Genome-Wide Identification of Allele-Specific Gene Expression in a Parent-of-Origin Specific Manner

2019 ◽  
pp. 129-139
Author(s):  
Chen Chen ◽  
Kevin Begcy
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Genome Wide ◽  
Specific Manner ◽  
Allele Specific ◽  
Parent Of Origin

scholarly journals A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression

2017 ◽  
Vol 7 (7) ◽  
pp. 2227-2234 ◽  
Author(s):  
Yasuaki Takada ◽  
Ryutaro Miyagi ◽  
Aya Takahashi ◽  
Toshinori Endo ◽  
Naoki Osada
Keyword(s):  
Gene Expression ◽  
Maternal Effects ◽  
Genomic Imprinting ◽  
Whole Body ◽  
Specific Gene ◽  
Rna Seq ◽  
Simple Method ◽  
Specific Gene Expression ◽  
Allele Specific ◽  
Parent Of Origin

Abstract Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype), genomic imprinting [i.e., parent-of-origin (PO)], and maternal [i.e., maternal genotype (MG)] effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.

scholarly journals Males that silence their father’s genes: genomic imprinting of a complete haploid genome

2020 ◽  
Author(s):  
Andrés G. de la Filia ◽  
Andrew J. Mongue ◽  
Jennifer Dorrens ◽  
Hannah Lemon ◽  
Dominik R. Laetsch ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genomic Imprinting ◽  
Mendelian Inheritance ◽  
Specific Gene ◽  
Paternal Genome ◽  
Genetic Conflict ◽  
Specific Gene Expression ◽  
Maternal Genome ◽  
Allele Specific ◽  
Parent Of Origin

AbstractGenetic conflict is considered a key driver in the evolution of new reproductive and sex determining systems. In particular, reproductive strategies with non-Mendelian inheritance, where parents do not contribute equally to the genetic makeup of their offspring. One of the most extraordinary examples of non-Mendelian inheritance is paternal genome elimination (PGE), a form of haplodiploidy which has evolved repeatedly across arthropods. Under PGE, males are diploid but only transmit maternally-inherited chromosomes to their offspring, while the paternal homologues are excluded from sperm. This asymmetric inheritance is thought to have evolved through an evolutionary arms race between paternal and maternal genomes over transmission to future generations. In several clades with PGE, such as the mealybugs (Hemiptera: Pseudococcidae), paternal chromosomes are not just eliminated from sperm, but also heterochromatinised early in development and thought to remain inactive. Such paternal genome silencing could alleviate genetic conflict between paternal alleles over transmission. However, it is unclear if paternal chromosomes are indeed genetically inert in both soma and germline. Here, we present a parent-of-origin allele-specific transcriptome analysis in male mealybugs. We show that expression is globally biased towards the maternal genome, but detect activity of paternal chromosomes in both somatic and reproductive tissues. Up to 70% of somatically-expressed genes are to some degree paternally-expressed. However, paternal genome expression is much more restricted in the testis, with only 20% of genes showing paternal contribution. Finally, we show that the patterns of parent-of-origin-specific gene expression are remarkably similar across genotypes and that those genes with biparental expression show elevated rates of molecular evolution. Our results provide the clearest example yet of genome-wide genomic imprinting (parent-of-origin specific gene expression) in insects. Furthermore, it enhances our understanding of PGE, which will aid future empirical tests of evolutionary theory regarding the origin of this unusual reproductive strategy.

scholarly journals Genome-wide comparison of allele-specific gene expression between African and European populations

2018 ◽  
Vol 27 (6) ◽  
pp. 1067-1077 ◽  
Author(s):  
Lei Tian ◽  
Asifullah Khan ◽  
Zhilin Ning ◽  
Kai Yuan ◽  
Chao Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Genome Wide ◽  
Allele Specific ◽  
European Populations

scholarly journals Changes in DNA Methylation in Response to 6-Benzylaminopurine Affect Allele-Specific Gene Expression in Populus tomentosa

2020 ◽  
Author(s):  
Anran Xuan ◽  
Yuepeng Song ◽  
Chenhao Bu ◽  
Panfei Chen ◽  
Yousry A. El-Kassaby ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Patterns ◽  
Populus Tomentosa ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Snp Analysis ◽  
Specific Gene Expression ◽  
Genome Wide ◽  
Allele Specific

The cytokinins play important roles in plant growth and development by regulating gene expression at genome wide level. DNA methylation is responsive to the external environment, but whether DNA methylation changes in response to cytokinin treatment to regulate gene expression is still unclear. Here, we used bisulfite sequencing and RNA sequencing to examine genome-wide DNA methylation and gene expression patterns in poplar (Populus tomentosa) after treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA). We identified 566 significantly differentially methylated regions (DMRs) in response to 6-BA treatment. Transcriptome analysis showed that 501 protein-coding genes, 262 long non-coding RNAs, and 15,793 24-nt small interfering RNAs were differentially expressed under 6-BA treatment. Among these, 79% were differentially expressed between alleles in P. tomentosa. Combined DNA methylation and gene expression analysis demonstrated that DNA methylation plays an important role in regulating allele-specific gene expression. To further investigate the relationship between these 6-BA-responsive genes and phenotypic variation, we performed SNP analysis of 507 6-BA-responsive DMRs via re-sequencing using a natural population of P. tomentosa and identified 206 SNPs that were significantly associated with growth and wood properties. Association analysis indicated that 53% of loci with allele-specific expression had primarily dominant effects on poplar traits. Our comprehensive analyses of P. tomentosa DNA methylation and the regulation of allele-specific gene expression suggest that DNA methylation is an important regulator of imbalanced expression between allelic loci.

scholarly journals SCALE: modeling allele-specific gene expression by single-cell RNA sequencing

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Yuchao Jiang ◽  
Nancy R. Zhang ◽  
Mingyao Li
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Scale Modeling ◽  
Single Cell Rna Sequencing ◽  
Allele Specific

scholarly journals Random X Inactivation and Extensive Mosaicism in Human Placenta Revealed by Analysis of Allele-Specific Gene Expression along the X Chromosome

PLoS ONE ◽  
2010 ◽  
Vol 5 (6) ◽  
pp. e10947 ◽  
Author(s):  
Joana Carvalho Moreira de Mello ◽  
Érica Sara Souza de Araújo ◽  
Raquel Stabellini ◽  
Ana Maria Fraga ◽  
Jorge Estefano Santana de Souza ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Human Placenta ◽  
X Inactivation ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Allele Specific

scholarly journals High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

BMC Genetics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 25 ◽  
Author(s):  
Caroline Daelemans ◽  
Matthew E Ritchie ◽  
Guillaume Smits ◽  
Sayeda Abu-Amero ◽  
Ian M Sudbery ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Specific Gene ◽  
Imprinted Genes ◽  
High Throughput Analysis ◽  
Human Term Placenta ◽  
Throughput Analysis ◽  
Term Placenta ◽  
Specific Gene Expression ◽  
Allele Specific

scholarly journals Allele-specific gene expression in a wild nonhuman primate population

2011 ◽  
Vol 20 (4) ◽  
pp. 725-739 ◽  
Author(s):  
J. TUNG ◽  
M. Y. AKINYI ◽  
S. MUTURA ◽  
J. ALTMANN ◽  
G. A. WRAY ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nonhuman Primate ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Allele Specific ◽  
Primate Population
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