scholarly journals Genomic imprinting and parent-of-origin effects on complex traits

2013 ◽  
Vol 14 (9) ◽  
pp. 609-617 ◽  
Author(s):  
Heather A. Lawson ◽  
James M. Cheverud ◽  
Jason B. Wolf
Keyword(s):  
Genomic Imprinting ◽  
Complex Traits ◽  
Parent Of Origin ◽  
Origin Effects

scholarly journals Parent-of-origin effects, allele-specific expression, genomic imprinting and paternal manipulation in social insects

2021 ◽  
Vol 376 (1826) ◽  
Author(s):  
Benjamin P. Oldroyd ◽  
Boris Yagound
Keyword(s):  
Gene Expression ◽  
Genomic Imprinting ◽  
Social Insects ◽  
Social Insect ◽  
Specific Gene ◽  
Specific Expression ◽  
Rna Molecules ◽  
Parent Of Origin ◽  
Origin Effects ◽  
Gene Expression Studies

Haplo-diploidy and the relatedness asymmetries it generates mean that social insects are prime candidates for the evolution of genomic imprinting. In single-mating social insect species, some genes may be selected to evolve genomic mechanisms that enhance reproduction by workers when they are inherited from a female. This situation reverses in multiple mating species, where genes inherited from fathers can be under selection to enhance the reproductive success of daughters. Reciprocal crosses between subspecies of honeybees have shown strong parent-of-origin effects on worker reproductive phenotypes, and this could be evidence of such genomic imprinting affecting genes related to worker reproduction. It is also possible that social insect fathers directly affect gene expression in their daughters, for example, by placing small interfering RNA molecules in semen. Gene expression studies have repeatedly found evidence of parent-specific gene expression in social insects, but it is unclear at this time whether this arises from genomic imprinting, paternal manipulation, an artefact of cyto-nuclear interactions, or all of these. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

scholarly journals Epistatic Networks Associated with Parent-of-Origin Effects on Metabolic Traits

2019 ◽  
Author(s):  
Juan F Macias-Velasco ◽  
Celine L. St. Pierre ◽  
Jessica P Wayhart ◽  
Li Yin ◽  
Larry Spears ◽  
...  
Keyword(s):  
Complex Traits ◽  
Reciprocal Cross ◽  
Expression Profiles ◽  
Specific Interaction ◽  
Imprinted Genes ◽  
Cross Model ◽  
Metabolic Traits ◽  
Parent Of Origin ◽  
Origin Effects ◽  
Context Specific

ABSTRACTParent-of-origin effects (POE) are unexpectedly common in complex traits, including metabolic and neurological diseases. POE can also be modified by the environment, but the architecture of these gene-by-environmental effects on phenotypes remains to be unraveled. Previously, quantitative trait loci (QTL) showing context-specific POE on metabolic traits were mapped in the F16 generation of an advanced intercross between LG/J and SM/J inbred mice. However, these QTL were not enriched for known imprinted genes, suggesting another mechanism is needed to explain these POE phenomena. Here, we use a simple yet powerful F1 reciprocal cross model to test the hypothesis that non-imprinted genes can generate complex POE on metabolic traits through genetic interactions with imprinted genes. Male and female mice from a F1 reciprocal cross of LG/J and SM/J strains were fed either high or low fat diets. We generated expression profiles from three metabolically-relevant tissues: hypothalamus, white adipose, and liver. We identified two classes of parent-of-origin expression biases: genes showing parent-of-origin-dependent allele-specific expression and biallelic genes that are differentially expressed by reciprocal cross. POE patterns of both gene classes are highly tissue-and context-specific, sometimes occurring only in one sex and/or diet cohort in a particular tissue. We then constructed tissue-specific interaction networks among genes from these two classes of POE. A key subset of gene pairs show significant epistasis in the F16 LG/J x SM/J advanced intercross data in cases where the biallelic gene fell within a previously-identified metabolic POE QTL interval. We highlight one such interaction in adipose, between Nnat and Mogat1, which associates with POE on multiple adiposity traits. Both genes localize to the endoplasmic reticulum of adipocytes and play a role in adipogenesis. Additionally, expression of both genes is significantly correlated in human visceral adipose tissue. The genes and networks we present here represent a set of actionable interacting candidates that can be probed to further identify the machinery driving POE on complex traits.

scholarly journals Lack of parent-of-origin effects in Nasonia jewel wasp: A replication and extension study

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252457
Author(s):  
Kimberly C. Olney ◽  
Joshua D. Gibson ◽  
Heini M. Natri ◽  
Avery Underwood ◽  
Juergen Gadau ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Sequence Data ◽  
Original Data ◽  
Paternal Allele ◽  
Analysis Strategy ◽  
Parent Of Origin ◽  
Origin Effects ◽  
New Processing ◽  
Diploid Cells ◽  
Origin Effect

In diploid cells, the paternal and maternal alleles are, on average, equally expressed. There are exceptions from this: a small number of genes express the maternal or paternal allele copy exclusively. This phenomenon, known as genomic imprinting, is common among eutherian mammals and some plant species; however, genomic imprinting in species with haplodiploid sex determination is not well characterized. Previous work reported no parent-of-origin effects in the hybrids of closely related haplodiploid Nasonia vitripennis and Nasonia giraulti jewel wasps, suggesting a lack of epigenetic reprogramming during embryogenesis in these species. Here, we replicate the gene expression dataset and observations using different individuals and sequencing technology, as well as reproduce these findings using the previously published RNA sequence data following our data analysis strategy. The major difference from the previous dataset is that they used an introgression strain as one of the parents and we found several loci that resisted introgression in that strain. Our results from both datasets demonstrate a species-of-origin effect, rather than a parent-of-origin effect. We present a reproducible workflow that others may use for replicating the results. Overall, we reproduced the original report of no parent-of-origin effects in the haplodiploid Nasonia using the original data with our new processing and analysis pipeline and replicated these results with our newly generated data.

scholarly journals Parent-of-origin effects propagate through networks to shape metabolic traits

2021 ◽  
Author(s):  
Juan F Macias-Velasco ◽  
Celine L. St. Pierre ◽  
Jessica P Wayhart ◽  
Li Yin ◽  
Larry Spears ◽  
...  
Keyword(s):  
Complex Traits ◽  
Neurological Diseases ◽  
Inbred Mice ◽  
Inbred Mouse ◽  
Serum Glucose ◽  
Physiological Data ◽  
Imprinted Genes ◽  
Metabolic Traits ◽  
Parent Of Origin ◽  
Origin Effects

ABSTRACTParent-of-origin effects are unexpectedly common in complex traits, including metabolic and neurological diseases. Parent-of-origin effects can be modified by the environment, but the architecture of these gene-by-environmental effects on phenotypes remains to be unraveled. Previously, quantitative trait loci (QTL) showing context-specific parent-of-origin effects on metabolic traits were mapped in the F16 generation of an advanced intercross between LG/J and SM/J inbred mice. However, these QTL were not enriched for known imprinted genes, suggesting another mechanism is needed to explain these parent-of-origin effects phenomena. We propose that non-imprinted genes can generate complex parent-of-origin effects on metabolic traits through interactions with imprinted genes. Here, we employ data from mouse populations at different levels of intercrossing (F0, F1, F2, F16) of the LG/J and SM/J inbred mouse lines to test this hypothesis. Using multiple populations and incorporating genetic, genomic, and physiological data, we leverage orthogonal evidence to identify networks of genes through which parent-of-origin effects propagate. We identify a network comprised of 3 imprinted and 6 non-imprinted genes that show parent-of-origin effects. This epistatic network forms a nutritional responsive pathway and the genes comprising it jointly serve cellular functions associated with growth. We focus on 2 genes, Nnat and F2r, whose interaction associates with serum glucose levels across generations in high fat-fed females. Single-cell RNAseq reveals that Nnat and F2r are negatively correlated in pre-adipocytes along an adipogenic trajectory, a result that is consistent with our observations in bulk white adipose tissue.

scholarly journals An Introduction to Genomic Imprinting and Parent of Origin Effects

1996 ◽  
Vol 45 (1-2) ◽  
pp. 59-61
Author(s):  
J.G. Hall ◽  
E. Lopez-Rangel
Keyword(s):  
Genomic Imprinting ◽  
Protein Interactions ◽  
Uniparental Disomy ◽  
Protein Protein Interactions ◽  
Human Heredity ◽  
Expression Of Genes ◽  
Recent Developments ◽  
Genetic Mechanisms ◽  
Parent Of Origin ◽  
Origin Effects

Recent developments in molecular genetics and cytogenetics have allowed for better understanding of the inheritance and expression of genes. Many newly recognized mechanisms such as genomic imprinting, mosaicism, allelic expansion, cytoplasmic inheritance and uniparental disomy have been recognized to play an important role in human heredity.Genomic imprinting refers to differences in the phenotype which are observed depending on whether the gene was inherited from the father or from the mother. Genomic imprinting is a difficult concept to understand because imprinting has been used loosely to refer to a number of different mechanisms including psychological development, endocrinological actions of cells and protein-protein interactions. Genomic imprinting produces parent-of-origin effects. Parent-of-origin effects is a term that encompasses many of the non-traditional types of inheritance and other genetic and non-genetic mechanisms which show an effect depending on whether they were paternally or maternally derived.

scholarly journals Parent-of-Origin Effects on mRNA Expression in Drosophila melanogaster Not Caused by Genomic Imprinting

Genetics ◽  
2006 ◽  
Vol 173 (3) ◽  
pp. 1817-1821 ◽  
Author(s):  
Patricia J. Wittkopp ◽  
Belinda K. Haerum ◽  
Andrew G. Clark
Keyword(s):  
Drosophila Melanogaster ◽  
Mrna Expression ◽  
Genomic Imprinting ◽  
Parent Of Origin ◽  
Origin Effects

scholarly journals Coping-Style Behavior Identified by a Survey of Parent-of-Origin Effects in the Rat

2018 ◽  
Author(s):  
Carme Mont ◽  
Polinka Hernandez Pilego ◽  
Toni Cañete ◽  
Ignasi Oliveras ◽  
Cristóbal Río-Álamos ◽  
...  
Keyword(s):  
Complex Traits ◽  
Coping Style ◽  
Additive Genetic Variance ◽  
Shared Environment ◽  
Parental Origin ◽  
Impulsive Behavior ◽  
Develop Theory ◽  
Parent Of Origin ◽  
Origin Effects ◽  
F1 Cross

AbstractWe develop theory, based on earlier work, to partition heritability into a component due to a combination of parent of origin, maternal, paternal and shared environment, and another component that estimates classical additive genetic variance. We then investigate the effects on heritability of the parental origin of alleles in outbred heterogeneous stock rats across 199 complex traits. Parent-of-origin-like heritability was on average 2.7-fold larger than classical additive heritability. Among the phenotypes with the most enhanced parent-of-origin heritability were 10 coping style behaviors, with average 3.2-fold heritability enrichment. To confirm these findings on coping behaviour, and to eliminate the possibility that the parent of origin effects are due to confounding with shared environment, we performed a reciprocal F1 cross between the behaviourally divergent RHA and RLA rat strains. We observed parent-of-origin effects on F1 rat anxiety/coping-related behavior in the Elevated Zero Maze test. Our results are the first to assess genetic parent-of-origin effects in rats, and confirm earlier findings in mice that such effects influence mammalian coping and impulsive behavior.

scholarly journals Lack of parent-of-origin effects in Nasonia jewel wasp: a replication and extension study

2021 ◽  
Author(s):  
Kimberly C. Olney ◽  
Joshua D. Gibson ◽  
Heini M. Natri ◽  
Avery Underwood ◽  
Juergen Gadau ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Sequence Data ◽  
Original Data ◽  
Paternal Allele ◽  
Analysis Strategy ◽  
Parent Of Origin ◽  
Origin Effects ◽  
New Processing ◽  
Diploid Cells ◽  
Origin Effect

AbstractIn diploid cells, the paternal and maternal alleles are, on average, equally expressed. There are exceptions from this: a small number of genes express the maternal or paternal allele copy exclusively. This phenomenon, known as genomic imprinting, is common among eutherian mammals and some plant species; however, genomic imprinting in species with haplodiploid sex determination is not well characterized. Previous work reported no parent-of-origin effects in the hybrids of closely related haplodiploid Nasonia vitripennis and Nasonia giraulti jewel wasps, suggesting a lack of epigenetic reprogramming during embryogenesis in these species. Here, we replicate the gene expression dataset and observations using different individuals and sequencing technology, as well as reproduce these findings using the previously published RNA sequence data following our data analysis strategy. The major difference from the previous dataset is that they used an introgression strain as one of the parents and we found several loci that resisted introgression in that strain. Our results from both datasets demonstrate a species-of-origin effect, rather than a parent-of-origin effect. We present a reproducible workflow that others may use for replicating the results. Overall, we reproduced the original report of no parent-of-origin effects in the haplodiploid Nasonia using the original data with our new processing and analysis pipeline and replicated these results with our newly generated data.

scholarly journals Maternal Effects as the Cause of Parent-of-Origin Effects That Mimic Genomic Imprinting

Genetics ◽  
2008 ◽  
Vol 178 (3) ◽  
pp. 1755-1762 ◽  
Author(s):  
Reinmar Hager ◽  
James M. Cheverud ◽  
Jason B. Wolf
Keyword(s):  
Maternal Effects ◽  
Genomic Imprinting ◽  
Parent Of Origin ◽  
Origin Effects
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