Structure of bacterial chromosome: An analysis of DNA-protein interactions in vivo

Hołówka, Joanna; Płachetka, Małgorzata

doi:10.5604/01.3001.0010.6696

Cited by 4 publications

(3 citation statements)

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“…[ 84 ] integrated the genome conformation capture data of E. coli with its genome, biological pathway, and protein interaction data, leading to the discovery of the spatial characteristics of E. coli genome organization. Meanwhile, Hołówka and Płachetka [ 85 ] used molecular biology techniques along with high-throughput DNA sequencing methods to analyze bacterial chromosome structures in a precise manner at both local and global scales. Tian et al .…”

Section: Perspectivementioning

confidence: 99%

Chromosome structure modeling tools and their evaluation in bacteria

Liu,

Qiu,

Hua

et al. 2024

Briefings in Bioinformatics

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The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained from Escherichia coli and Caulobacter crescentus, as well as simulated datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms.

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Section: Perspectivementioning

confidence: 99%

Chromosome structure modeling tools and their evaluation in bacteria

Liu,

Qiu,

Hua

et al. 2024

Briefings in Bioinformatics

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“…For instance, Xie et al [86] integrated the genome conformation capture data of E. coli with its genome, biological pathway, and protein interaction data, leading to the discovery of the spatial characteristics of E. coli genome organization. Meanwhile, Hołówka and Płachetka [87] used molecular biology techniques along with high-throughput DNA sequencing methods to analyze bacterial chromosome structures in a precise manner at both local and global scales. Tian et al [88] investigated the spatial organization characteristics of bacterial transcriptional regulatory network (TRN) using gene regulation and chromatin interaction data.…”

Section: Integration Of Structure Models With Multi-omics Datamentioning

confidence: 99%

Evaluation of chromosome structure modelling tools in bacteria

Liu,

Qiu,

Hua

et al. 2023

Preprint

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The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained fromEscherichia coliandCaulobacter crescentus, as well as simulating datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms.

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“…Among the four core histone proteins constituting the nucleosome, histone H3 is highly conserved in eukaryotes [15]. On the contrary, bacterial DNA, as well as the plastid and mitochondrion DNA that originated from ancient bacterial endosymbionts, are naked [16,17]. Nucleoids in bacteria are folded into a range of different conformations by nucleoid-associated proteins (NAPs) that have few similarities in amino acid sequence with histones [18].…”

Section: Introductionmentioning

confidence: 99%

ChIP-Based Nuclear DNA Isolation for Genome Sequencing in Pyropia to Remove Cytosol and Bacterial DNA Contamination

zhang

Wang

Zhang

et al. 2023

Plants

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Contamination from cytosolic DNA (plastid and mitochondrion) and epiphytic bacteria is challenging the efficiency and accuracy of genome-wide analysis of nori-producing marine seaweed Pyropia yezoensis. Unlike bacteria and organellar DNA, Pyropia nuclear DNA is closely associated with histone proteins. In this study, we applied Chromatin Immunoprecipitation (ChIP) of histone H3 to isolate nuclear DNA, followed by high-throughput sequencing. More than 99.41% of ChIP-sequencing data were successfully aligned to the reference nuclear genome; this was remarkably higher than those from direct extraction and direct extraction data, in which 40.96% to 42.95% are from plastids. The proportion of data that were mapped to the bacterial database when using ChIP extraction was very low. Additionally, ChIP data can cover up to 89.00% of the nuclear genome, higher than direct extraction data at equal data size and comparable to the latter at equal sequencing depth. The uncovered regions from the three methods are mostly overlapping, suggesting that incomplete sequencing accounts for the missing data, rather than failed chromatin-antibody binding in the ChIP extraction method. This ChIP extraction method can successfully separate nuclear DNA from cytosolic DNA and bacterial DNA, thus overwhelmingly reducing the sequencing cost in a genome resequencing project and providing strictly purified reference data for genome assembly. The method’s applicability to other macroalgae makes it a valuable contribution to the algal research community.

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Structure of bacterial chromosome: An analysis of DNA-protein interactions in vivo

Cited by 4 publications

References 0 publications

Chromosome structure modeling tools and their evaluation in bacteria

Chromosome structure modeling tools and their evaluation in bacteria

Evaluation of chromosome structure modelling tools in bacteria

ChIP-Based Nuclear DNA Isolation for Genome Sequencing in Pyropia to Remove Cytosol and Bacterial DNA Contamination

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