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The Bitome: digitized genomic features reveal fundamental genome organization.

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.

SUBMITTER: Lamoureux CR

PROVIDER: S-EPMC7544223 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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The Bitome: digitized genomic features reveal fundamental genome organization.

Lamoureux Cameron R CR Choudhary Kumari Sonal KS King Zachary A ZA Sandberg Troy E TE Gao Ye Y Sastry Anand V AV Phaneuf Patrick V PV Choe Donghui D Cho Byung-Kwan BK Palsson Bernhard O BO

Nucleic acids research 20201001 18

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 reso ...[more]

PMID: 32976587

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