scholarly journals Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Qin Xu ◽  
Caiyun Zhu ◽  
Yangyang Fan ◽  
Zhihong Song ◽  
Shilai Xing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Gene Expression Variation ◽  
Changing Environment ◽  
Expression Variation

scholarly journals Massively parallel gene expression variation measurement of a synonymous codon library

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alexander Schmitz ◽  
Fuzhong Zhang
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Single Cells ◽  
Massively Parallel ◽  
Protein Abundance ◽  
Translation Efficiency ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Change In Mean ◽  
Adaptation Index

Abstract Background Cell-to-cell variation in gene expression strongly affects population behavior and is key to multiple biological processes. While codon usage is known to affect ensemble gene expression, how codon usage influences variation in gene expression between single cells is not well understood. Results Here, we used a Sort-seq based massively parallel strategy to quantify gene expression variation from a green fluorescent protein (GFP) library containing synonymous codons in Escherichia coli. We found that sequences containing codons with higher tRNA Adaptation Index (TAI) scores, and higher codon adaptation index (CAI) scores, have higher GFP variance. This trend is not observed for codons with high Normalized Translation Efficiency Index (nTE) scores nor from the free energy of folding of the mRNA secondary structure. GFP noise, or squared coefficient of variance (CV2), scales with mean protein abundance for low-abundant proteins but does not change at high mean protein abundance. Conclusions Our results suggest that the main source of noise for high-abundance proteins is likely not originating at translation elongation. Additionally, the drastic change in mean protein abundance with small changes in protein noise seen from our library implies that codon optimization can be performed without concerning gene expression noise for biotechnology applications.

scholarly journals Gene expression variation increase in trisomy 21 tissues

2008 ◽  
Vol 19 (6) ◽  
pp. 398-405 ◽  
Author(s):  
Ching Yu Chou ◽  
Li Yu Liu ◽  
Chien Yu Chen ◽  
Cheng Hsien Tsai ◽  
Hsiao Lin Hwa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Trisomy 21 ◽  
Gene Expression Variation ◽  
Expression Variation

Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae)

2017 ◽  
Vol 303 (8) ◽  
pp. 1061-1079 ◽  
Author(s):  
Julie Ferreira de Carvalho ◽  
Julien Boutte ◽  
Pierre Bourdaud ◽  
Houda Chelaifa ◽  
Kader Ainouche ◽  
...  
Keyword(s):  
Gene Expression ◽  
Natural Populations ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Spartina Species

scholarly journals Correlating Gene Expression Variation with cis-Regulatory Polymorphism in Saccharomyces cerevisiae

2010 ◽  
Vol 2 ◽  
pp. 697-707 ◽  
Author(s):  
Kevin Chen ◽  
Erik van Nimwegen ◽  
Nikolaus Rajewsky ◽  
Mark L. Siegal
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Regulatory Polymorphism

scholarly journals Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture

2019 ◽  
Vol 116 (3) ◽  
pp. 677-692 ◽  
Author(s):  
Inmaculada Hernandez ◽  
Heena Dhiman ◽  
Gerald Klanert ◽  
Vaibhav Jadhav ◽  
Norbert Auer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Batch Culture ◽  
Epigenetic Regulation ◽  
Chinese Hamster Ovary ◽  
Chinese Hamster Ovary Cells ◽  
Regulation Of Gene Expression ◽  
Chinese Hamster ◽  
Changing Environment ◽  
Ovary Cells

scholarly journals Population-scale long-read sequencing uncovers transposable elements contributing to gene expression variation and associated with adaptive signatures in Drosophila melanogaster

2021 ◽  
Author(s):  
Gabriel Rech ◽  
Santiago Radio ◽  
Sara Guirao-Rico ◽  
Laura Aguilera ◽  
Vivien Horvath ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Transposable Elements ◽  
Natural Populations ◽  
Gene Expression Variation ◽  
High Quality ◽  
Expression Variation ◽  
Climatic Regions ◽  
Genomic Studies ◽  
Reference Genomes

High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generated 32 high-quality reference genomes for the well-known model species D. melanogaster and focused on the identification and analysis of transposable element variation as they are the most common type of structural variant. We showed that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identified hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.

scholarly journals An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster

PLoS Genetics ◽  
2016 ◽  
Vol 12 (4) ◽  
pp. e1005987 ◽  
Author(s):  
Ana Catalán ◽  
Amanda Glaser-Schmitt ◽  
Eliza Argyridou ◽  
Pablo Duchen ◽  
John Parsch
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Local Adaptation ◽  
Untranslated Region ◽  
Indel Polymorphism ◽  
Gene Expression Variation ◽  
Expression Variation

scholarly journals Iron deficiency modifies gene expression variation induced by augmented hypoxia sensing

2014 ◽  
Vol 52 (1) ◽  
pp. 35-45 ◽  
Author(s):  
Xu Zhang ◽  
Wei Zhang ◽  
Shwu-Fan Ma ◽  
Galina Miasniakova ◽  
Adelina Sergueeva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Iron Deficiency ◽  
Gene Expression Variation ◽  
Expression Variation
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