scholarly journals SNPs in Sites for DNA Methylation, Transcription Factor Binding, and miRNA Targets Leading to Allele-Specific Gene Expression and Contributing to Complex Disease Risk: A Systematic Review

2020 ◽  
pp. 1-16
Author(s):  
Manik Vohra ◽  
Anu Radha Sharma ◽  
Navya Prabhu B ◽  
Padmalatha S. Rai
Keyword(s):  
Gene Expression ◽  
Systematic Review ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Complex Disease ◽  
Disease Risk ◽  
Specific Gene ◽  
Factor Binding ◽  
Specific Gene Expression ◽  
Allele Specific

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 Changes in DNA Methylation in Response to 6-Benzylaminopurine Affect Allele-Specific Gene Expression in Populus Tomentosa

2020 ◽  
Vol 21 (6) ◽  
pp. 2117
Author(s):  
Anran Xuan ◽  
Yuepeng Song ◽  
Chenhao Bu ◽  
Panfei Chen ◽  
Yousry A. El-Kassaby ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Growth And Development ◽  
Populus Tomentosa ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Specific Gene Expression ◽  
Allele Specific

Cytokinins play important roles in the growth and development of plants. Physiological and photosynthetic characteristics are common indicators to measure the growth and development in plants. However, few reports have described the molecular mechanisms of physiological and photosynthetic changes in response to cytokinin, particularly in woody plants. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression in response to the external environment. In this study, we examined genome-wide DNA methylation variation and transcriptional variation in poplar (Populus tomentosa) after short-term treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA). We identified 460 significantly differentially methylated regions (DMRs) in response to 6-BA treatment. Transcriptome analysis showed that 339 protein-coding genes, 262 long non-coding RNAs (lncRNAs), and 15,793 24-nt small interfering RNAs (siRNAs) were differentially expressed under 6-BA treatment. Among these, 79% were differentially expressed between alleles in P. tomentosa, and 102,819 allele-specific expression (ASE) loci in 19,200 genes were detected showing differences in ASE levels after 6-BA treatment. 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 460 6-BA-responsive DMRs via re-sequencing using a natural population of P. tomentosa, and we 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 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

scholarly journals A SAGE study of apolipoprotein E3/3, E3/4 and E4/4 allele-specific gene expression in hippocampus in Alzheimer disease

2007 ◽  
Vol 36 (3) ◽  
pp. 313-331 ◽  
Author(s):  
Pu-Ting Xu ◽  
Yi-Ju Li ◽  
Xue-Jun Qin ◽  
Charles Kroner ◽  
Anya Green-Odlum ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alzheimer Disease ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Allele Specific
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