scholarly journals Natural Gene-Expression Variation in Down Syndrome Modulates the Outcome of Gene-Dosage Imbalance

2007 ◽  
Vol 81 (2) ◽  
pp. 252-263 ◽  
Author(s):  
Paola Prandini ◽  
Samuel Deutsch ◽  
Robert Lyle ◽  
Maryline Gagnebin ◽  
Celine Delucinge Vivier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Down Syndrome ◽  
Gene Dosage ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Dosage Imbalance

Gene expression variation in three brain tissues of a mouse model of down syndrome

2005 ◽  
Vol 2005 (Fall) ◽  
Author(s):  
Marc Sultan ◽  
Daniela Balzereit ◽  
Nidhi G Saran ◽  
Simone Guenther ◽  
Karl Guegler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Down Syndrome ◽  
Mouse Model ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Brain Tissues

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 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.

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