scholarly journals Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F1 hybrids

2013 ◽  
Vol 13 (1) ◽  
pp. 221 ◽  
Author(s):  
Gaoyuan Song ◽  
Zhibin Guo ◽  
Zhenwei Liu ◽  
Qin Cheng ◽  
Xuefeng Qu ◽  
...  
Keyword(s):  
Differential Expression ◽  
Rna Sequencing ◽  
F1 Hybrids ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

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

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.

Genome-wide analysis of spatiotemporal allele-specific expression in F1 hybrids of meat- and egg-type chickens

Gene ◽  
2020 ◽  
Vol 747 ◽  
pp. 144671 ◽  
Author(s):  
Peng Ren ◽  
Feilong Deng ◽  
Ye Wang ◽  
Jinshan Ran ◽  
Jingjing Li ◽  
...  
Keyword(s):  
F1 Hybrids ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Allele Specific

scholarly journals Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

2009 ◽  
Vol 25 (24) ◽  
pp. 3207-3212 ◽  
Author(s):  
Jacob F. Degner ◽  
John C. Marioni ◽  
Athma A. Pai ◽  
Joseph K. Pickrell ◽  
Everlyne Nkadori ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Sequencing Data ◽  
Read Mapping ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

scholarly journals Allele-specific expression reveals interactions between genetic variation and environment

2015 ◽  
Author(s):  
David A Knowles ◽  
Joe R Davis ◽  
Anil Raj ◽  
Xiaowei Zhu ◽  
James B Potash ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cellular Level ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Sequencing Studies ◽  
Allele Specific ◽  
Gxe Interactions ◽  
Over Dispersion ◽  
The Impact

The impact of environment on human health is dramatic, with major risk factors including substance use, diet and exercise. However, identifying interactions between the environment and an individual's genetic background (GxE) has been hampered by statistical and computational challenges. By combining RNA sequencing of whole blood and extensive environmental annotations collected from 922 individuals, we have evaluated GxE interactions at a cellular level. We have developed EAGLE, a hierarchical Bayesian model for identifying GxE interactions based on association between environment and allele-specific expression (ASE). EAGLE increases power by leveraging the controlled, within-sample comparison of environmental impact on different genetic backgrounds provided by ASE, while also taking into account technical covariates and over-dispersion of sequencing read counts. EAGLE identifies 35 GxE interactions, a substantial increase over standard GxE testing. Among EAGLE hits are variants that modulate response to smoking, exercise and blood pressure medication. Further, application of EAGLE identifies GxE interactions to infection response that replicate results reported in vitro, demonstrating the power of EAGLE to accurately identify GxE candidates from large RNA sequencing studies.

scholarly journals ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing

PLoS Genetics ◽  
2020 ◽  
Vol 16 (5) ◽  
pp. e1008786 ◽  
Author(s):  
Jiaxin Fan ◽  
Jian Hu ◽  
Chenyi Xue ◽  
Hanrui Zhang ◽  
Katalin Susztak ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific

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

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.

Sign in / Sign up

Export Citation Format

Share Document