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Fedorova L, Crossley ER, Mulyar OA, Qiu S, Freeman R, Fedorov A. Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome. BIOLOGY 2023; 12:1125. [PMID: 37627009 PMCID: PMC10452674 DOI: 10.3390/biology12081125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
Long human ultra-conserved non-coding elements (UCNEs) do not have any sequence similarity to each other or other characteristics that make them unalterable during vertebrate evolution. We hypothesized that UCNEs have unique dinucleotide (DN) composition and arrangements compared to the rest of the genome. A total of 4272 human UCNE sequences were analyzed computationally and compared with the whole genomes of human, chicken, zebrafish, and fly. Statistical analysis was performed to assess the non-randomness in DN spacing arrangements within the entire human genome and within UCNEs. Significant non-randomness in DN spacing arrangements was observed in the entire human genome. Additionally, UCNEs exhibited distinct patterns in DN arrangements compared to the rest of the genome. Approximately 83% of all DN pairs within UCNEs showed significant (>10%) non-random genomic arrangements at short distances (2-6 nucleotides) relative to each other. At the extremes, non-randomness in DN spacing distances deviated up to 40% from expected values and were frequently associated with GpC, CpG, ApT, and GpG/CpC dinucleotides. The described peculiarities in DN arrangements have persisted for hundreds of millions of years in vertebrates. These distinctive patterns may suggest that UCNEs have specific DNA conformations.
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Affiliation(s)
- Larisa Fedorova
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Emily R. Crossley
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA;
| | - Oleh A. Mulyar
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Shuhao Qiu
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA;
| | - Ryan Freeman
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Alexei Fedorov
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA;
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA;
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Abstract
Periodic occurrences of oligonucleotide sequences can impact the physical properties of DNA. For example, DNA bendability is modulated by 10-bp periodic occurrences of WW (W = A/T) dinucleotides. We present periodicDNA, an R package to identify k-mer periodicity and generate continuous tracks of k-mer periodicity over genomic loci of interest, such as regulatory elements. periodicDNA will facilitate investigation and improve understanding of how periodic DNA sequence features impact function.
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Affiliation(s)
- Jacques Serizay
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, CB2 1QN, UK
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Denis A, Martínez-Núñez MA, Tenorio-Salgado S, Perez-Rueda E. Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638. Life (Basel) 2018; 8:life8040040. [PMID: 30248960 PMCID: PMC6316755 DOI: 10.3390/life8040040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 01/06/2023] Open
Abstract
In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.
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Affiliation(s)
- Antonia Denis
- Facultad de Medicina, Universidad Juárez Autónoma de Tabasco, C.P. 86100, Tabasco, Mexico.
| | - Mario Alberto Martínez-Núñez
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
| | - Silvia Tenorio-Salgado
- Tecnológico Nacional de México, Instituto Tecnológico de Mérida, C.P. 97000, Mérida, Yucatán, Mexico.
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, C.P. 97302, Mérida, Yucatán, Mexico.
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Pugacheva V, Korotkov A, Korotkov E. Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming. Stat Appl Genet Mol Biol 2017; 15:381-400. [PMID: 27337743 DOI: 10.1515/sagmb-2015-0079] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of this study was to show that amino acid sequences have a latent periodicity with insertions and deletions of amino acids in unknown positions of the analyzed sequence. Genetic algorithm, dynamic programming and random weight matrices were used to develop a new mathematical algorithm for latent periodicity search. A multiple alignment of periods was calculated with help of the direct optimization of the position-weight matrix without using pairwise alignments. The developed algorithm was applied to analyze amino acid sequences of a small number of proteins. This study showed the presence of latent periodicity with insertions and deletions in the amino acid sequences of such proteins, for which the presence of latent periodicity was not previously known. The origin of latent periodicity with insertions and deletions is discussed.
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Chechetkin VR, Lobzin VV. Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique. J Theor Biol 2017; 426:162-179. [PMID: 28552553 DOI: 10.1016/j.jtbi.2017.05.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 04/23/2017] [Accepted: 05/23/2017] [Indexed: 12/15/2022]
Abstract
Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the rapidly growing structural data on the chromosome folding and the large-scale genome organization. Could a part of information on the chromosome folding be obtained directly from underlying genomic DNA sequences abundantly stored in the databanks? To answer this question, we developed an original discrete double Fourier transform (DDFT). DDFT serves for the detection of large-scale genome regularities associated with domains/units at the different levels of hierarchical chromosome folding. The method is versatile and can be applied to both genomic DNA sequences and corresponding physico-chemical parameters such as base-pairing free energy. The latter characteristic is closely related to the replication and transcription and can also be used for the assessment of temperature or supercoiling effects on the chromosome folding. We tested the method on the genome of E. coli K-12 and found good correspondence with the annotated domains/units established experimentally. As a brief illustration of further abilities of DDFT, the study of large-scale genome organization for bacteriophage PHIX174 and bacterium Caulobacter crescentus was also added. The combined experimental, modeling, and bioinformatic DDFT analysis should yield more complete knowledge on the chromosome architecture and genome organization.
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Affiliation(s)
- V R Chechetkin
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Vavilov str., 32, Moscow 119334, Russia; Theoretical Department of Division for Perspective Investigations, Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI), Moscow, Troitsk District 108840, Russia.
| | - V V Lobzin
- School of Physics, University of Sydney, Sydney, NSW 2006, Australia.
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Database of Periodic DNA Regions in Major Genomes. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7949287. [PMID: 28182099 PMCID: PMC5274682 DOI: 10.1155/2017/7949287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/07/2016] [Accepted: 12/21/2016] [Indexed: 12/11/2022]
Abstract
Summary. We analyzed several prokaryotic and eukaryotic genomes looking for the periodicity sequences availability and employing a new mathematical method. The method envisaged using the random position weight matrices and dynamic programming. Insertions and deletions were allowed inside periodicities, thus adding a novelty to the results we obtained. A periodicity length, one of the key periodicity features, varied from 2 to 50 nt. Totally over 60,000 periodicity sequences were found in 15 genomes including some chromosomes of the H. sapiens (partial), C. elegans, D. melanogaster, and A. thaliana genomes.
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Korotkov EV, Korotkova MA. Developing a mathematical method to search for latent periodicity in protein amino-acid sequences with deletions and insertions. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915060159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: The role of mixing statistics and frame shift of neighboring genes. Comput Biol Chem 2014; 53 Pt A:15-25. [DOI: 10.1016/j.compbiolchem.2014.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Valenzuela CY. The structure of selective dinucleotide interactions and periodicities in D melanogaster mtDNA. Biol Res 2014; 47:18. [PMID: 25027717 PMCID: PMC4101722 DOI: 10.1186/0717-6287-47-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 04/26/2014] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND We found a strong selective 3-sites periodicity of deviations from randomness of the dinucleotide (DN) distribution, where both bases of DN were separated by 1, 2, K sites in prokaryotes and mtDNA. Three main aspects are studied. I) the specific 3 K-sites periodic structure of the 16 DN. II) to discard the possibility that the periodicity was produced by the highly nonrandom interactive association of contiguous bases, by studying the interaction of non-contiguous bases, the first one chosen each I sites and the second chosen J sites downstream. III) the difference between this selective periodicity of association (distance to randomness) of the four bases with the described fixed periodicities of base sequences. RESULTS I) The 16 pairs presented a consistent periodicity in the strength of association of both bases of the pairs; the most deviated pairs are those where G and C are involved and the least deviated ones are those where A and T are involved. II) we found significant non-random interactions when the first nucleotide is chosen every I sites and the second J sites downstream until I=J=76. III) we showed conclusive differences between these internucleotide association periodicities and sequence periodicities. CONCLUSIONS This relational selective periodicity is different from sequence periodicities and indicates that any base strongly interacts with the bases of the residual genome; this interaction and periodicity is highly structured and systematic for every pair of bases. This interaction should be destroyed in few generations by recurrent mutation; it is only compatible with the Synthetic Theory of Evolution and agrees with the Wright's adaptive landscape conception and evolution by shifting balanced adaptive peaks.
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Muskhelishvili G, Travers A. Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell Mol Life Sci 2013; 70:4555-67. [PMID: 23771629 PMCID: PMC11113758 DOI: 10.1007/s00018-013-1394-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 11/29/2022]
Abstract
Understanding genetic regulation is a problem of fundamental importance. Recent studies have made it increasingly evident that, whereas the cellular genetic regulation system embodies multiple disparate elements engaged in numerous interactions, the central issue is the genuine function of the DNA molecule as information carrier. Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer. These two DNA information types are intrinsically coupled in the primary sequence organisation, and this coupling is directly relevant to regulation of the genetic function. In this review, we emphasise the critical need of holistic integration of the DNA information as a prerequisite for understanding the organisational complexity of the genetic regulation system.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany,
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Kravatskaya GI, Chechetkin VR, Kravatsky YV, Tumanyan VG. Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: how to relate microarray expression data with genomic sequences. Genomics 2012; 101:1-11. [PMID: 23085385 DOI: 10.1016/j.ygeno.2012.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 09/10/2012] [Accepted: 10/11/2012] [Indexed: 11/18/2022]
Abstract
The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression enhanced and decreased in response to loss of chromosomal supercoiling in Escherichia coli. Fourier analysis of promoter sequences for supercoiling-sensitive genes reveals the tendency in selection of sequences with helical periodicities close to 10nt for relaxation-induced genes and to 11nt for relaxation-repressed genes. The helical periodicities in the subsets of promoters recognized by RNA polymerase with different sigma factors were also studied. A special procedure was developed for the study of correlations between the intensities of periodicities in promoter sequences and the expression levels of corresponding genes. Significant correlations of expression with the AT content and with AT periodicities about 10, 11, and 50nt indicate their role in regulation of supercoiling-sensitive genes.
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Affiliation(s)
- Galina I Kravatskaya
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Russia.
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