Genomic Imprinting in the Rat: Linkage ofIgf2andH19Genes and Opposite Parental Allele-Specific Expression during Embryogenesis

Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.

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Analysis of Genomic Imprinting by Quantitative Allele-Specific Expression by Pyrosequencing®

Methods in Molecular Biology - Plant Epigenetics and Epigenomics ◽

10.1007/978-1-62703-773-0_6 ◽

2014 ◽

pp. 85-104 ◽

Cited By ~ 2

Author(s):

Peter C. McKeown ◽

Antoine Fort ◽

Charles Spillane

Keyword(s):

Genomic Imprinting ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific

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Allele specific expression in worker reproduction genes in the bumblebee Bombus terrestris

10.7287/peerj.preprints.878 ◽

2015 ◽

Author(s):

Harindra E Amarasinghe ◽

Bradley J Toghill ◽

Eamonn B Mallon

Keyword(s):

Differential Expression ◽

Genomic Imprinting ◽

Bombus Terrestris ◽

Worker Reproduction ◽

Specific Expression ◽

Allele Specific Expression ◽

Potential Models ◽

Allele Specific ◽

Hymenopteran Insects

Genomic imprinting is the differential expression of alleles, with the expression being dependent upon the sex of the parent from which it was inherited. Hymenopteran insects (ants, bees and wasps) are emerging as potential models for genomic imprinting and epigenetics. As a first step in establishing the possibility of genomic imprinting in the bumblebee, Bombus terrestris, we search for allele specific expression in twelve genes associated with worker reproduction. We found that the patrigene (allele from the father) is more expressed than the matrigene (allele from the mother) in Ecdysone 20 monooxygenase. This enzyme catalyses the reaction which turns the ecdysteroid ecdysone into 20-hydroxyecdysone, also an ecdysteroid. Both of these ecdysteroids are important for worker reproduction in the bumblebee.

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RNA-Seq Analyses Identify Frequent Allele Specific Expression and No Evidence of Genomic Imprinting in Specific Embryonic Tissues of Chicken

Scientific Reports ◽

10.1038/s41598-017-12179-9 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 23

Author(s):

Zhu Zhuo ◽

Susan J. Lamont ◽

Behnam Abasht

Keyword(s):

Genomic Imprinting ◽

Rna Seq ◽

Specific Expression ◽

Allele Specific Expression ◽

Embryonic Tissues ◽

Allele Specific ◽

Frequent Allele

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Known unknowns for allele-specific expression and genomic imprinting effects

F1000Prime Reports ◽

10.12703/p6-75 ◽

2014 ◽

Vol 6 ◽

Cited By ~ 11

Author(s):

Christopher Gregg

Keyword(s):

Genomic Imprinting ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific ◽

Known Unknowns

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Allele specific expression in worker reproduction genes in the bumblebee Bombus terrestris

10.7287/peerj.preprints.878v1 ◽

2015 ◽

Author(s):

Harindra E Amarasinghe ◽

Bradley J Toghill ◽

Eamonn B Mallon

Keyword(s):

Differential Expression ◽

Genomic Imprinting ◽

Bombus Terrestris ◽

Worker Reproduction ◽

Specific Expression ◽

Allele Specific Expression ◽

Potential Models ◽

Allele Specific ◽

Hymenopteran Insects

Genomic imprinting is the differential expression of alleles, with the expression being dependent upon the sex of the parent from which it was inherited. Hymenopteran insects (ants, bees and wasps) are emerging as potential models for genomic imprinting and epigenetics. As a first step in establishing the possibility of genomic imprinting in the bumblebee, Bombus terrestris, we search for allele specific expression in twelve genes associated with worker reproduction. We found that the patrigene (allele from the father) is more expressed than the matrigene (allele from the mother) in Ecdysone 20 monooxygenase. This enzyme catalyses the reaction which turns the ecdysteroid ecdysone into 20-hydroxyecdysone, also an ecdysteroid. Both of these ecdysteroids are important for worker reproduction in the bumblebee.

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Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

Scientific Reports ◽

10.1038/s41598-021-83459-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Joseph Tomlinson ◽

Shawn W. Polson ◽

Jing Qiu ◽

Juniper A. Lake ◽

William Lee ◽

...

Keyword(s):

Broiler Chickens ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Specific Expression ◽

Single Nucleotide ◽

Allele Specific Expression ◽

Detection Tool ◽

Commercial Broiler ◽

Significant Phenomenon ◽

Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

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