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DLm6Am: A Deep-Learning-Based Tool for Identifying N6,2′-O-Dimethyladenosine Sites in RNA Sequences. Int J Mol Sci 2022; 23:ijms231911026. [PMID: 36232325 PMCID: PMC9570463 DOI: 10.3390/ijms231911026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/10/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
N6,2′-O-dimethyladenosine (m6Am) is a post-transcriptional modification that may be associated with regulatory roles in the control of cellular functions. Therefore, it is crucial to accurately identify transcriptome-wide m6Am sites to understand underlying m6Am-dependent mRNA regulation mechanisms and biological functions. Here, we used three sequence-based feature-encoding schemes, including one-hot, nucleotide chemical property (NCP), and nucleotide density (ND), to represent RNA sequence samples. Additionally, we proposed an ensemble deep learning framework, named DLm6Am, to identify m6Am sites. DLm6Am consists of three similar base classifiers, each of which contains a multi-head attention module, an embedding module with two parallel deep learning sub-modules, a convolutional neural network (CNN) and a Bi-directional long short-term memory (BiLSTM), and a prediction module. To demonstrate the superior performance of our model’s architecture, we compared multiple model frameworks with our method by analyzing the training data and independent testing data. Additionally, we compared our model with the existing state-of-the-art computational methods, m6AmPred and MultiRM. The accuracy (ACC) for the DLm6Am model was improved by 6.45% and 8.42% compared to that of m6AmPred and MultiRM on independent testing data, respectively, while the area under receiver operating characteristic curve (AUROC) for the DLm6Am model was increased by 4.28% and 5.75%, respectively. All the results indicate that DLm6Am achieved the best prediction performance in terms of ACC, Matthews correlation coefficient (MCC), AUROC, and the area under precision and recall curves (AUPR). To further assess the generalization performance of our proposed model, we implemented chromosome-level leave-out cross-validation, and found that the obtained AUROC values were greater than 0.83, indicating that our proposed method is robust and can accurately predict m6Am sites.
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2
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Liu G, Zhao H, Meng H, Xing Y, Cai L. A deformation energy model reveals sequence-dependent property of nucleosome positioning. Chromosoma 2021; 130:27-40. [PMID: 33452566 PMCID: PMC7889546 DOI: 10.1007/s00412-020-00750-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 11/18/2022]
Abstract
We present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from crystal structures of nucleosomes was used to calculate the DNA deformation energy. The model is successful in predicting nucleosome occupancy genome-wide in budding yeast, nucleosome free energy, and rotational positioning of nucleosomes. Our model also indicates that the genomic regions underlying the MNase-sensitive nucleosomes in budding yeast have high deformation energy and, consequently, low nucleosome-forming ability, while the MNase-sensitive non-histone particles are characterized by much lower DNA deformation energy and high nucleosome preference. In addition, we also revealed that remodelers, SNF2 and RSC8, are likely to act in chromatin remodeling by binding to broad nucleosome-depleted regions that are intrinsically favorable for nucleosome positioning. Our data support the important role of position-dependent physical properties of DNA in nucleosome positioning.
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Affiliation(s)
- Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
| | - Hongyu Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Hu Meng
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yongqiang Xing
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Lu Cai
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
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3
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The dynamics and regulation of chromatin remodeling during spermiogenesis. Gene 2019; 706:201-210. [DOI: 10.1016/j.gene.2019.05.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 01/06/2023]
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4
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Zhao H, Zhang F, Guo M, Xing Y, Liu G, Zhao X, Cai L. The affinity of DNA sequences containing R5Y5 motif and TA repeats with 10.5-bp periodicity to histone octamer in vitro. J Biomol Struct Dyn 2018; 37:1935-1943. [PMID: 30044196 DOI: 10.1080/07391102.2018.1477621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nucleosome positioning along the genome is partially determined by the intrinsic DNA sequence preferences on histone. RRRRRYYYYY (R5Y5, R = Purine and Y = Pyrimidine) motif in nucleosome DNA, which was presented based on several theoretical models by Trifonov et al., might be a facilitating sequence pattern for nucleosome assembly. However, there is not a high conformity experimental evidence to support the concept that R5Y5 motif is a key element for the determination of nucleosome positioning. In this work, the ability of the canonical, H2A.Z- and H3.3-containing octamers to assemble nucleosome on DNA templates containing R5Y5 motif and TA repeats within 10.5-bp periodicity was investigated by using salt-dialysis method in vitro. The results showed that the10.5-bp periodical distributions of both R5Y5 motif and TA repeats along DNA templates can significantly promote canonical nucleosome assembly and may be key sequence factors for canonical nucleosome assembly. Compared with TA repeats within 10.5-bp periodicity, R5Y5 motif in DNA templates did not elevate H2A.Z- and H3.3-containing nucleosome formation efficiency in vitro. This result indicates that R5Y5 motif probably isn't a pivotal factor to regulate nucleosome assembly on histone variants. It is speculated that the regulatory mechanism of nucleosome assembly is different between canonical and variant histone. These conclusions can provide a deeper insight on the mechanism of nucleosome positioning. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hongyu Zhao
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Fenghui Zhang
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China
| | - Mingxin Guo
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China
| | - Yongqiang Xing
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Guoqing Liu
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Xiujuan Zhao
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Lu Cai
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
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5
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Liu G, Liu GJ, Tan JX, Lin H. DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions. Genomics 2018; 111:1167-1175. [PMID: 30055231 DOI: 10.1016/j.ygeno.2018.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/07/2018] [Accepted: 07/15/2018] [Indexed: 12/15/2022]
Abstract
The nucleosome is the fundamental structural unit of eukaryotic chromatin and plays an essential role in the epigenetic regulation of cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to identify nucleosome positions in the genome. Our previous model based on DNA deformation energy, in which a set of DNA physical descriptors was used, performed well in predicting nucleosome dyad positions and occupancy. In this study, we established a machine-learning model for predicting nucleosome occupancy in order to further verify the physical descriptors. Results showed that (1) our model outperformed several other sequence compositional information-based models, indicating a stronger dependence of nucleosome positioning on DNA physical properties; (2) nucleosome-enriched and -depleted regions have distinct features in terms of DNA physical descriptors like sequence-dependent flexibility and equilibrium structure parameters; (3) gene transcription start sites and termination sites can be well characterized with the distribution patterns of the physical descriptors, indicating the regulatory role of DNA physical properties in gene transcription. In addition, we developed a web server for the model, which is freely accessible at http://lin-group.cn/server/iNuc-force/.
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Affiliation(s)
- Guoqing Liu
- The School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.
| | - Guo-Jun Liu
- School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620000, Russia
| | - Jiu-Xin Tan
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
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6
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The implication of DNA bending energy for nucleosome positioning and sliding. Sci Rep 2018; 8:8853. [PMID: 29891930 PMCID: PMC5995830 DOI: 10.1038/s41598-018-27247-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 05/24/2018] [Indexed: 11/24/2022] Open
Abstract
Nucleosome not only directly affects cellular processes, such as DNA replication, recombination, and transcription, but also severs as a fundamentally important target of epigenetic modifications. Our previous study indicated that the bending property of DNA is important in nucleosome formation, particularly in predicting the dyad positions of nucleosomes on a DNA segment. Here, we investigated the role of bending energy in nucleosome positioning and sliding in depth to decipher sequence-directed mechanism. The results show that bending energy is a good physical index to predict the free energy in the process of nucleosome reconstitution in vitro. Our data also imply that there are at least 20% of the nucleosomes in budding yeast do not adopt canonical positioning, in which underlying sequences wrapped around histones are structurally symmetric. We also revealed distinct patterns of bending energy profile for distinctly organized chromatin structures, such as well-positioned nucleosomes, fuzzy nucleosomes, and linker regions and discussed nucleosome sliding in terms of bending energy. We proposed that the stability of a nucleosome is positively correlated with the strength of the bending anisotropy of DNA segment, and both accessibility and directionality of nucleosome sliding is likely to be modulated by diverse patterns of DNA bending energy profile.
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Jia C, Yang Q, Zou Q. NucPosPred: Predicting species-specific genomic nucleosome positioning via four different modes of general PseKNC. J Theor Biol 2018; 450:15-21. [PMID: 29678692 DOI: 10.1016/j.jtbi.2018.04.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 11/20/2022]
Abstract
The nucleosome is the basic structure of chromatin in eukaryotic cells, with essential roles in the regulation of many biological processes, such as DNA transcription, replication and repair, and RNA splicing. Because of the importance of nucleosomes, the factors that determine their positioning within genomes should be investigated. High-resolution nucleosome-positioning maps are now available for organisms including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans, enabling the identification of nucleosome positioning by application of computational tools. Here, we describe a novel predictor called NucPosPred, which was specifically designed for large-scale identification of nucleosome positioning in C. elegans and D. melanogaster genomes. NucPosPred was separately optimized for each species for four types of DNA sequence feature extraction, with consideration of two classification algorithms (gradient-boosting decision tree and support vector machine). The overall accuracy obtained with NucPosPred was 92.29% for C. elegans and 88.26% for D. melanogaster, outperforming previous methods and demonstrating the potential for species-specific prediction of nucleosome positioning. For the convenience of most experimental scientists, a web-server for the predictor NucPosPred is available at http://121.42.167.206/NucPosPred/index.jsp.
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Affiliation(s)
- Cangzhi Jia
- Science of College, Dalian Maritime University, No. 1 Linghai Road, Dalian 116026, China.
| | - Qing Yang
- Science of College, Dalian Maritime University, No. 1 Linghai Road, Dalian 116026, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, China.
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8
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Meng H, Li H, Zheng Y, Yang Z, Jia Y, Bo S. Evolutionary analysis of nucleosome positioning sequences based on New Symmetric Relative Entropy. Genomics 2017; 110:154-161. [PMID: 28917635 DOI: 10.1016/j.ygeno.2017.09.007] [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: 07/04/2017] [Revised: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 10/18/2022]
Abstract
New Symmetric Relative Entropy (NSRE) was applied innovatively to analyze the nucleosome sequences in S. cerevisiae, S. pombe and Drosophila. NSRE distributions could well reflect the characteristic differences of nucleosome sequences among three organisms, and the differences indicate a concerted evolution in the sequence usage of nucleosome. Further analysis about the nucleosomes around TSS shows that the constitutive property of +1/-1 nucleosomes in S. cerevisiae is different from that in S. pombe and Drosophila, which indicates that S. cerevisiae has a different transcription regulation mechanism based on nucleosome. However, in either case, the nucleosome dyad region is conserved and always has a higher NSRE. Base composition analysis shows that this conservative property in nucleosome dyad region is mainly determined by base A and T, and the dependence degrees on base A and T are consistent in three organisms.
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Affiliation(s)
- Hu Meng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Hong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
| | - Yan Zheng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Zhenhua Yang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Yun Jia
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Suling Bo
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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9
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Liu G, Xing Y, Zhao H, Wang J, Shang Y, Cai L. A deformation energy-based model for predicting nucleosome dyads and occupancy. Sci Rep 2016; 6:24133. [PMID: 27053067 PMCID: PMC4823781 DOI: 10.1038/srep24133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/21/2016] [Indexed: 12/14/2022] Open
Abstract
Nucleosome plays an essential role in various cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to decode the mechanism of nucleosome positioning and identify nucleosome positions in the genome. In this paper, we present a model for predicting nucleosome positioning based on DNA deformation, in which both bending and shearing of the nucleosomal DNA are considered. The model successfully predicted the dyad positions of nucleosomes assembled in vitro and the in vitro map of nucleosomes in Saccharomyces cerevisiae. Applying the model to Caenorhabditis elegans and Drosophila melanogaster, we achieved satisfactory results. Our data also show that shearing energy of nucleosomal DNA outperforms bending energy in nucleosome occupancy prediction and the ability to predict nucleosome dyad positions is attributed to bending energy that is associated with rotational positioning of nucleosomes.
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Affiliation(s)
- Guoqing Liu
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.,Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Yongqiang Xing
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Hongyu Zhao
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jianying Wang
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.,State Key Laboratory for Utilization of Bayan Obo Multi-Metallic Resources, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yu Shang
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,College of Computer Science and Technology, Jilin University, Changchun, Jilin 130021, China
| | - Lu Cai
- The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
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Xing YQ, Liu GQ, Zhao XJ, Zhao HY, Cai L. Genome-wide characterization and prediction of Arabidopsis thaliana replication origins. Biosystems 2014; 124:1-6. [PMID: 25050475 DOI: 10.1016/j.biosystems.2014.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 03/25/2014] [Accepted: 07/15/2014] [Indexed: 01/25/2023]
Abstract
Identification of replication origins is crucial for the faithful duplication of genomic DNA. The frequencies of single nucleotides and dinucleotides, GC/AT bias and GC/AT profile in the vicinity of Arabidopsis thaliana replication origins were analyzed in the present work. The guanine content or cytosine content is higher in origin of replication (Ori) than in non-Ori. The SS (S=G or C) dinucleotides are favoured in Ori whereas WW (W=A or T) dinucleotides are favoured in non-Ori. GC/AT bias and GC/AT profile in Ori are significantly different from that in non-Ori. Furthermore, by inputting DNA sequence features into support vector machine, we distinguished between the Ori and non-Ori regions in A. thaliana. The total prediction accuracy is about 69.5% as evaluated by the 10-fold cross-validation. This result suggested that apart from DNA sequence, deciphering the selection of replication origin must integrate many other factors including nucleosome positioning, DNA methylation, histone modification, etc. In addition, by comparing predictive performance we found that the predictive accuracy of SVM using sequence features on the context of WS language is significantly better than that of RY language. Furthermore, the same conclusion was also obtained in S. cerevisiae and D. melanogaster.
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Affiliation(s)
- Yong-Qiang Xing
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China; School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China; The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Guo-Qing Liu
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China; The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Xiu-Juan Zhao
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China; The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Hong-Yu Zhao
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China; The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China; Inner Mongolia Key Laboratory of Biomass-Energy Conversion, Baotou, 014010, China
| | - Lu Cai
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China; The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China; Inner Mongolia Key Laboratory of Biomass-Energy Conversion, Baotou, 014010, China.
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11
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Guo SH, Deng EZ, Xu LQ, Ding H, Lin H, Chen W, Chou KC. iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. ACTA ACUST UNITED AC 2014; 30:1522-9. [PMID: 24504871 DOI: 10.1093/bioinformatics/btu083] [Citation(s) in RCA: 312] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
MOTIVATION Nucleosome positioning participates in many cellular activities and plays significant roles in regulating cellular processes. With the avalanche of genome sequences generated in the post-genomic age, it is highly desired to develop automated methods for rapidly and effectively identifying nucleosome positioning. Although some computational methods were proposed, most of them were species specific and neglected the intrinsic local structural properties that might play important roles in determining the nucleosome positioning on a DNA sequence. RESULTS Here a predictor called 'iNuc-PseKNC' was developed for predicting nucleosome positioning in Homo sapiens, Caenorhabditis elegans and Drosophila melanogaster genomes, respectively. In the new predictor, the samples of DNA sequences were formulated by a novel feature-vector called 'pseudo k-tuple nucleotide composition', into which six DNA local structural properties were incorporated. It was observed by the rigorous cross-validation tests on the three stringent benchmark datasets that the overall success rates achieved by iNuc-PseKNC in predicting the nucleosome positioning of the aforementioned three genomes were 86.27%, 86.90% and 79.97%, respectively. Meanwhile, the results obtained by iNuc-PseKNC on various benchmark datasets used by the previous investigators for different genomes also indicated that the current predictor remarkably outperformed its counterparts. AVAILABILITY A user-friendly web-server, iNuc-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iNuc-PseKNC.
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Affiliation(s)
- Shou-Hui Guo
- Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - En-Ze Deng
- Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Li-Qin Xu
- Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi ArabiaKey Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi ArabiaKey Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kuo-Chen Chou
- Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi ArabiaKey Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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12
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Xing YQ, Liu GQ, Zhao XJ, Cai L. An analysis and prediction of nucleosome positioning based on information content. Chromosome Res 2013; 21:63-74. [PMID: 23435498 DOI: 10.1007/s10577-013-9338-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/20/2013] [Accepted: 01/24/2013] [Indexed: 11/26/2022]
Abstract
Nucleosome positioning plays a key role in the regulation of many biological processes. In this study, the statistical difference of information content was investigated in nucleosome and linker DNA regions across eukaryotic organisms. By analyzing the information redundancy, D k , in Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans genomes, the short-range dominance of nucleotide correlation in nucleosome and linker DNA regions was confirmed. Significant difference of the D k value between the nucleosome and linker DNA regions was also found. The underlying reason for many successful oligonucleotide-based predictions of nucleosome positioning in eukaryotic model organisms may be attributed to the short-range dominance of nucleotide correlation in the nucleosome and linker DNA regions. When applying power spectrum analysis to the nucleosome and linker DNA regions, some obvious differences in sequence periodic signals were observed. The parameter F k was introduced to describe particular base correlation. Furthermore, the support vector machine combining F k was used to classify nucleosome and linker DNA regions in Homo sapiens, Oryzias latipes, C. elegans, Candida albicans, and S. cerevisiae. Independent test demonstrated that a good performance can be achieved by using this algorithm. This result further revealed that base correlation information has an important role in nucleosome positioning.
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Affiliation(s)
- Yong-qiang Xing
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
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13
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Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning. Chromosome Res 2012; 20:889-902. [DOI: 10.1007/s10577-012-9328-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/09/2012] [Accepted: 11/15/2012] [Indexed: 10/27/2022]
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14
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Predicting nucleosome binding motif set and analyzing their distributions around functional sites of human genes. Chromosome Res 2012; 20:685-98. [DOI: 10.1007/s10577-012-9305-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 07/13/2012] [Accepted: 07/17/2012] [Indexed: 01/30/2023]
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