Copy number variation is associated with gene expression change in archaea

Microbial Genomics
Keely A DulmageAmy K Schmid

Abstract

Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness remains unclear. Here we use DNA segmentation methods to detect and quantify genome-wide copy number variation (CNV) in large compendia of high-throughput datasets in a model archaeal species, Halobacterium salinarum. CNV hotspots were identified throughout the genome. Some hotspots were strongly associated with changes in gene expression, suggesting a mechanism for phenotypic innovation. In contrast, CNV hotspots in other genomic loci left expression unchanged, suggesting buffering of certain phenotypes. The correspondence of CNVs with gene expression was validated with strain- and condition-matched transcriptomics and DNA quantification experiments at specific loci. Significant correlation of CNV hotspot locations with the positions of known insertion sequence (IS) elements suggested a mechanism for generating genomic instability. Given the efficient recombination capabilities in H. salinarum despite stability at the single nucleotide level, these results suggest that genomic pl...Continue Reading

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Citations

Jun 14, 2019·Biochemical Society Transactions·Katharina Ludt, Jörg Soppa
May 12, 2019·Current Genetics·Stephanie Lauer, David Gresham
Sep 29, 2019·International Journal of Molecular Sciences·Sungmin HwangJulie A Maupin-Furlow
Oct 30, 2020·Biomolecules·Craig J Marshall, Thomas J Santangelo

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Datasets Mentioned

BETA
SRP108734
GPL23553
GSE99730

Methods Mentioned

BETA
ChIP
ChIP-chip
immunoprecipitation
PCR
Feature Extraction
RNA-Seq
glycosylation

Software Mentioned

Cutadapt
Agilent Feature Extraction
R
R package limma
limma
Bowtie2
R scripts
TrimGalore !
samtools
Python

Related Concepts

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