mandibular regions and a negative effect on frontal regions of the face.Effects of CNV on craniofacial development in human are well conserved in rat and mouse models of 16p11.2 deletion and duplication.7/30 genes each independently have significant effects on the shape of the mandible in zebrafish; these include SPN, C16orf54, SEZ6L2, ASPHD1, TAOK2, INO80E and FAM57B. Others (MAPK3, MVP, KCTD13) have detectable effects only in combination.Overexpression of 30 genes individually showed a distribution of effects that was skewed in the same direction as that of the full duplication, suggesting that specific facial features represent the net of all individual effects combined.

Reflections on studies of gene expression in aneuploids

2010 ◽  
Vol 426 (2) ◽  
pp. 119-123 ◽  
Author(s):  
James A. Birchler
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Gene Dosage ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Different Types ◽  
Chromosomal Copy Number ◽  
Cancerous Cells ◽  
Insight Into ◽  
Careful Documentation

Aneuploidy involves changes in chromosomal copy number compared with normal euploid genotypes. Studies of gene expression in aneuploids in a variety of species have claimed many different types of responses. Studies of individual genes suggest that there are both structural gene dosage effects and compensation in aneuploids, and that subtle trans-acting effects across the genome are quite prevalent. A discussion is presented concerning the normalization procedures for studying gene expression in aneuploids. A careful documentation of the modulations of gene expression in aneuploids should provide insight into the nature of cancerous cells and the basis of aneuploid syndromes.

scholarly journals Evolutionary Rescue and Drug Resistance on Multicopy Plasmids

Genetics ◽  
2020 ◽  
Vol 215 (3) ◽  
pp. 847-868
Author(s):  
Mario Santer ◽  
Hildegard Uecker
Keyword(s):  
Copy Number ◽  
Gene Dosage ◽  
Branching Processes ◽  
Plasmid Copy Number ◽  
Wild Type ◽  
Plasmid Copy ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Evolutionary Rescue ◽  
Establishment Probability

Bacteria often carry “extra DNA” in the form of plasmids in addition to their chromosome. Many plasmids have a copy number greater than one such that the genes encoded on these plasmids are present in multiple copies per cell. This has evolutionary consequences by increasing the mutational target size, by prompting the (transitory) co-occurrence of mutant and wild-type alleles within the same cell, and by allowing for gene dosage effects. We develop and analyze a mathematical model for bacterial adaptation to harsh environmental change if adaptation is driven by beneficial alleles on multicopy plasmids. Successful adaptation depends on the availability of advantageous alleles and on their establishment probability. The establishment process involves the segregation of mutant and wild-type plasmids to the two daughter cells, allowing for the emergence of mutant homozygous cells over the course of several generations. To model this process, we use the theory of multitype branching processes, where a type is defined by the genetic composition of the cell. Both factors—the availability of advantageous alleles and their establishment probability—depend on the plasmid copy number, and they often do so antagonistically. We find that in the interplay of various effects, a lower or higher copy number may maximize the probability of evolutionary rescue. The decisive factor is the dominance relationship between mutant and wild-type plasmids and potential gene dosage effects. Results from a simple model of antibiotic degradation indicate that the optimal plasmid copy number may depend on the specific environment encountered by the population.

scholarly journals Evolutionary rescue and drug resistance on multicopy plasmids

2019 ◽  
Author(s):  
Mario Santer ◽  
Hildegard Uecker
Keyword(s):  
Copy Number ◽  
Gene Dosage ◽  
Branching Processes ◽  
Plasmid Copy Number ◽  
Wild Type ◽  
Plasmid Copy ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Evolutionary Rescue ◽  
Establishment Probability

AbstractBacteria often carry “extra DNA” in form of plasmids in addition to their chromosome. Many plasmids have a copy number greater than one such that the genes encoded on these plasmids are present in multiple copies per cell. This has evolutionary consequences by increasing the mutational target size, by prompting the (transitory) co-occurrence of mutant and wild-type alleles within the same cell, and by allowing for gene dosage effects. We develop and analyze a mathematical model for bacterial adaptation to harsh environmental change if adaptation is driven by beneficial alleles on multicopy plasmids. Successful adaptation depends on the availability of advantageous alleles and on their establishment probability. The establishment process involves the segregation of mutant and wild-type plasmids to the two daughter cells, allowing for the emergence of mutant-homozygous cells over the course of several generations. To model this process, we use the theory of multi-type branching processes, where a type is defined by the genetic composition of the cell. Both factors – the number of adaptive alleles and their establishment probability – depend on the plasmid copy number, and they often do so antagonistically. We find that in the interplay of various effects, a lower or higher copy number may maximize the probability of evolutionary rescue. The decisive factor is the dominance relationship between mutant and wild-type plasmids and potential gene dosage effects. Results from a simple model of antibiotic degradation indicate that the optimal plasmid copy number may depend on the specific environment encountered by the population.

scholarly journals Selection of SHV Extended-Spectrum-β-Lactamase-Dependent Cefotaxime and Ceftazidime Resistance in Klebsiella pneumoniae Requires a Plasmid-Borne blaSHV Gene

2007 ◽  
Vol 52 (2) ◽  
pp. 441-445 ◽  
Author(s):  
David S. Hammond ◽  
Tegan Harris ◽  
Jan Bell ◽  
John Turnidge ◽  
Philip M. Giffard
Keyword(s):  
Klebsiella Pneumoniae ◽  
Copy Number ◽  
Gene Dosage ◽  
Single Cells ◽  
The Other ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Extended Spectrum ◽  
Copy Number Amplification ◽  
Selection Of

ABSTRACT In Klebsiella pneumoniae, it is common for plasmid-located and chromosome-located bla SHV copies to coexist within single cells. The plasmid-borne genes are mainly derived from two separate IS26-mediated mobilizations of bla SHV. The objective of this study was to test the hypothesis that the presence of a non-extended-spectrum β-lactamase (non-ESBL) encoding plasmid-borne form of bla SHV facilitates the cefotaxime (CTX)-mediated selection of ESBL-expressing mutants, even when there is a chromosomal copy of the same gene. Twenty-one diverse ESBL-negative, bla TEM-negative K. pneumoniae clinical isolates were tested for the IS26 insertions characteristic of the two mobilization events. The isolates were then tested for their ability to be selected for ESBL-mediated CTX resistance by serial subculturing with a doubling of the CTX concentration at every subculture. Fourteen isolates possessed neither of the IS26 insertions. None of these became ESBL positive, and all died during the course of the experiment, despite possessing chromosomal bla SHV copies. The other isolates all became ESBL positive and grew abundantly up to a CTX concentration of 128 μg/ml. Similar results were obtained with ceftazidime. ESBL expression was associated with the appearance of the expected G→A mutation at position 1 of codon 238 and also with bla SHV copy number amplification. It was concluded that plasmid-borne bla SHV greatly facilitates the selection of ESBL expression, even when the same gene is on the chromosome, and that gene dosage effects are likely to contribute to this phenomenon.

scholarly journals Genetics advances and learning disability

2000 ◽  
Vol 176 (1) ◽  
pp. 12-19 ◽  
Author(s):  
Walter J. Muir
Keyword(s):  
Learning Disability ◽  
Gene Dosage ◽  
Genetic Disorders ◽  
Molecular Medicine ◽  
Gene Dosage Effects ◽  
Dosage Effects ◽  
Rapid Changes ◽  
Basic Understanding ◽  
Genetic Mechanisms ◽  
Dynamic Mutations

BackgroundMedicine is rapidly becoming molecular medicine, and little escapes the grasp of modern genetics. Most disorders associated with learning disability have at least a genetic component influencing their expression; in many disorders, disturbances of genetic mechanisms play a pivotal role.AimsDynamic mutations, imprinting mechanisms and gene-dosage effects are explained with reference to genetic disorders that lead to learning disability.MethodA review of recent important studies in the genetics of learning disability.ResultsA host of new genetic connections to conditions associated with learning disability have been made.ConclusionsA basic understanding of these genetic connections is important for all learning disability psychiatrists if they are to follow the rapid changes – already beginning to influence our practice – that hold immense promise for the future.

Gene Dosage Effects at the ae Locus on Amylose Content of Corn Endosperm

1966 ◽  
Vol 57 (3) ◽  
pp. 90-90 ◽  
Author(s):  
V. L. FERG ASON ◽  
J. L. HELM ◽  
M. S. ZUBER
Keyword(s):  
Gene Dosage ◽  
Amylose Content ◽  
Gene Dosage Effects ◽  
Dosage Effects
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