The Bitome: Digitized genomic features reveal fundamental genome organization

Cameron R. Lamoureux; Kumari Sonal Choudhary; Zachary A. King; Troy E. Sandberg; Ye Gao; Anand V. Sastry; Patrick V. Phaneuf; Donghui Choe; Byung Kwan Cho; Bernhard O. Palsson

doi:10.1093/nar/gkaa774

The Bitome: Digitized genomic features reveal fundamental genome organization

Cameron R. Lamoureux, Kumari Sonal Choudhary, Zachary A. King, Troy E. Sandberg, Ye Gao, Anand V. Sastry, Patrick V. Phaneuf, Donghui Choe, Byung Kwan Cho, Bernhard O. Palsson^*

^*Corresponding author for this work

University of Iceland

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Abstract

A genome contains the information underlying an organism's form and function. Yet, we lack formal framework to represent and study this information. Here, we introduce the Bitome, a matrix composed of binary digits (bits) representing the genomic positions of genomic features. We form a Bitome for the genome of Escherichia coli K-12 MG1655. We find that: (i) genomic features are encoded unevenly, both spatially and categorically; (ii) coding and intergenic features are recapitulated at high resolution; (iii) adaptive mutations are skewed towards genomic positions with fewer features; and (iv) the Bitome enhances prediction of adaptively mutated and essential genes. The Bitome is a formal representation of a genome and may be used to study its fundamental organizational properties.

Original language	English
Pages (from-to)	10157-10163
Number of pages	7
Journal	Nucleic Acids Research
Volume	48
Issue number	18
DOIs	https://doi.org/10.1093/nar/gkaa774
Publication status	Published - 9 Oct 2020

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© 2020 The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

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abstract = "A genome contains the information underlying an organism's form and function. Yet, we lack formal framework to represent and study this information. Here, we introduce the Bitome, a matrix composed of binary digits (bits) representing the genomic positions of genomic features. We form a Bitome for the genome of Escherichia coli K-12 MG1655. We find that: (i) genomic features are encoded unevenly, both spatially and categorically; (ii) coding and intergenic features are recapitulated at high resolution; (iii) adaptive mutations are skewed towards genomic positions with fewer features; and (iv) the Bitome enhances prediction of adaptively mutated and essential genes. The Bitome is a formal representation of a genome and may be used to study its fundamental organizational properties. ",

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AU - Gao, Ye

AU - Sastry, Anand V.

AU - Phaneuf, Patrick V.

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AU - Cho, Byung Kwan

AU - Palsson, Bernhard O.

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The Bitome: Digitized genomic features reveal fundamental genome organization

Abstract

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