Data and scripts from: Copy number variation is associated with gene expression change in archaea

Schmid, Amy K.; Vreugdenhil, A.; Dulmage, Keely A.; Darnell, Cynthia L.

Data and scripts from: Copy number variation is associated with gene expression change in archaea

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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 quantitation experiments at specific loci. Significant correlation of CNV hotspot locations with the positions of known 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 plasticity mediated by IS element activity can provide a source of phenotypic innovation in extreme environments. ... [Read More]

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Data Citation

Dulmage, Keely A., Darnell, Cynthia L., Vreugdenhil, A., Schmid, Amy K. (2018). Data and scripts from: Copy number variation is associated with gene expression change in archaea. Duke Digital Repository. https://doi.org/doi:10.7924/r4pz54w7h

Creator: Schmid, Amy K.
Vreugdenhil, A.
Dulmage, Keely A.
Darnell, Cynthia L.
DOI: 10.7924/r4pz54w7h
Subject: Microarray
Genomics
Transcriptomics
Archaea
Biological data
ChIP-chip
Copy number variation
Publication Date: May 4, 2018
ARK: ark:/87924/r4pz54w7h
Contributor: Pan, Min
Facciotti, Marc T.
Brooks, Aaron
Kaur, Amardeep
Whitehead, Kenia
Baliga, Nitin S.
Affiliation: Duke Center for Genomic and Computational Biology
Biology
Publisher: Duke Digital Repository
Collection Dates: 2004-2014
Language: eng
Type: Dataset
Format: CSV
TXT
XLSX
PY
Related Materials: Schmid et al., 2007, Genome Research 17(10): 1399-413. https://genome.cshlp.org/content/17/10/1399
Facciotti et al., 2007, PNAS 104(11):4630-5. https://doi.org/10.1073/pnas.0611663104
Schmid et al., 2009, Molecular Systems Biology 5:282. https://doi.org/10.1038/msb.2009.40
Bonneau et al., 2007, Cell 131(7):1354-64. https://doi.org/10.1016/j.cell.2007.10.053
Schmid et al., 2011, Nucleic Acids Research 39(7):2519-32. https://doi.org/10.1093/nar/gkq1211
Sharma et al., 2012, BMC Genomics 13:351. https://dx.doi.org/10.1186%2F1471-2164-13-351
Kaur et al., 2006, Genome Research 16(7):841-53. http://www.genome.org/cgi/doi/10.1101/gr.5189606
Baliga et al., 2004, Genome Research 14(6):1025-35. doi: 10.1101/gr.1993504
Kaur et al., 2010, Molecular Systems Biology 6:393. https://doi.org/10.1038/msb.2010.50
Whitehead et al., 2009, PLoS One 4(5):e5484.
Brooks et al., 2014, Molecular Systems Biology 10:740. https://doi.org/10.15252/msb.20145160
Whitehead et al., 2006, Molecular Systems Biology 2:47. https://doi.org/10.1038/msb4100091
Facciotti et al., 2010, BMC Systems Biology 4:64. https://doi.org/10.1186/1752-0509-4-64
Contact: Amy Schmid: amy.schmid@duke.edu, ORCID: 0000-0001-5821-8000
License: Creative Commons CC0 1.0 Universal
Title: Data and scripts from: Copy number variation is associated with gene expression change in archaea
License: http://creativecommons.org/publicdomain/zero/1.0/
Repository: Duke Research Data Repository

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Title	Date Uploaded	Visibility	Actions
collectionReadme.rtf	2018-09-13	Public	Download
ChIP	2018-09-13	Public
Expression	2018-09-13	Public

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