scholarly journals Faster-X evolution of gene expression is driven by recessive adaptivecis-regulatory variation inDrosophila

2018 ◽  
Vol 27 (19) ◽  
pp. 3811-3821 ◽  
Author(s):  
Ana Llopart
Keyword(s):  
Gene Expression ◽  
Regulatory Variation

scholarly journals The genetic basis of evolutionary change in gene expression levels

2010 ◽  
Vol 365 (1552) ◽  
pp. 2581-2590 ◽  
Author(s):  
J. J. Emerson ◽  
Wen-Hsiung Li
Keyword(s):  
Gene Expression ◽  
Genetic Basis ◽  
Regulation Of Gene Expression ◽  
Specific Expression ◽  
Genetic Changes ◽  
Expression Variation ◽  
Regulatory Variation ◽  
Global Mapping ◽  
History Of ◽  
Trait Locus

The regulation of gene expression is an important determinant of organismal phenotype and evolution. However, the widespread recognition of this fact occurred long after the synthesis of evolution and genetics. Here, we give a brief sketch of thoughts regarding gene regulation in the history of evolution and genetics. We then review the development of genome-wide studies of gene regulatory variation in the context of the location and mode of action of the causative genetic changes. In particular, we review mapping of the genetic basis of expression variation through expression quantitative trait locus studies and measuring the cis / trans component of expression variation in allele-specific expression studies. We conclude by proposing a systematic integration of ideas that combines global mapping studies, cis / trans tests and modern population genetics methodologies, in order to directly estimate the forces acting on regulatory variation within and between species.

scholarly journals Author response: Genetics of trans-regulatory variation in gene expression

2018 ◽  
Author(s):  
Frank Wolfgang Albert ◽  
Joshua S Bloom ◽  
Jake Siegel ◽  
Laura Day ◽  
Leonid Kruglyak
Keyword(s):  
Gene Expression ◽  
Author Response ◽  
Regulatory Variation

scholarly journals Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yujuan Gui ◽  
Kamil Grzyb ◽  
Mélanie H. Thomas ◽  
Jochen Ohnmacht ◽  
Pierre Garcia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cell Types ◽  
Mouse Strains ◽  
Cell Type ◽  
Data Set ◽  
Cell Identity ◽  
Regulatory Variation ◽  
Ventral Midbrain ◽  
Cell Type Specific

Abstract Background Cell types in ventral midbrain are involved in diseases with variable genetic susceptibility, such as Parkinson’s disease and schizophrenia. Many genetic variants affect regulatory regions and alter gene expression in a cell-type-specific manner depending on the chromatin structure and accessibility. Results We report 20,658 single-nuclei chromatin accessibility profiles of ventral midbrain from two genetically and phenotypically distinct mouse strains. We distinguish ten cell types based on chromatin profiles and analysis of accessible regions controlling cell identity genes highlights cell-type-specific key transcription factors. Regulatory variation segregating the mouse strains manifests more on transcriptome than chromatin level. However, cell-type-level data reveals changes not captured at tissue level. To discover the scope and cell-type specificity of cis-acting variation in midbrain gene expression, we identify putative regulatory variants and show them to be enriched at differentially expressed loci. Finally, we find TCF7L2 to mediate trans-acting variation selectively in midbrain neurons. Conclusions Our data set provides an extensive resource to study gene regulation in mesencephalon and provides insights into control of cell identity in the midbrain and identifies cell-type-specific regulatory variation possibly underlying phenotypic and behavioural differences between mouse strains.

scholarly journals TIGER: The gene expression regulatory variation landscape of human pancreatic islets

Cell Reports ◽  
2021 ◽  
Vol 37 (2) ◽  
pp. 109807
Author(s):  
Lorena Alonso ◽  
Anthony Piron ◽  
Ignasi Morán ◽  
Marta Guindo-Martínez ◽  
Sílvia Bonàs-Guarch ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Islets ◽  
Human Pancreatic Islets ◽  
Regulatory Variation

scholarly journals Genetics of trans-regulatory variation in gene expression

2017 ◽  
Author(s):  
Frank W. Albert ◽  
Joshua S. Bloom ◽  
Jake Siegel ◽  
Laura Day ◽  
Leonid Kruglyak
Keyword(s):  
Gene Expression ◽  
Statistical Power ◽  
Target Genes ◽  
Transcriptome Profiling ◽  
Mrna Levels ◽  
Heritable Variation ◽  
Altered Expression ◽  
Regulatory Variation ◽  
Transcription Factor Genes ◽  
Transcriptome Variation

AbstractHeritable variation in gene expression provides a critical bridge between differences in genome sequence and the biology of many traits, including common human diseases. However, the sources of most regulatory genetic variation remain unknown. Here, we used transcriptome profiling in 1,012 yeast segregants to map the genetic basis of variation in gene expression with high statistical power. We identified expression quantitative trait loci (eQTL) that together account for over 70% of the total genetic contribution to variation in mRNA levels, allowing us to examine the sources of regulatory variation comprehensively. We found that variation in the expression of a typical gene has a complex genetic architecture involving multiple eQTL. We also detected hundreds of eQTL pairs with significant non-additive interactions in an unbiased genome-wide scan. Although most genes were influenced by a local eQTL located close to the gene, most expression variation arose from distant, trans-acting eQTL located far from their target genes. Nearly all distant eQTL clustered at 102 “hotspot” locations, some of which influenced the expression of thousands of genes. Hotspot regions were enriched for transcription factor genes and altered expression of their target genes though both direct and indirect mechanisms. Many local eQTL had no detectable effects on the expression of other genes in trans. These results reveal the complexity of genetic influences on transcriptome variation in unprecedented depth and detail.

scholarly journals Transposable elements contribute to activation of maize genes in response to abiotic stress

2014 ◽  
Author(s):  
Irina Makarevitch ◽  
Amanda J Waters ◽  
Patrick T West ◽  
Michelle C Stitzer ◽  
Jeffrey Ross-Ibarra ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Transposable Elements ◽  
Environmental Changes ◽  
Stress Conditions ◽  
Gene Expression Response ◽  
Regulatory Variation ◽  
Ideal System ◽  
Response To Stress ◽  
Regulated Gene Expression

Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as "junk" DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress- induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize.

scholarly journals Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

Science ◽  
2009 ◽  
Vol 325 (5945) ◽  
pp. 1246-1250 ◽  
Author(s):  
A. S. Dimas ◽  
S. Deutsch ◽  
B. E. Stranger ◽  
S. B. Montgomery ◽  
C. Borel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dependent Manner ◽  
Cell Type ◽  
Regulatory Variation ◽  
A Cell

scholarly journals Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development

2019 ◽  
Vol 12 (3) ◽  
pp. 410-425 ◽  
Author(s):  
Peng Zhou ◽  
Candice N. Hirsch ◽  
Steven P. Briggs ◽  
Nathan M. Springer
Keyword(s):  
Gene Expression ◽  
Regulatory Variation ◽  
Dynamic Patterns
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