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Lenzini L, Di Patti F, Livi R, Fondi M, Fani R, Mengoni A. A Method for the Structure-Based, Genome-Wide Analysis of Bacterial Intergenic Sequences Identifies Shared Compositional and Functional Features. Genes (Basel) 2019; 10:genes10100834. [PMID: 31652625 PMCID: PMC6826451 DOI: 10.3390/genes10100834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/07/2019] [Accepted: 10/16/2019] [Indexed: 11/16/2022] Open
Abstract
In this paper, we propose a computational strategy for performing genome-wide analyses of intergenic sequences in bacterial genomes. Following similar directions of a previous paper, where a method for genome-wide analysis of eucaryotic Intergenic sequences was proposed, here we developed a tool for implementing similar concepts in bacteria genomes. This allows us to (i) classify intergenic sequences into clusters, characterized by specific global structural features and (ii) draw possible relations with their functional features.
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Affiliation(s)
- Leonardo Lenzini
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
- Istituto Nazionale di Fisica Nucleare, Sesto Fiorentino, 50019, Italy.
| | - Francesca Di Patti
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse, Sesto Fiorentino, 50019, Italy.
| | - Roberto Livi
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
- Istituto Nazionale di Fisica Nucleare, Sesto Fiorentino, 50019, Italy.
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse, Sesto Fiorentino, 50019, Italy.
- Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, 50019, Italy.
| | - Marco Fondi
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
| | - Renato Fani
- Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, 50019, Italy.
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
| | - Alessio Mengoni
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Italy.
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Li X, Doukhan P, Feugeas JP. Statistical inference for DNA sequences of promoters: a non-stationary qualitative model. STATISTICS-ABINGDON 2016. [DOI: 10.1080/02331888.2016.1261474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Xiaoyin Li
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Paul Doukhan
- AGM, Department of Mathematics, University of Cergy-Pontoise & IUF, Ile de France, Cergy-Pontoise, France
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Maximiano RV, Weber G. Deoxyinosine mismatch parameters calculated with a mesoscopic model result in uniform hydrogen bonding and strongly variable stacking interactions. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Variation and constraints in species-specific promoter sequences. J Theor Biol 2014; 363:357-66. [PMID: 25149367 DOI: 10.1016/j.jtbi.2014.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/30/2014] [Accepted: 08/04/2014] [Indexed: 11/24/2022]
Abstract
A vast literature is nowadays devoted to the search of correlations between transcription related functions and the composition of sequences upstream the Transcription Start Site. Little is known about the possible functional effects of nucleotide distributions on the conformational landscape of DNA in such regions. We have used suitable statistical indicators for identifying sequences that may play an important role in regulating transcription processes. In particular, we have analyzed base composition, periodicity and information content in sets of aligned promoters clustered according to functional information in order to obtain an insight on the main structural differences between promoters regulating genes with different functions. Our results show that when we select promoters according to some biological information, in a single species, at least in vertebrates, we observe structurally different classes of sequences. The highly variable and differentiated gene expression patterns may explain the great extent of structural differentiation observed in complex organisms. In fact, despite our analysis is focused on Homo sapiens, we provide also a comparison with other species, selected at different positions in the phylogenetic tree.
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