Role of special cross-links in structure formation of bacterial DNA polymer

Agarwal, Tejal; Manjunath, Geetha; Habib, Farhat; Vaddavalli, Pavana Lakshmi; Chatterji, A. C.

doi:10.1088/1361-648x/aa9e66

Cited by 8 publications

(36 citation statements)

References 43 publications

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“…For details see supplementary section: Construction of 2-D map. Corresponding structural quantities/colormaps for E. Coli can be found in [25]; the interpretation and conclusions are similar to what is discussed above for C.Crescentus.…”

Section: The Interpretation Of Data Presented Insupporting

confidence: 71%

“…As a consequence multiple segments of the chain are pulled in together towards the center of the coil with loops remaining on the outside. This can be reconfirmed also for E.Coli in [25]. In contrast for RC-2 set of CLs the CLs are scattered in space.…”

Section: The Interpretation Of Data Presented Insupporting

confidence: 60%

“…Quantities like pair correlation function g(r) between monomers are insufficient as we would like more individualized information about arrangement of different segments of the DNA. We use the following four quantities to identify the global organization of C.Crecentus DNA-polymers; similar detailed data for E.coli is given in [25] 1. We estimate the radius of gyration R g of the DNApolymer of C.Crescentus.…”

Section: Resultsmentioning

confidence: 99%

“…By lowering the frequency cutoff, we can have more cross-linked monomers. For details, refer [25]. So, we take 47 or 159 CLs for E. Coli.…”

mentioning

confidence: 99%

“…Removing such over-counts, there are 26 and 60 effective CLs for C.Crescentus. For E. Coli we have 27 and 82 effective CLs, CL-list and other details are in [25]. We also investigate large scale organization of the chain when we have a set of CLs, where pairs of monomers are chosen randomly and cross-linked.…”

mentioning

confidence: 99%

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Origin of spatial organization of DNA-polymer in bacterial chromosomes

Agarwal¹,

Manjunath²,

Habib³

et al. 2018

EPL

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In-vivo DNA organization at large length scales (∼ 100nm) is highly debated and polymer modelshave proved useful to understand the principle of DNA-organization. Here, we show that < 2% cross-links at specific points in a ring polymer can lead to a distinct spatial organization of the polymer. The specific pairs of cross-linked monomers were extracted from contact maps of bacterial DNA.We are able to predict the structure of 2 DNAs using Monte Carlo simulations of the beadspring polymer with cross-links at these special positions. Simulations with cross-links at random positions along the chain show that the organization of the polymer is different in nature from the previous case.PACS numbers: 87.15.ak,82.35.Lr,82.35.Pq,87.16.Sr,61.25.hp It is established that DNA-polymer is not a random coil in either bacterial cells [1][2][3] or in eukaryotic cells [4][5][6][7]. Experimental methods such as CCC (chromosomal conformation capture) which was then further developed as 5C and then Hi-C have consistently shown the presence of topologically associated domains (TADs) in the contact maps (C-maps) of DNA-chains [8][9][10]. The Hi-C technique gives us the C-map which is the map of frequencies that a segment of the DNA chain (say i) is found in spatial proximity to another segment (say j) for all combinations i, j of segments along the contour length of the DNA-polymer. TADs are patches in Cmaps which indicate that some segments of the chain (at 1 mega-base pair(BP) to 1 kilo-BP resolution), are found spatially close to other particular segments with higher frequencies compared to the rest of the segments.The ds-DNA is stiff at length scales of 1nm but can be considered to be a flexible chain at length scales beyond 100nm [11] . The persistence length ℓ p of a naked DNA is 150 Base Pairs (BP) ≡ 50 nm [12] and the value of ℓ p in vivo is debated [13]. Since, the resolution of Hi-C experiments are well above this length scale [1,4], there has a focussed attempts in the last few years trying to understand the DNA organization and in particular origin of formation of TADs from the principles of polymer physics [14][15][16][17][18]. A series of studies indicate that TADs in eukaryotic cells are indicative of fractal globule organization of the polymer (as opposed to equilibrium globule) [4,19]. Recently, more detailed polymer models with either different lengths of loops or with many distinct (coarse-grained) diffusing binder molecules which cross-link different segments of the chain have reproduced TADs of sections of a particular eukaryotic DNA by performing optimizations in multi-parameter space. Distinct kinds of binder molecules link correspondingly distinct monomers (DNA-segments) along the chain, and the optimization parameters include the number of distinct kind of binders/monomers as well as the position and number of distinct monomers as well as diffusing cross-links along the contour [16,[20][21][22].We propose a much simpler model for shorter bacterial DNAs and ask a more general question: Does fixed cross-links...

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Section: The Interpretation Of Data Presented Insupporting

confidence: 71%

Section: The Interpretation Of Data Presented Insupporting

confidence: 60%

Section: Resultsmentioning

confidence: 99%

“…By lowering the frequency cutoff, we can have more cross-linked monomers. For details, refer [25]. So, we take 47 or 159 CLs for E. Coli.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

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Origin of spatial organization of DNA-polymer in bacterial chromosomes

Agarwal¹,

Manjunath²,

Habib³

et al. 2018

EPL

Self Cite

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Development of a Data-Driven Integrative Model of a Bacterial Chromosome

Wasim

Bera

Mondal

2023

J. Chem. Theory Comput.

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The chromosome of archetypal bacteria E. coli is known for a complex topology with a 4.6 × 10 6 base pairs (bp) long sequence of nucleotides packed within a micrometer-sized cellular confinement. The inherent organization underlying this chromosome eludes general consensus due to the lack of a high-resolution picture of its conformation. Here we present our development of an integrative model of E. coli at a 500 bp resolution (https://github.com/JMLab-tifrh/ecoli_finer), which optimally combines a set of multiresolution genome-wide experimentally measured data within a framework of polymer based architecture. In particular the model is informed with an intragenome contact probability map at 5000 bp resolution derived via the Hi-C experiment and RNA-sequencing data at 500 bp resolution. Via dynamical simulations, this data-driven polymer based model generates an appropriate conformational ensemble commensurate with chromosome architectures that E. coli adopts. As a key hallmark of the E. coli chromosome the model spontaneously self-organizes into a set of nonoverlapping macrodomains and suitably locates plectonemic loops near the cell membrane. As novel extensions, it predicts a contact probability map simulated at a higher resolution than precedent experiments and can demonstrate segregation of chromosomes in a partially replicating cell. Finally, the modular nature of the model helps us devise control simulations to quantify the individual role of key features in hierarchical organization of the bacterial chromosome.

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