 Software
 Open Access
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EVR: reconstruction of bacterial chromosome 3D structure models using errorvector resultant algorithm
BMC Genomics volume 20, Article number: 738 (2019)
Abstract
Background
More and more 3C/HiC experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structure models is an important task and in great need.
Results
We have developed a new reconstruction program for bacterial chromosome 3D structure models called EVR that exploits a simple ErrorVector Resultant (EVR) algorithm. This software tool is particularly optimized for the closedloop structural features of prokaryotic chromosomes. The parallel implementation of the program can utilize the computing power of both multicore CPUs and GPUs.
Conclusions
EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/HiC experimental data quickly and precisely.
Background
Like eukaryotes, the prokaryotic genomes also fold with regular patterns. The spatial organization plays very important roles in many cellular activities such as transcriptional regulation [1], gene expression [2] and DNA replication [3]. Many approaches, e.g., FISH (Fluorescence in situ hybridization) [4] and 3C (chromosome conformation capture) technology [5] have been adopted to study the 3D architecture of prokaryotic chromosome. In FISH experiments, fluorescence is generated by binding a labeled probe to a specific DNA fragment, and the position of target DNA fragment in cell can be visually observed under a microscope [6]. However, due to the low throughput and limited resolution of FISH, it is difficult to be applied in the genomewide study of chromosome structure. The 3C technology and its derivative technologies such as 4C (circular chromosome conformation capture) [7], 5C (3Ccarbon copy) [8] and HiC (Highthroughput/resolution chromosome conformation capture) [9] have significantly promoted the research of threedimensional genomics in the past decade [1]. In 3C technology, the genome is crosslinked by formaldehyde and then broken into fragments which are further ligated by enzymes and sequenced for subsequent analysis [10]. In the process of crosslinking, the probability that the fragments close to each other in space are connected is high. This feature is an important clue to study the spatial structure of chromosome [11]. In 2011, Umbarger et al. used 5C technology to generate a genomewide DNA interaction map of Caulobacter crescentus with fragment size of approximately 13 kb [12], and established the 3D structure of chromosome using the integrated modeling platform (IMP) [13, 14]. Subsequently in 2013, Cagliero et al. obtained the chromosome interaction data of E. coli [15], but the final interaction map contained a large amount of noise, and it was difficult to use the data to reconstruct structures. In the same year, Le et al. produced the fullgenome interaction maps of 10 kb resolution for C. crescentus using HiC and built its spatial structure with their own method [16]. With this research, they demonstrated the existence of CID (chromosomal interaction domains) boundaries and their roles in gene expression. In 2015, Marbouty et al. applied HiC to the chromosome research of Bacillus subtilis [17] and reconstructed 3D models with the ShRec3D program [18], and then they combined the 3D genome structure with superresolution microscopy to unravel the role of chromosome 3D folding pattern in the regulation of replication initiation, chromosome organization and DNA segregation. In the meanwhile, Wang et al. also studied B. subtilis with HiC and a large number of chromosome interaction maps were generated at various physiological stages [19, 20], and their research revealed the mechanism of SMC condensin complexes in compacting and resolving replicated chromosomes. Recently, Lioy et al. succeeded in applying HiC in the study of E. coli and obtained interaction maps in a high resolution of 5 kb, and the 3D chromosome structures were reconstructed with the ShRec3D program [18, 21] to demonstrate the role of nucleoid associated proteins (NAPs) in chromosome organizing.
Years of investigation have yielded many discoveries of bacterial chromosome features, such as cyclic pseudonucleation [22], supercoiled regions [23] and plectoneme structures [16], etc. With the knowledge of these features, scientists can build the structure of bacterial chromosome by combining experimental data with elaborately developed calculation methods. In 2017, a research work divided E coli chromatin into plectonemeabundant regions and plectonemefree regions based on ChIPchip data [24], and built its structure by using multiscale modeling and Brownian dynamics approaches, resulting in a chromosome model with a resolution of 1NTB (nucleotide per bead) [25]. More recently, a lattice model of E. coli chromatin with resolution of 20 bp was constructed by giving the position and size of the plectoneme fragments [26] using a mesoscale modeling pipeline method [27], and the chromosome structure model of C. crescentus with 15 bp resolution was obtained by using HiC data combined with Monte Carlo sampling and molecular dynamics [28].
With the application of 3C technology, more and more chromosome interaction maps of prokaryotes emerge and the 3D models of chromosome structure are in great need for the studies of chromosome function and transcriptional regulation. Several software tools have been published for the reconstruction of chromosome 3D structures. These tools can be classified into two categories according to their modeling strategies: modeling based on restraints and modeling based on thermodynamics [29]. Restraintbased modeling is a commonly used method to derive 3D models from DNA interaction data. In restraintbased modeling, the DNA interaction data is first converted to the expected space distance, and then heuristic methods are used to optimize the structure under given restraint conditions, such as the gradient ascent method in MOGEN [30], Monte Carlo sampling in TADbit [31], multidimensional scaling algorithm in miniMDS [32], and shortestpath method in ShRec3D [18]. In these methods, ShRec3D [18] has been applied to reconstruct the chromosome 3D structures of two model bacteria species (B. subtilis and E. coli) [17, 21], but it is sensitive to resolution and highly depends on data normalization.
In this study, a new algorithm was proposed specially for the chromosome structure reconstruction of prokaryotes, which used error vectors to guide structural optimization and added constraints of a circular genome shape on the implementation of program. This program can robustly deal with prokaryotic data and has high calculation speed by fully utilizing the computing power of multicore CPUs and GPUs. With this algorithm, the 3D structures of the chromosomes of three prokaryotic model organisms (C. crescentus, B. subtilis and E. coli) were reconstructed and analyzed.
Implementation
Data source
The sequencing data from 3C/HiC experiments can be processed by pipelines such as HiCPro [33] or HiCUP [34] to obtain chromosome interaction information. In these pipelines, genomes are divided into equallength segments and each segment is called a bin. The interaction information of bins is generally presented in the form of a matrix whose element is the number of interactions between two bins. Then the matrix will be normalized to remove some biases such as GC content, mappability, and fragment length, etc. [35], resulting in the interaction frequency (IF) matrix, which will be used to construct the spatial structure of chromosome (namely, determine the spatial coordinates of each bin).
We used the published chromosome interaction data of three bacteria species: normalized chromosome interaction frequency matrix (referred to as IF matrix) with 10 kb resolution of Bacillus subtilis (GEO accession number: GSE68418) [19], normalized IF matrix with 10 kb resolution of Caulobacter crescentus (GEO accession number: GSE45966) [16], and the raw IF matrix with 5 kb resolution of Escherichia coli (GEO accession number: GSE107301) [21].
Algorithm
The EVR algorithm consists of the following steps: (i) transform IF matrix to the expected distance matrix D by Eq. 1; (ii) an initial conformation is generated by randomly assigning coordinates to DNA bins; (iii) calculate error vectors for each bin; (iv) a new conformation is obtained by moving bins according to the guidance of error vectors; (v) repeat steps (iii) and (iv) until the iteration stop condition is satisfied. The chromosome structure is the final conformation (coordinates of bins) after iteration (Fig. 1).
Generation of the expected distance matrix
In crosslinked chromatin, the closer the spatial distance is, the higher the probability of crosslinking is. Therefore, Eq. 1 is usually used to express the relationship between interaction frequency and the expected spatial distance [11]. In Eq. 1, F_{ij} is the interaction frequency of bin i and bin j (1 ≤ i, j ≤ N where N is bin number), and D_{ij} is the corresponding expected spatial distance. If F_{ij} is not equal to 0, a power function is used to convert F_{ij} into D_{ij}; otherwise, the power function is invalid, and then the distance constraint of adjacent bins will be used to optimize the coordinates. Here, the power exponent α is set to 0.5 by reference [21].
Error vectors
An initial chromosome conformation is generated by randomly assigning coordinates to all bins. With the distance matrix D, error vectors are calculated between every two bins. The error vectors are expressed as in Eq. 2 for bins that are not directly adjacent on the linear genome. Here, \( \overrightarrow{P_i} \) and \( \overrightarrow{P_j} \) are the coordinates of bin i and bin j in vector form, respectively, and D_{ij} (Eq. 1) is the expected distance between the two bins.
For bins that are directly adjacent on the linear genome (namely, i – j = 1, 1 ≤ i, j ≤ N), error vectors are defined as in Eq. 3, where D_{max} and D_{min} are the allowed maximum and minimum distances between any two adjacent bins, respectively. In a conformation, D_{max} and D_{min} will be used to calculate the error vector between two adjacent bins if the distance of the two bins is less than D_{min} or greater than D_{max}; otherwise, the expected distance D_{ij} is used. Owing to the fact that most prokaryotic chromosomes are circular, the first bin and the last bin are set as adjacent bins (namely, (ij)%N = 1 if i = 1, j = N or (ji)%N = 1 if i = N, j = 1, where % is modulus operator), which means the error vectors as defined in Eq. 3 also exist between the first and the last bins.
For each bin, all its error vectors are summed up with certain weights to a resultant vector (EVR). As shown in Eq. 4, \( \overrightarrow{E_j} \) is the EVR for bin j which indicates the direction and distance that bin j should move in the next iteration step (Fig. 2a) and a weight w_{ij} determines the step size. When w_{ij} is large, the length of EVR is large, and the structure changes greatly compared with the previous one after one iteration step, and the optimization speed is fast, but the result may not converge. Conversely, when w_{ij} is small, the structural change in each iteration step is small, and the optimization speed is slow, but it is easier to converge. In our algorithm, w_{ij} = 1/N, where N is the number of bins.
An example of EVR calculation is shown in Fig. 2a, in which black arrows are error vectors that can be calculated according to Eq. 2 and Eq. 3 and red arrows are the resultant vectors calculated according to parallelogram law; these resultant vectors can guide the position optimization of bins.
Iterative optimization
Starting with an initial random conformation, error vectors and resultant vectors can be calculated based on the expected distance matrix for all bins. The resultant vector of each bin indicates the direction and distance according to which the bin should move to change its position towards the target position. The chromosome structure is optimized by an iteration process during which all bins change their positions (coordinates) guided by their resultant vectors, resulting in the minimization of the sum of EVR lengths (Eq. 5). For example, the motion trajectories of the 3 bins P_{j1}, P_{j2}, P_{j3} are shown as light blue circles (Fig. 2a) and the distances of the 3 bins to their target positions decrease quickly during iteration (Fig. 2b).
In the iterative process, the value of F becomes smaller and smaller to approach a stable value. As shown in Eq. 6, ΔF is defined as the difference between two successive F values of iterative steps t and t1. When a level of ΔF < 1E5 or the given maximum number of steps is reached, the iteration stops and an optimized conformation is obtained which is the final structure of a chromosome. A general issue in optimization is local optima; see Supplementary Information (Additional file 1) for the analysis of our algorithm in this respect.
Programming
The main part of EVR program is implemented in Python with Numpy arrays for storing data. Two acceleration schemes are adopted in the iterative optimization part: Cython and OpenCL. In Cython scheme, the core code is written in CythonC language and compiled into a dynamic library that can be accelerated by OpenMP. The Cython scheme can make full use of the computing power of multicore CPUs. In OpenCL scheme, the core code is written in OpenCLC language, and it can be compiled and invoked directly by the PyOpenCL library functions. The OpenCL scheme can use not only multicore CPUs but also GPUs and other devices that support OpenCL to accelerate computing.
Results
First, we compared our EVR program with some published software tools for chromosome reconstruction, including: miniMDS [32], MOGEN [30] and ShRec3D [18]. All these software tools ran on multicore CPUs with default parameter setting. The comparisons involve the speed, accuracy and sensitivity to noise level of calculations. Subsequently, our EVR program was applied to the chromosome structure reconstruction of 3 model species of prokaryotes with published 3C/HiC data. The obtained chromosome structures were analyzed in a biological background.
EVR is fast
Among the compared software tools, miniMDS is written in Python and accelerated using the pymp library, and the computational complexity of a single iteration is O(N^{2}); MOGEN is written in java and can use multicore CPUs for accelerating calculation and the computational complexity of a single iteration is O(N^{2}); ShRec3D is written in MATLAB, and the program itself is not parallelized, but the new version of MATLAB supports automatic parallelization. Because eigenvalue and feature vector decomposition are used in the algorithm, the computational complexity of ShRec3D is O(N^{3}). The computational complexity of EVR’s single iteration is also O(N^{2}). Following convention [11], standard structures were generated for algorithm assessment. Here, toroidal spiral curves were generated and cut into fragments (bins) with bin numbers from 100 to 5000, and the IF matrixes of these structures were calculated to simulate a prokaryotic circular chromosome. Then, the above software tools were used to reconstruct the standard structures with these IF matrixes. See Supplementary Information (Additional file 1) for more details. The time efficiency of structure reconstruction is shown in Fig. 3.
Testing platform is Ubuntu 16.04 (64 bit) with Intel Core i5–2400 CPU@3.10 GHz and 16GB DDR3–1600 memory. The GPU platform is Geforce GTX 1050Ti. The comparison results show that EVR running on GPU with OpenCL used the least time, followed by EVR running on CPUs with OpenCL and MOGEN; meanwhile, their computation time is not sensitive to the bin numbers within a reasonable range. The running speed of EVR with Cython is slightly slower but still relatively fast. The computation time of miniMDS and ShRec3D shows a rapid rise with the increase of bin numbers.
EVR is robust
To assess robustness, different levels of noise were added to the IF matrix generated from the structures of toroidal spiral curves, and then the noisy data were used in the 3D structure reconstruction by using the above four software tools. Noises were added to the IF matrix by randomly selecting values from the range of −0.5 × P × IF_{max} to 0.5 × P × IF_{max} ; here, P is noise level and IF_{max} is the maximum value in IF matrix. The resulting structure reconstructed from the noisy data was compared to the original noisefree structure and the RMSD (rootmeansquare deviation) value was calculated. See Supplementary Information (Additional file 1) for more details. At each noise level, the above steps of adding noise, reconstructing structures, and comparing structures were repeated 100 times. The average RMSD values obtained are plotted against noise level as Fig. 4.
Since the IF matrix does not provide structural scale information, the scales of the structures obtained by different software tools may be not the same. When comparing structures, in order to ensure scale consistency, all the structures are scaled and compared with the original structure, and the structural alignment with the smallest RMSD value is selected for comparison. As shown in Fig. 4, our EVR algorithm always has the smallest RMSD values at different levels of noise, meaning that the structures reconstructed based on the noisy data are always very similar to the original structures based on the noisefree data, i.e., our EVR algorithm is robust to noise.
Since the initial conformation is randomly assigned in our algorithm, the dependency of the final structure on the initial conformation was also evaluated. As shown in Supplementary Information (Additional file 1: Figure S5), our EVR algorithm is not sensitive to the random initial conformations.
EVR is accurate
To assess accuracy, the reconstructed chromosome structures of E. coli by using the four software tools were compared with the published experimental fluorescence microscopy data (Additional file 1: Table S1) [36]. The E. coli chromosome structure reconstruction was based on the recently published IF matrixes [21]. By mapping the fluorescence marker sites onto the reconstructed structures (Additional file 1: Figure S6), the 3D coordinates of these sites could be determined and the spatial distances between them were calculated and correlated with the experimentally measured distances in fluorescence microscopy. Results show that there are high correlations (indicated by PCC: Pearson Correlation Coefficient) between the structurebased distances and the experimental distances (Fig. 5) for the EVR (PCC = 0.869, p − value = 1.079E − 10) and ShRec3D (PCC = 0.781, p − value = 1.324E − 7) software tools; The correlations for miniMDS (PCC = 0.552, p − value = 1.053E − 3) and MOGEN (PCC = 0.495, p − value = 3.932E − 3 PCC = 0.495, pvalue = 3.932E3) are relatively lower but still significant, possibly because they are developed for eukaryotes, not suitable or optimized for prokaryotes. The significant and high correlation between the experimentally measured and structurebased distances indicate that the reconstructed structure is close to the real structure and that our EVR algorithm is accurate. More datasets from different species could be used to further test these algorithms when they become available.
Application of EVR to prokaryotes
Our EVR algorithm was applied in the reconstruction of 3D chromosome structures of three prokaryotic model species Escherichia coli (MG1655), Caulobacter crescentus (CB15) and Bacillus subtilis (PY79) based on 3C data, and the obtained structures were divided into 4 macrodomains [1, 37]: origin and terminus of replication, left and right chromosomal arms (Fig. 6).
After transforming the interaction matrix into a spatial structure, we can visually examine the structure from a global perspective and observe features that are difficult to find in the interaction matrix. For example, Fis is a very important nucleoidassociated protein in E. coli, and it plays a variety of roles in regulating DNA transactions and modulating DNA topology [38]. By comparing the interaction matrixes of wildtype and fisdeficient (Δfis) E. coli, it can be seen that the interaction intensity is significantly reduced at the terminus region but conserved at other sites [21]. While converting these two IF matrixes into structures by using our EVR program and comparing them, the overall effect of Fis protein on the 3D structure is even more obvious (Fig. 7): compared to the wild type, there is a clear angle in the terminus region of the Δfis type, although other regions are substantially overlapping. Running many times of our software this angle persists and it cannot be found in the interaction map. Why the lack of fis causes the bending of the terminus region and what biological effects this bending will cause remain to be further investigated.
Discussion
We have developed a software tool called EVR for the reconstruction of 3D chromosome structure models from the DNA interaction data measured by 3C/HiC experiments. This tool added constraints related to a circular shape in the reconstruction process and thus it is particularly suitable for the reconstruction of chromosome structures of prokaryotes. Assessed based on standard structures, our EVR program is very fast and robust compared with other software tools, and the reconstructed structure is accurate evaluated based on the fluorescence labeling data. Our EVR program was used in the reconstruction of the 3D chromosome structures of three model prokaryotic species with published DNA interaction data. The obtained structures provided consistent understanding on the 3D genomes of these species.
Limited by the resolution of 3C/HiC experiment data [39, 40], our EVR program as well as other programs can only establish the backbone structure models of the prokaryotic chromosomes at domain levels. Combined with other modeling approaches such as the thermodynamicsbased methods used in a recent paper [25], more reliable and higher resolution chromosome models may be built to assist the fundamental research on the 3D genomics of prokaryotes. Another noticeable aspect is about the storage file format of the reconstructed chromosome structures. Currently, since the resulting structures contain only the spatial coordinate information of bins, they are usually saved in a simple PDBfilelike format such as the modified PDB file format [30] or “xyz” format [18]. With the development of 3D genomics, more specific format may be explored to accommodate more information such as domain partition, gene annotation and levels of transcription etc. in order to be readily integrated into a systems biology context.
Conclusions
Our EVR software is optimized for closedloop structures and can be used to reconstruct the bacterial 3D chromosome models based on the contact frequency matrix derived from 3C/HiC experimental data with high accuracy and robustness. Owing to its parallel implementation, this software tool also runs fast. The application of EVR to the model organism E. coli revealed a large structural variation between mutant and wild types, which provides clues for experimental investigation. In summary, EVR is a readily available software tool for the studies of prokaryotic 3D genomes and related fields.
Availability of data and materials
The source code and data of the program are available at https://github.com/mbglab/EVR.
Abbreviations
 1NTB:

Nucleotide per bead
 3C:

Chromosome Conformation Capture
 4C:

Circular Chromosome Conformation Capture
 5C:

3CCarbon copy
 ChIPchip:

Chromatin immunoprecipitation on chip
 CID:

Chromosomal Interaction Domains
 EVR:

ErrorVector Resultant
 FISH:

Fluorescence in situ Hybridization
 GEO:

Gene Expression Omnibus
 HiC:

Highthroughput/resolution Chromosome conformation capture
 IF matrix:

Interaction Frequency matrix
 IMP:

Integrated Modeling Platform
 NAPs:

Nucleoid Associated Proteins
 PCC:

Pearson Correlation Coefficient
 RMSD:

RootMeanSquare Deviation
 SMC:

Structural Maintenance of Chromosomes
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Acknowledgements
We’d like to thank Yang Yi for his help in polishing the manuscript.
Funding
This work was supported by the National Natural Science Foundation of China (Grant 31570844), Project 2662016PY094 supported by the Fundamental Research Funds for the Central Universities, and the National Basic Research Program of China (973 project, Grant 2013CB127103). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
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BGM conceived and designed the study. KJH designed the algorithm and software supervised by BGM. KJH and BGM wrote the manuscript. All authors have read and approved the final manuscript.
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Supplementary information
Additional file 1.
Supplementary materials for the evaluation of EVR algorithm.
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Hua, KJ., Ma, BG. EVR: reconstruction of bacterial chromosome 3D structure models using errorvector resultant algorithm. BMC Genomics 20, 738 (2019). https://doi.org/10.1186/s1286401960960
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Keywords
 Chromatin architecture
 HiC
 Prokaryotes
 3D genome
 Structure modelling