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

Research output: Contribution to journalJournal articleResearchpeer-review

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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.
Original languageEnglish
Article numbergkaa774
JournalNucleic acids research
Volume48
Issue number18
Pages (from-to)10157-10163
Number of pages7
ISSN0305-1048
DOIs
Publication statusPublished - 2020

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