1
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Masoudi-Sobhanzadeh Y, Li S, Peng Y, Panchenko A. Interpretable deep residual network uncovers nucleosome positioning and associated features. Nucleic Acids Res 2024; 52:8734-8745. [PMID: 39036965 PMCID: PMC11347144 DOI: 10.1093/nar/gkae623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/31/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024] Open
Abstract
Nucleosomes represent elementary building units of eukaryotic chromosomes and consist of DNA wrapped around a histone octamer flanked by linker DNA segments. Nucleosomes are central in epigenetic pathways and their genomic positioning is associated with regulation of gene expression, DNA replication, DNA methylation and DNA repair, among other functions. Building on prior discoveries that DNA sequences noticeably affect nucleosome positioning, our objective is to identify nucleosome positions and related features across entire genome. Here, we introduce an interpretable framework based on the concepts of deep residual networks (NuPoSe). Trained on high-coverage human experimental MNase-seq data, NuPoSe is able to learn sequence and structural patterns associated with nucleosome organization in human genome. NuPoSe can be also applied to unseen data from different organisms and cell types. Our findings point to 43 informative features, most of them constitute tri-nucleotides, di-nucleotides and one tetra-nucleotide. Most features are significantly associated with the nucleosomal structural characteristics, namely, periodicity of nucleosomal DNA and its location with respect to a histone octamer. Importantly, we show that features derived from the 27 bp linker DNA flanking nucleosomes contribute up to 10% to the quality of the prediction model. This, along with the comprehensive training sets, deep-learning architecture, and feature selection method, may contribute to the NuPoSe's 80-89% classification accuracy on different independent datasets.
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Affiliation(s)
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L3N6, Canada
| | - Yunhui Peng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L3N6, Canada
- Department of Biology and Molecular Sciences, Queen's University, Kingston, K7L3N6, Canada
- School of Computing, Queen's University, Kingston, K7L3N6, Canada
- Ontario Institute of Cancer Research, Toronto, M5G 0A3, Canada
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2
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Sahrhage M, Paul NB, Beißbarth T, Haubrock M. The importance of DNA sequence for nucleosome positioning in transcriptional regulation. Life Sci Alliance 2024; 7:e202302380. [PMID: 38830772 PMCID: PMC11147951 DOI: 10.26508/lsa.202302380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Nucleosome positioning is a key factor for transcriptional regulation. Nucleosomes regulate the dynamic accessibility of chromatin and interact with the transcription machinery at every stage. Influences to steer nucleosome positioning are diverse, and the according importance of the DNA sequence in contrast to active chromatin remodeling has been the subject of long discussion. In this study, we evaluate the functional role of DNA sequence for all major elements along the process of transcription. We developed a random forest classifier based on local DNA structure that assesses the sequence-intrinsic support for nucleosome positioning. On this basis, we created a simple data resource that we applied genome-wide to the human genome. In our comprehensive analysis, we found a special role of DNA in mediating the competition of nucleosomes with cis-regulatory elements, in enabling steady transcription, for positioning of stable nucleosomes in exons, and for repelling nucleosomes during transcription termination. In contrast, we relate these findings to concurrent processes that generate strongly positioned nucleosomes in vivo that are not mediated by sequence, such as energy-dependent remodeling of chromatin.
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Affiliation(s)
- Malte Sahrhage
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - Niels Benjamin Paul
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
- Department of Cardiology and Pneumology, University Medical Center, Göttingen, Germany
| | - Tim Beißbarth
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - Martin Haubrock
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
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3
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Tan WY, Nagabhyrava S, Ang-Olson O, Das P, Ladel L, Sailo B, He L, Sharma A, Ahuja N. Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology. Curr Issues Mol Biol 2024; 46:6533-6565. [PMID: 39057032 PMCID: PMC11276574 DOI: 10.3390/cimb46070390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/21/2024] [Accepted: 06/23/2024] [Indexed: 07/28/2024] Open
Abstract
Technological advancements in cell-free DNA (cfDNA) liquid biopsy have triggered exponential growth in numerous clinical applications. While cfDNA-based liquid biopsy has made significant strides in personalizing cancer treatment, the exploration and translation of epigenetics in liquid biopsy to clinical practice is still nascent. This comprehensive review seeks to provide a broad yet in-depth narrative of the present status of epigenetics in cfDNA liquid biopsy and its associated challenges. It highlights the potential of epigenetics in cfDNA liquid biopsy technologies with the hopes of enhancing its clinical translation. The momentum of cfDNA liquid biopsy technologies in recent years has propelled epigenetics to the forefront of molecular biology. We have only begun to reveal the true potential of epigenetics in both our understanding of disease and leveraging epigenetics in the diagnostic and therapeutic domains. Recent clinical applications of epigenetics-based cfDNA liquid biopsy revolve around DNA methylation in screening and early cancer detection, leading to the development of multi-cancer early detection tests and the capability to pinpoint tissues of origin. The clinical application of epigenetics in cfDNA liquid biopsy in minimal residual disease, monitoring, and surveillance are at their initial stages. A notable advancement in fragmentation patterns analysis has created a new avenue for epigenetic biomarkers. However, the widespread application of cfDNA liquid biopsy has many challenges, including biomarker sensitivity, specificity, logistics including infrastructure and personnel, data processing, handling, results interpretation, accessibility, and cost effectiveness. Exploring and translating epigenetics in cfDNA liquid biopsy technology can transform our understanding and perception of cancer prevention and management. cfDNA liquid biopsy has great potential in precision oncology to revolutionize conventional ways of early cancer detection, monitoring residual disease, treatment response, surveillance, and drug development. Adapting the implementation of liquid biopsy workflow to the local policy worldwide and developing point-of-care testing holds great potential to overcome global cancer disparity and improve cancer outcomes.
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Affiliation(s)
- Wan Ying Tan
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Internal Medicine, Norwalk Hospital, Norwalk, CT 06850, USA
- Hematology & Oncology, Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030, USA
| | | | - Olivia Ang-Olson
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Paromita Das
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Luisa Ladel
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Internal Medicine, Norwalk Hospital, Norwalk, CT 06850, USA
| | - Bethsebie Sailo
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Linda He
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Anup Sharma
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Nita Ahuja
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520-8000, USA
- Biological and Biomedical Sciences Program (BBS), Yale University, New Haven, CT 06520-8084, USA
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4
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Beati P, Massimino Stepñicka M, Vilchez Larrea SC, Smircich P, Alonso GD, Ocampo J. Improving genome-wide mapping of nucleosomes in Trypanosome cruzi. PLoS One 2023; 18:e0293809. [PMID: 37988351 PMCID: PMC10662739 DOI: 10.1371/journal.pone.0293809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/19/2023] [Indexed: 11/23/2023] Open
Abstract
In Trypanosoma cruzi DNA is packaged into chromatin by octamers of histone proteins that form nucleosomes. Transcription of protein coding genes in trypanosomes is constitutive producing polycistronic units and gene expression is primarily regulated post-transcriptionally. However, chromatin organization influences DNA dependent processes. Hence, determining nucleosome position is of uppermost importance to understand the peculiarities found in trypanosomes. To map nucleosomes genome-wide in several organisms, digestion of chromatin with micrococcal nuclease followed by deep sequencing has been applied. Nonetheless, the special requirements for cell manipulation and the uniqueness of the chromatin organization in trypanosomes entails a customized analytical approach. In this work, we adjusted this broadly used method to the hybrid reference strain, CL Brener. Particularly, we implemented an exhaustive and thorough computational workflow to overcome the difficulties imposed by this complex genome. We tested the performance of two aligners, Bowtie2 and HISAT2, and discuss their advantages and caveats. Specifically, we highlight the relevance of using the whole genome as a reference instead of the commonly used Esmeraldo-like haplotype to avoid spurious alignments. Additionally, we show that using the whole genome refines the average nucleosome representation, but also the quality of mapping for every region represented. Moreover, we show that the average nucleosome organization around trans-splicing acceptor site described before, is not just an average since the same chromatin pattern is detected for most of the represented regions. In addition, we extended the study to a non-hybrid strain applying the experimental and analytical approach to Sylvio-X10 strain. Furthermore, we provide a source code for the construction of 2D plots and heatmaps which are easy to adapt to any T. cruzi strain.
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Affiliation(s)
- Paula Beati
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Milena Massimino Stepñicka
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Salomé C. Vilchez Larrea
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pablo Smircich
- Laboratorio de Bioinformática, Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Sección Genómica Funcional, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Guillermo D. Alonso
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Josefina Ocampo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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Sokolova DA, Halych TV, Zhuk VV, Kravets AP. Relationship of radiation-induced genomic instability and antioxidant production in the chamomile plant. Int J Radiat Biol 2023; 99:1631-1638. [PMID: 36881557 DOI: 10.1080/09553002.2023.2188934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/27/2023] [Indexed: 03/08/2023]
Abstract
PURPOSE To verify the hypothesis about the preservation of signs of radiation-induced genomic instability at the flowering stage of the chamomile plant after pre-sowing seed irradiation, the interaction of dose-dependent changes in the level of DNA damage and stimulation of antioxidant production. MATERIALS AND METHODS The study was carried out on two genotypes of chamomile, Perlyna Lisostepu variety and its mutant, using pre-sowing seed radiation exposure at dose levels 5-15 Gy. Studies of the rearrangement of the primary DNA structure of under different doses were studied on plant tissues at the flowering stage using - ISSR and RAPD DNA markers. Dose-dependent changes relative to the control of the amplicons' spectra were analyzed using the Jacquard similarity index. Antioxidants such as flavonoids and phenols were isolated from pharmaceutical raw materials (inflorescences) using traditional methods. RESULTS Preservation of multiple DNA damages at the stage of plant flowering under pre-sowing seed irradiation at low doses was confirmed. It was found that the largest rearrangements of the primary DNA structure of both genotypes, manifested in reduced similarity with the control spectra of amplicons, were observed under irradiation dose levels 5-10 Gy. There was a tendency to approach this indicator to the control under 15 Gy dose, which means increasing efficiency of the reparative processes. The relationship between the polymorphism of the primary structure of DNA by ISSR-RAPD-markers in different genotypes and the nature of its rearrangement under radiation exposure was shown. Dose dependences of changes in the specific content of antioxidants were non-monotonic with a maximum at 5-10 Gy. CONCLUSIONS Comparison of dose dependences of changes in the coefficient of similarity of the spectrum of amplicons between irradiated and control variants with nonmonotonic dose curves in the specific content of antioxidants allowed to suggest that there was the antioxidant protection stimulation under the doses corresponding to low efficiency of repair processes. The decrease in the specific content of antioxidants followed the restoration of the genetic material normal state. The interpretation of the identified phenomenon has been based on both known connection between the effects of genomic instability and the increasing yield of the reactive oxygen species and general principles of antioxidant protection.
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Affiliation(s)
- Daryna A Sokolova
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Taras V Halych
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Vladyslav V Zhuk
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alexandra P Kravets
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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6
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Johnston AD, Ross JP, Ma C, Fung KYC, Locke WJ. Epigenetic liquid biopsies for minimal residual disease, what's around the corner? Front Oncol 2023; 13:1103797. [PMID: 37081990 PMCID: PMC10110851 DOI: 10.3389/fonc.2023.1103797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/23/2023] [Indexed: 04/22/2023] Open
Abstract
Liquid biopsy assays for minimal residual disease (MRD) are used to monitor and inform oncological treatment and predict the risk of relapse in cancer patients. To-date, most MRD assay development has focused on targeting somatic mutations. However, epigenetic changes are more frequent and universal than genetic alterations in cancer and circulating tumor DNA (ctDNA) retains much of these changes. Here, we review the epigenetic signals that can be used to detect MRD, including DNA methylation alterations and fragmentation patterns that differentiate ctDNA from noncancerous circulating cell-free DNA (ccfDNA). We then summarize the current state of MRD monitoring; highlight the advantages of epigenetics over genetics-based approaches; and discuss the emerging paradigm of assaying both genetic and epigenetic targets to monitor treatment response, detect disease recurrence, and inform adjuvant therapy.
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7
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Sokolova DO, Halych TV, Zhuk VV, Kravets OP, Kuchuk MV. Association of the Stimulation of Plant Antioxidant Protection with Traits of Genome Instability. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722050103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Kadam S, Bameta T, Padinhateeri R. Nucleosome sliding can influence the spreading of histone modifications. Phys Rev E 2022; 106:024408. [PMID: 36110002 DOI: 10.1103/physreve.106.024408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Nucleosomes are the fundamental building blocks of chromatin that not only help in the folding of chromatin, but also in carrying epigenetic information. It is known that nucleosome sliding is responsible for dynamically organizing chromatin structure and the resulting gene regulation. Since sliding can move two neighboring nucleosomes physically close or away, can it play a role in the spreading of histone modifications? We investigate this by simulating a stochastic model that couples nucleosome dynamics with the kinetics of histone modifications. We show that the sliding of nucleosomes can affect the modification pattern as well as the time it takes to modify a given region of chromatin. Exploring different nucleosome densities and modification kinetic parameters, we show that nucleosome sliding can be important for creating histone modification domains. Our model predicts that nucleosome density coupled with sliding dynamics can create an asymmetric histone modification profile around regulatory regions. We also compute the probability distribution of modified nucleosomes and relaxation kinetics of modifications. Our predictions are comparable with known experimental results.
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Affiliation(s)
- Shantanu Kadam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Tripti Bameta
- Department of Medical Oncology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai 410210, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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9
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Kong S, Lu Y, Tan S, Li R, Gao Y, Li K, Zhang Y. Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape. Genes (Basel) 2022; 13:1114. [PMID: 35885897 PMCID: PMC9323251 DOI: 10.3390/genes13071114] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 12/04/2022] Open
Abstract
Genetic information is loaded on chromatin, which involves DNA sequence arrangement and the epigenetic landscape. The epigenetic information including DNA methylation, nucleosome positioning, histone modification, 3D chromatin conformation, and so on, has a crucial impact on gene transcriptional regulation. Out of them, nucleosomes, as basal chromatin structural units, play an important central role in epigenetic code. With the discovery of nucleosomes, various nucleosome-level technologies have been developed and applied, pushing epigenetics to a new climax. As the underlying methodology, next-generation sequencing technology has emerged and allowed scientists to understand the epigenetic landscape at a genome-wide level. Combining with NGS, nucleosome-omics (or nucleosomics) provides a fresh perspective on the epigenetic code and 3D genome landscape. Here, we summarized and discussed research progress in technology development and application of nucleosome-omics. We foresee the future directions of epigenetic development at the nucleosome level.
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Affiliation(s)
| | | | | | | | | | | | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (S.K.); (Y.L.); (S.T.); (R.L.); (Y.G.); (K.L.)
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10
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Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns. Int J Mol Sci 2022; 23:ijms23094869. [PMID: 35563261 PMCID: PMC9102330 DOI: 10.3390/ijms23094869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/25/2023] Open
Abstract
Nucleosomes are basic units of DNA packing in eukaryotes. Their structure is well conserved from yeast to human and consists of the histone octamer core and 147 bp DNA wrapped around it. Nucleosomes are bound to a majority of the eukaryotic genomic DNA, including its regulatory regions. Hence, they also play a major role in gene regulation. For the latter, their precise positioning on DNA is essential. In the present paper, we describe Galaxy dnpatterntools—software package for nucleosome DNA sequence analysis and mapping. This software will be useful for computational biologists practitioners to conduct more profound studies of gene regulatory mechanisms.
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11
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NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma 2022; 131:19-28. [PMID: 35061087 PMCID: PMC8776978 DOI: 10.1007/s00412-021-00766-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 11/24/2021] [Accepted: 12/20/2021] [Indexed: 01/25/2023]
Abstract
Nucleosome positioning is involved in many gene regulatory processes happening in the cell, and it may change as cells differentiate or respond to the changing microenvironment in a healthy or diseased organism. One important implication of nucleosome positioning in clinical epigenetics is its use in the “nucleosomics” analysis of cell-free DNA (cfDNA) for the purpose of patient diagnostics in liquid biopsies. The rationale for this is that the apoptotic nucleases that digest chromatin of the dying cells mostly cut DNA between nucleosomes. Thus, the short pieces of DNA in body fluids reflect the positions of nucleosomes in the cells of origin. Here, we report a systematic nucleosomics database — NucPosDB — curating published nucleosome positioning datasets in vivo as well as datasets of sequenced cell-free DNA (cfDNA) that reflect nucleosome positioning in situ in the cells of origin. Users can select subsets of the database by a number of criteria and then obtain raw or processed data. NucPosDB also reports the originally determined regions with stable nucleosome occupancy across several individuals with a given condition. An additional section provides a catalogue of computational tools for the analysis of nucleosome positioning or cfDNA experiments and theoretical algorithms for the prediction of nucleosome positioning preferences from DNA sequence. We provide an overview of the field, describe the structure of the database in this context, and demonstrate data variability using examples of different medical conditions. NucPosDB is useful both for the analysis of fundamental gene regulation processes and the training of computational models for patient diagnostics based on cfDNA. The database currently curates ~ 400 publications on nucleosome positioning in cell lines and in situ as well as cfDNA from > 10,000 patients and healthy volunteers. For open-access cfDNA datasets as well as key MNase-seq datasets in human cells, NucPosDB allows downloading processed mapped data in addition to the regions with stable nucleosome occupancy. NucPosDB is available at https://generegulation.org/nucposdb/.
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12
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Teubl F, Schwank K, Ohmayer U, Griesenbeck J, Tschochner H, Milkereit P. Tethered MNase Structure Probing as Versatile Technique for Analyzing RNPs Using Tagging Cassettes for Homologous Recombination in Saccharomyces cerevisiae. Methods Mol Biol 2022; 2533:127-145. [PMID: 35796986 PMCID: PMC9761527 DOI: 10.1007/978-1-0716-2501-9_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Micrococcal nuclease (MNase) originating from Staphylococcus aureus is a calcium dependent ribo- and desoxyribonuclease which has endo- and exonucleolytic activity of low sequence preference. MNase is widely used to analyze nucleosome positions in chromatin by probing the enzyme's DNA accessibility in limited digestion reactions. Probing reactions can be performed in a global way by addition of exogenous MNase , or locally by "chromatin endogenous cleavage " (ChEC ) reactions using MNase fusion proteins . The latter approach has recently been adopted for the analysis of local RNA environments of MNase fusion proteins which are incorporated in vivo at specific sites of ribonucleoprotein (RNP ) complexes. In this case, ex vivo activation of MNase by addition of calcium leads to RNA cleavages in proximity to the tethered anchor protein thus providing information about the folding state of its RNA environment.Here, we describe a set of plasmids that can be used as template for PCR-based MNase tagging of genes by homologous recombination in S. cerevisiae . The templates enable both N- and C-terminal tagging with MNase in combination with linker regions of different lengths and properties. In addition, an affinity tag is included in the recombination cassettes which can be used for purification of the particle of interest before or after induction of MNase cleavages in the surrounding RNA or DNA. A step-by-step protocol is provided for tagging of a gene of interest, followed by affinity purification of the resulting fusion protein together with associated RNA and subsequent induction of local MNase cleavages.
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Affiliation(s)
- Fabian Teubl
- Regensburg Center for Biochemistry (RCB), Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Katrin Schwank
- Regensburg Center for Biochemistry (RCB), Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Uli Ohmayer
- Regensburg Center for Biochemistry (RCB), Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany
- Evotec München GmbH, Martinsried, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry (RCB), Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany.
| | - Herbert Tschochner
- Regensburg Center for Biochemistry (RCB), Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany.
| | - Philipp Milkereit
- Regensburg Center for Biochemistry (RCB), Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, Regensburg, Germany.
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13
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Xu B, Li X, Gao X, Jia Y, Liu J, Li F, Zhang Z. DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data. Brief Bioinform 2021; 23:6454261. [PMID: 34875002 DOI: 10.1093/bib/bbab469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 12/25/2022] Open
Abstract
As the basal bricks, the dynamics and arrangement of nucleosomes orchestrate the higher architecture of chromatin in a fundamental way, thereby affecting almost all nuclear biology processes. Thanks to its rather simple protocol, assay for transposase-accessible chromatin using sequencing (ATAC)-seq has been rapidly adopted as a major tool for chromatin-accessible profiling at both bulk and single-cell levels; however, to picture the arrangement of nucleosomes per se remains a challenge with ATAC-seq. In the present work, we introduce a novel ATAC-seq analysis toolkit, named decoding nucleosome organization profile based on ATAC-seq data (deNOPA), to predict nucleosome positions. Assessments showed that deNOPA outperformed state-of-the-art tools with ultra-sparse ATAC-seq data, e.g. no more than 0.5 fragment per base pair. The remarkable performance of deNOPA was fueled by the short fragment reads, which compose nearly half of sequenced reads in the ATAC-seq libraries and are commonly discarded by state-of-the-art nucleosome positioning tools. However, we found that the short fragment reads enrich information on nucleosome positions and that the linker regions were predicted by reads from both short and long fragments using Gaussian smoothing. Last, using deNOPA, we showed that the dynamics of nucleosome organization may not directly couple with chromatin accessibility in the cis-regulatory regions when human cells respond to heat shock stimulation. Our deNOPA provides a powerful tool with which to analyze the dynamics of chromatin at nucleosome position level with ultra-sparse ATAC-seq data.
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Affiliation(s)
- Bingxiang Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China.,School of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Xiaoli Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Xiaomeng Gao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Yan Jia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Jing Liu
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Feifei Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China.,School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P.R. China
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14
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Chen X, Yang H, Liu G, Zhang Y. NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes. BMC Bioinformatics 2021; 22:321. [PMID: 34120586 PMCID: PMC8201709 DOI: 10.1186/s12859-021-04239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/06/2021] [Indexed: 12/02/2022] Open
Abstract
Background Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC) assessment and uneven data quality of public data sets. Results The NUCOME is a database focused on filtering qualified nucleosome organization referenced landscapes covering various cell types in human and mouse based on QC metrics. The filtering strategy guarantees the quality of nucleosome organization referenced landscapes and exempts users from redundant data set selection and processing. The NUCOME database provides standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci. Conclusions The NUCOME provides valuable data resources for integrative analyses focus on nucleosome organization. The NUCOME is freely available at http://compbio-zhanglab.org/NUCOME. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04239-9.
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Affiliation(s)
- Xiaolan Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Hui Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Guifen Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
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15
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Kato H, Shimizu M, Urano T. Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos. BMC Bioinformatics 2021; 22:322. [PMID: 34120589 PMCID: PMC8201924 DOI: 10.1186/s12859-021-04240-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Assessing the nucleosome-forming potential of specific DNA sequences is important for understanding complex chromatin organization. Methods for predicting nucleosome positioning include bioinformatics and biophysical approaches. An advantage of bioinformatics methods, which are based on in vivo nucleosome maps, is the use of natural sequences that may contain previously unknown elements involved in nucleosome positioning in vivo. The accuracy of such prediction attempts reflects the genomic coordinate resolution of the nucleosome maps applied. Nucleosome maps are constructed using micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq). However, as MNase has a strong preference for A/T-rich sequences, MNase-seq may not be appropriate for this purpose. In addition to MNase-seq-based maps, base pair-resolution chemical maps of in vivo nucleosomes from three different species (budding and fission yeasts, and mice) are currently available. However, these chemical maps have yet to be integrated into publicly available computational methods. Results We developed a Bioconductor package (named nuCpos) to demonstrate the superiority of chemical maps in predicting nucleosome positioning. The accuracy of chemical map-based prediction in rotational settings was higher than that of the previously developed MNase-seq-based approach. With our method, predicted nucleosome occupancy reasonably matched in vivo observations and was not affected by A/T nucleotide frequency. Effects of genetic alterations on nucleosome positioning that had been observed in living yeast cells could also be predicted. nuCpos calculates individual histone binding affinity (HBA) scores for given 147-bp sequences to examine their suitability for nucleosome formation. We also established local HBA as a new parameter to predict nucleosome formation, which was calculated for 13 overlapping nucleosomal DNA subsequences. HBA and local HBA scores for various sequences agreed well with previous in vitro and in vivo studies. Furthermore, our results suggest that nucleosomal subsegments that are disfavored in different rotational settings contribute to the defined positioning of nucleosomes. Conclusions Our results demonstrate that chemical map-based statistical models are beneficial for studying nucleosomal DNA features. Studies employing nuCpos software can enhance understanding of chromatin regulation and the interpretation of genetic alterations and facilitate the design of artificial sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04240-2.
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Affiliation(s)
- Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan.
| | - Mitsuhiro Shimizu
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan
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16
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Han GS, Li Q, Li Y. Comparative analysis and prediction of nucleosome positioning using integrative feature representation and machine learning algorithms. BMC Bioinformatics 2021; 22:129. [PMID: 34078256 PMCID: PMC8170966 DOI: 10.1186/s12859-021-04006-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/01/2022] Open
Abstract
Background Nucleosome plays an important role in the process of genome expression, DNA replication, DNA repair and transcription. Therefore, the research of nucleosome positioning has invariably received extensive attention. Considering the diversity of DNA sequence representation methods, we tried to integrate multiple features to analyze its effect in the process of nucleosome positioning analysis. This process can also deepen our understanding of the theoretical analysis of nucleosome positioning. Results Here, we not only used frequency chaos game representation (FCGR) to construct DNA sequence features, but also integrated it with other features and adopted the principal component analysis (PCA) algorithm. Simultaneously, support vector machine (SVM), extreme learning machine (ELM), extreme gradient boosting (XGBoost), multilayer perceptron (MLP) and convolutional neural networks (CNN) are used as predictors for nucleosome positioning prediction analysis, respectively. The integrated feature vector prediction quality is significantly superior to a single feature. After using principal component analysis (PCA) to reduce the feature dimension, the prediction quality of H. sapiens dataset has been significantly improved. Conclusions Comparative analysis and prediction on H. sapiens, C. elegans, D. melanogaster and S. cerevisiae datasets, demonstrate that the application of FCGR to nucleosome positioning is feasible, and we also found that integrative feature representation would be better.
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Affiliation(s)
- Guo-Sheng Han
- Department of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, Hunan, China. .,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China.
| | - Qi Li
- Department of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, Hunan, China.,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China
| | - Ying Li
- Department of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, Hunan, China.,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China
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17
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Barbier J, Vaillant C, Volff JN, Brunet FG, Audit B. Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution. Genes (Basel) 2021; 12:genes12060851. [PMID: 34205881 PMCID: PMC8228248 DOI: 10.3390/genes12060851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.
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Affiliation(s)
- Jérémy Barbier
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Cédric Vaillant
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Correspondence: (J.-N.V.); (B.A.)
| | - Frédéric G. Brunet
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
| | - Benjamin Audit
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
- Correspondence: (J.-N.V.); (B.A.)
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18
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Routhier E, Pierre E, Khodabandelou G, Mozziconacci J. Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics. Genome Res 2021; 31:317-326. [PMID: 33355297 PMCID: PMC7849406 DOI: 10.1101/gr.264416.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022]
Abstract
Genetically modified genomes are often used today in many areas of fundamental and applied research. In many studies, coding or noncoding regions are modified in order to change protein sequences or gene expression levels. Modifying one or several nucleotides in a genome can also lead to unexpected changes in the epigenetic regulation of genes. When designing a synthetic genome with many mutations, it would thus be very informative to be able to predict the effect of these mutations on chromatin. We develop here a deep learning approach that quantifies the effect of every possible single mutation on nucleosome positions on the full Saccharomyces cerevisiae genome. This type of annotation track can be used when designing a modified S. cerevisiae genome. We further highlight how this track can provide new insights on the sequence-dependent mechanisms that drive nucleosomes' positions in vivo.
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Affiliation(s)
- Etienne Routhier
- Sorbonne Universite, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
| | - Edgard Pierre
- Sorbonne Universite, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
| | | | - Julien Mozziconacci
- Sorbonne Universite, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
- Muséum National d'Histoire Naturelle, Structure et Instabilité des Génomes, UMR7196, Paris 75231, France
- Institut Universitaire de France, Paris 75005, France
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19
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Liu G, Zhao H, Meng H, Xing Y, Yang H, Lin H. Deform-nu: A DNA Deformation Energy-Based Predictor for Nucleosome Positioning. Front Cell Dev Biol 2021; 8:596341. [PMID: 33425904 PMCID: PMC7785812 DOI: 10.3389/fcell.2020.596341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/26/2020] [Indexed: 12/01/2022] Open
Abstract
The structure and function of chromatin can be regulated through positioning patterns of nucleosomes. DNA-based processes are regulated via nucleosomes. Therefore, it is significant to determine nucleosome positions in DNA-based processes. A deformation energy model was proposed to predict nucleosome positions in our previous study. A free web server based on the model (http://lin-group.cn/server/deform-nu/) was firstly established to estimate the occupancy and rotational positioning of nucleosomes in the study. Then, the performance of the model was verified by several examples. The results indicated that nucleosome positioning relied on the physical properties of DNA, such as deformation energy.
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Affiliation(s)
- Guoqing Liu
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hongyu Zhao
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hu Meng
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Yongqiang Xing
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hui Yang
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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20
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Maji A, Padinhateeri R, Mitra MK. The Accidental Ally: Nucleosome Barriers Can Accelerate Cohesin-Mediated Loop Formation in Chromatin. Biophys J 2020; 119:2316-2325. [PMID: 33181117 PMCID: PMC7732762 DOI: 10.1016/j.bpj.2020.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/21/2020] [Accepted: 10/13/2020] [Indexed: 01/26/2023] Open
Abstract
An important question in the context of the three-dimensional organization of chromosomes is the mechanism of formation of large loops between distant basepairs. Recent experiments suggest that the formation of loops might be mediated by loop extrusion factor proteins such as cohesin. Experiments on cohesin have shown that cohesins walk diffusively on the DNA and that nucleosomes act as obstacles to the diffusion, lowering the permeability and hence reducing the effective diffusion constant. An estimation of the times required to form the loops of typical sizes seen in Hi-C experiments using these low-effective-diffusion constants leads to times that are unphysically large. The puzzle then is the following: how does a cohesin molecule diffusing on the DNA backbone achieve speeds necessary to form the large loops seen in experiments? We propose a simple answer to this puzzle and show that although at low densities, nucleosomes act as barriers to cohesin diffusion, beyond a certain concentration they can reduce loop formation times because of a subtle interplay between the nucleosome size and the mean linker length. This effect is further enhanced on considering stochastic binding kinetics of nucleosomes on the DNA backbone and leads to predictions of lower loop formation times than might be expected from a naive obstacle picture of nucleosomes.
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Affiliation(s)
- Ajoy Maji
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mithun K Mitra
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India.
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21
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Kravets AP, Sokolova DA. Epigenetic factors of individual radiosensitivity and adaptive capacity. Int J Radiat Biol 2020; 96:999-1007. [PMID: 32396015 DOI: 10.1080/09553002.2020.1767819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Purpose: Studying the relationship between epigenetic variability with different individual radiosensitivity and adaptive capacity.Material and method: Using a simple and convenient experimental model - maize seedlings with different germination terms and epigenetic patterns - the hypothesis was tested that homogeneous genetically but epigenetic different organisms have different radiosensitivity and radioadaptive capacity. Differences in the DNA methylation profiles of individual subpopulations of seedlings were used as a marker of epigenetic differences and the yield of chromosomal aberration was used as an indicator of DNA vulnerability and its changes under different UV-C irradiation modes. In two series of experiments involving а UV-C acute single and exposure according to the scheme 'adaptive - challenging', the investigation of possible biological importance of epigenetic polymorphism has been performed. The study used a cytogenetic analysis of the yield of chromosomal aberrations and restriction analysis followed by ITS-ISSR- PCR.Results: Significant differences have been established in chromosome aberration yield and DNA methylation profile in control and under UV-C exposure for seedlings of subpopulations differing in time of germination. The differences in the DNA methylation profiles and the yield of chromosomal aberrations in the control subpopulations of seedlings of different germination term indicate the influence of the DNA methylation profile on DNA damage by regular metabolic factors, such as thermal vibrations or reactive oxygen species (ROS). This phenomenon can be explained with different chromatin conformation determining structural or 'passive' resistance, which provides different DNA availability to damage. Methylation switching into de novo under different mode radiation exposure could become a marker of gene expression changes due to induced repair and protecting.Conclusions: The obtained data indicate the importance of epigenetic factors in determining the radio-resistance and adaptive capacity of organisms. It points out that the epigenetic mechanisms that determine the choice of the metabolic pattern also contribute to the individual radiosensitivity and adaptive capacity of the organisms. This contribution is determined by two ways. First, the DNA methylation profile affects the initial damage processes and secondly, the type of methylation switching into de novo is associated with the further development of protection and repair processes.
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Affiliation(s)
- Alexandra P Kravets
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Science of Ukraine, Kiev, Ukraine
| | - Daryna A Sokolova
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Science of Ukraine, Kiev, Ukraine
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22
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Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang Z, Zhao W, Bao Y, Zhang Z, Wu J, Asmann YW, Li R, Xiao J. NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Res 2020; 47:D163-D169. [PMID: 30335176 PMCID: PMC6323900 DOI: 10.1093/nar/gky980] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/10/2018] [Indexed: 12/16/2022] Open
Abstract
Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation.
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Affiliation(s)
- Yongbing Zhao
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jinyue Wang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Liang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanxia Liu
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Wang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiye Jiang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhewen Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenming Zhao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiming Bao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Rujiao Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingfa Xiao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
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23
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Epigenome Regulation by Dynamic Nucleosome Unwrapping. Trends Biochem Sci 2020; 45:13-26. [PMID: 31630896 PMCID: PMC10168609 DOI: 10.1016/j.tibs.2019.09.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Gene regulation in eukaryotes requires the controlled access of sequence-specific transcription factors (TFs) to their sites in a chromatin landscape dominated by nucleosomes. Nucleosomes are refractory to TF binding, and often must be removed from regulatory regions. Recent genomic studies together with in vitro measurements suggest that the nucleosome barrier to TF binding is modulated by dynamic nucleosome unwrapping governed by ATP-dependent chromatin remodelers. Genome-wide occupancy and the regulation of subnucleosomal intermediates have gained recent attention with the application of high-resolution approaches for precision mapping of protein-DNA interactions. We summarize here recent findings on nucleosome substructures and TF binding dynamics, and highlight how unwrapped nucleosomal intermediates provide a novel signature of active chromatin.
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24
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Q-Nuc: a bioinformatics pipeline for the quantitative analysis of nucleosomal profiles. Interdiscip Sci 2019; 12:69-81. [PMID: 31845186 DOI: 10.1007/s12539-019-00354-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/20/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022]
Abstract
Nucleosomal profiling is an effective method to determine the positioning and occupancy of nucleosomes, which is essential to understand their roles in genomic processes. However, the positional randomness across the genome and its relationship with nucleosome occupancy remains poorly understood. Here we present a computational method that segments the profile into nucleosomal domains and quantifies their randomness and relative occupancy level. Applying this method to published data, we find on average ~ 3-fold differences in the degree of positional randomness between regions typically considered "well-ordered", as well as an unexpected predominance of only two types of domains of positional randomness in yeast cells. Further, we find that occupancy levels between domains actually differ maximally by ~ 2-3-fold in both cells, which has not been described before. We also developed a procedure by which one can estimate the sequencing depth that is required to identify nucleosomal positions even when regional positional randomness is high. Overall, we have developed a pipeline to quantitatively characterize domain-level features of nucleosome randomness and occupancy genome-wide, enabling the identification of otherwise unknown features in nucleosomal organization.
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25
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Buitrago D, Codó L, Illa R, de Jorge P, Battistini F, Flores O, Bayarri G, Royo R, Del Pino M, Heath S, Hospital A, Gelpí JL, Heath IB, Orozco M. Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning. Nucleic Acids Res 2019; 47:9511-9523. [PMID: 31504766 PMCID: PMC6765203 DOI: 10.1093/nar/gkz759] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/23/2019] [Accepted: 08/22/2019] [Indexed: 02/03/2023] Open
Abstract
We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.
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Affiliation(s)
- Diana Buitrago
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Laia Codó
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain
| | - Ricard Illa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Pau de Jorge
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Oscar Flores
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Genis Bayarri
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain
| | - Marc Del Pino
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Josep Lluís Gelpí
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain.,Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
| | - Isabelle Brun Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain.,Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
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26
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Abstract
Nucleosome positioning controls the accessible regions of chromatin and plays essential roles in DNA-templated processes. ATP driven remodeling enzymes are known to be crucial for its establishment in vivo, but their nonequilibrium nature has hindered the development of a unified theoretical framework for nucleosome positioning. Using a perturbation theory, we show that the effect of these enzymes can be well approximated by effective equilibrium models with rescaled temperatures and interactions. Numerical simulations support the accuracy of the theory in predicting both kinetic and steady-state quantities, including the effective temperature and the radial distribution function, in biologically relevant regimes. The energy landscape view emerging from our study provides an intuitive understanding for the impact of remodeling enzymes in either reinforcing or overwriting intrinsic signals for nucleosome positioning, and may help improve the accuracy of computational models for its prediction in silico.
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27
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ZCMM: A Novel Method Using Z-Curve Theory- Based and Position Weight Matrix for Predicting Nucleosome Positioning. Genes (Basel) 2019; 10:genes10100765. [PMID: 31569414 PMCID: PMC6827144 DOI: 10.3390/genes10100765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 02/04/2023] Open
Abstract
Nucleosomes are the basic units of eukaryotes. The accurate positioning of nucleosomes plays a significant role in understanding many biological processes such as transcriptional regulation mechanisms and DNA replication and repair. Here, we describe the development of a novel method, termed ZCMM, based on Z-curve theory and position weight matrix (PWM). The ZCMM was trained and tested using the nucleosomal and linker sequences determined by support vector machine (SVM) in Saccharomyces cerevisiae (S. cerevisiae), and experimental results showed that the sensitivity (Sn), specificity (Sp), accuracy (Acc), and Matthews correlation coefficient (MCC) values for ZCMM were 91.40%, 96.56%, 96.75%, and 0.88, respectively, and the average area under the receiver operating characteristic curve (AUC) value was 0.972. A ZCMM predictor was developed to predict nucleosome positioning in Homo sapiens (H. sapiens), Caenorhabditis elegans (C. elegans), and Drosophila melanogaster (D. melanogaster) genomes, and the accuracy (Acc) values were 77.72%, 85.34%, and 93.62%, respectively. The maximum AUC values of the four species were 0.982, 0.861, 0.912 and 0.911, respectively. Another independent dataset for S. cerevisiae was used to predict nucleosome positioning. Compared with the results of Wu's method, it was found that the Sn, Sp, Acc, and MCC of ZCMM results for S. cerevisiae were all higher, reaching 96.72%, 96.54%, 94.10%, and 0.88. Compared with the Guo's method 'iNuc-PseKNC', the results of ZCMM for D. melanogaster were better. Meanwhile, the ZCMM was compared with some experimental data in vitro and in vivo for S. cerevisiae, and the results showed that the nucleosomes predicted by ZCMM were highly consistent with those confirmed by these experiments. Therefore, it was further confirmed that the ZCMM method has good accuracy and reliability in predicting nucleosome positioning.
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28
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Santamaría R, Therón R, Durán L, García A, González S, Sánchez M, Antequera F. Genome-wide search of nucleosome patterns using visual analytics. Bioinformatics 2019; 35:2185-2192. [PMID: 30496344 PMCID: PMC6596885 DOI: 10.1093/bioinformatics/bty971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/19/2018] [Accepted: 11/28/2018] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The Burrows-Wheeler transform (BWT) is widely used for the fast alignment of high-throughput sequence data. This method also has potential applications in other areas of bioinformatics, and it can be specially useful for the fast searching of patterns on coverage data from different sources. RESULTS We present a nucleosome pattern search method that converts levels of nucleosomal occupancy to a sequence-like format to which BWT searches can be applied. The method is embedded in a nucleosome map browser, 'Nucleosee', an interactive visual tool specifically designed to enhance BWT searches, giving them context and making them suitable for visual discourse analysis of the results. The proposed method is fast, flexible and sufficiently generic for the exploration of data in a broad and interactive way. AVAILABILITY AND IMPLEMENTATION The proposed algorithm and visual browser are available for testing at http://cpg3.der.usal.es/nucleosee. The source code and installation packages are also available at https://github.com/rodrigoSantamaria/nucleosee. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rodrigo Santamaría
- Departmento de Informática y Automática, Universidad de Salamanca, Salamanca, Spain
| | - Roberto Therón
- Departmento de Informática y Automática, Universidad de Salamanca, Salamanca, Spain
| | - Laura Durán
- Instituto de Biología Funcional y Genómica, Unidad de Dinámica del Genoma y Epigenética, CSIC.USAL, Salamanca, Spain
| | - Alicia García
- Instituto de Biología Funcional y Genómica, Unidad de Dinámica del Genoma y Epigenética, CSIC.USAL, Salamanca, Spain
| | - Sara González
- Instituto de Biología Funcional y Genómica, Unidad de Dinámica del Genoma y Epigenética, CSIC.USAL, Salamanca, Spain
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica, Unidad de Dinámica del Genoma y Epigenética, CSIC.USAL, Salamanca, Spain
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica, Unidad de Dinámica del Genoma y Epigenética, CSIC.USAL, Salamanca, Spain
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29
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Jiang Z, Zhang B. Theory of active chromatin remodeling.. [DOI: 10.1101/687145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Nucleosome positioning controls the accessible regions of chromatin and plays essential roles in DNA-templated processes. ATP driven remodeling enzymes are known to be crucial for its establishment in vivo, but their non-equilibrium nature has hindered the development of a unified theoretical framework for nucleosome positioning. Using a perturbation theory, we show that the effect of these enzymes can be well approximated by effective equilibrium models with rescaled temperatures and interactions. Numerical simulations support the accuracy of the theory in predicting both kinetic and steady-state quantities, including the effective temperature and the radial distribution function, in biologically relevant regimes. The energy landscape view emerging from our study provides an intuitive understanding for the impact of remodeling enzymes in either reinforcing or overwriting intrinsic signals for nucleosome positioning, and may help improve the accuracy of computational models for its prediction in silico.
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30
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NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule. Sci Rep 2019; 9:8140. [PMID: 31148571 PMCID: PMC6544651 DOI: 10.1038/s41598-019-44597-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/20/2019] [Indexed: 11/15/2022] Open
Abstract
Recent technical advances highlight that to understand mammalian development and human disease we need to consider transcriptional and epigenetic cell-to-cell differences within cell populations. This is particularly important in key areas of biomedicine like stem cell differentiation and intratumor heterogeneity. The recently developed nucleosome occupancy and methylome (NOMe) assay facilitates the simultaneous study of DNA methylation and nucleosome positioning on the same DNA strand. NOMe-treated DNA can be sequenced by sanger (NOMe-PCR) or high throughput approaches (NOMe-seq). NOMe-PCR provides information for a single locus at the single molecule while NOMe-seq delivers genome-wide data that is usually interrogated to obtain population-averaged measures. Here, we have developed a bioinformatic tool that allow us to easily obtain locus-specific information at the single molecule using genome-wide NOMe-seq datasets obtained from bulk populations. We have used NOMePlot to study mouse embryonic stem cells and found that polycomb-repressed bivalent gene promoters coexist in two different epigenetic states, as defined by the nucleosome binding pattern detected around their transcriptional start site.
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31
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Hu G, Wendel JF. Cis-trans controls and regulatory novelty accompanying allopolyploidization. THE NEW PHYTOLOGIST 2019; 221:1691-1700. [PMID: 30290011 DOI: 10.1111/nph.15515] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/30/2018] [Indexed: 05/20/2023]
Abstract
Allopolyploidy is a prevalent process in plants, having important physiological, ecological and evolutionary consequences. Transcriptomic responses to genomic merger and doubling have been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena including homoeolog expression bias, genome dominance, expression-level dominance and revamping of co-expression networks. Notwithstanding the foregoing, there remains a need to develop a conceptual framework that will stimulate a deeper understanding of these diverse phenomena and their mechanistic interrelationships. Here we introduce considerations relevant to this framework with a focus on cis-trans interactions among duplicated genes and alleles in hybrids and allopolyploids. By extending classic allele-specific expression analysis to the allopolyploid level, we distinguish the distinct effects of progenitor regulatory interactions from the novel intergenomic interactions that arise from genome merger and allopolyploidization. This perspective informs experiments designed to reveal the molecular genetic basis of gene regulatory control, and will facilitate the disentangling of genetic from epigenetic and higher-order effects that impact gene expression. Finally, we suggest that the extended cis-trans model may help conceptually unify several presently disparate hallmarks of allopolyploid evolution, including genome-wide expression dominance and biased fractionation, and lead to a new level of understanding of phenotypic novelty accompanying polyploidy.
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Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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32
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Di Gangi M, Lo Bosco G, Rizzo R. Deep learning architectures for prediction of nucleosome positioning from sequences data. BMC Bioinformatics 2018; 19:418. [PMID: 30453896 PMCID: PMC6245688 DOI: 10.1186/s12859-018-2386-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background Nucleosomes are DNA-histone complex, each wrapping about 150 pairs of double-stranded DNA. Their function is fundamental for one of the primary functions of Chromatin i.e. packing the DNA into the nucleus of the Eukaryote cells. Several biological studies have shown that the nucleosome positioning influences the regulation of cell type-specific gene activities. Moreover, computational studies have shown evidence of sequence specificity concerning the DNA fragment wrapped into nucleosomes, clearly underlined by the organization of particular DNA substrings. As the main consequence, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using a sequence features representation. Results In this work, we propose a deep learning model for nucleosome identification. Our model stacks convolutional layers and Long Short-term Memories to automatically extract features from short- and long-range dependencies in a sequence. Using this model we are able to avoid the feature extraction and selection steps while improving the classification performances. Conclusions Results computed on eleven data sets of five different organisms, from Yeast to Human, show the superiority of the proposed method with respect to the state of the art recently presented in the literature.
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Affiliation(s)
- Mattia Di Gangi
- Fondazione Bruno Kessler, Via Sommarive, 18, Trento, 38123, Italy.,ICT International Doctoral School, Via Sommarive, 9, Trento, 38123, Italy
| | - Giosuè Lo Bosco
- Dipartimento di Matematica e Informatica, Università degli studi di Palermo, Via Archirafi, 34, Palermo, 90123, Italy. .,Dipartimento di Scienze per l'Innovazione tecnologica, Istituto Euro-Mediterraneo di Scienza e Tecnologia, Via Michele Miraglia, 20, Palermo, 90139, Italy.
| | - Riccardo Rizzo
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, 90146, Italy
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33
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Challenges and guidelines toward 4D nucleome data and model standards. Nat Genet 2018; 50:1352-1358. [PMID: 30262815 DOI: 10.1038/s41588-018-0236-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 07/19/2018] [Indexed: 11/09/2022]
Abstract
Due to recent advances in experimental and theoretical approaches, the dynamic three-dimensional organization (3D) of the nucleus has become a very active area of research in life sciences. We now understand that the linear genome is folded in ways that may modulate how genes are expressed during the basic functioning of cells. Importantly, it is now possible to build 3D models of how the genome folds within the nucleus and changes over time (4D). Because genome folding influences its function, this opens exciting new possibilities to broaden our understanding of the mechanisms that determine cell fate. However, the rapid evolution of methods and the increasing complexity of data can result in ambiguity and reproducibility challenges, which may hamper the progress of this field. Here, we describe such challenges ahead and provide guidelines to think about strategies for shared standardized validation of experimental 4D nucleome data sets and models.
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34
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Kravets AP, Sokolova DA. Evaluation of Factors Indicating Epigenetic Polymorphism through Population of Maize Seedlings. CYTOL GENET+ 2018. [DOI: 10.3103/s0095452718030088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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35
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Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq). Methods Mol Biol 2018; 1689:83-101. [PMID: 29027167 DOI: 10.1007/978-1-4939-7380-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
MNase-seq allows the genome-wide examination of the nucleosome landscape by determination of nucleosome positioning and occupancy. Typically, native or formaldehyde fixed chromatin is subjected to digestion by micrococcal nuclease (MNase), which degrades linker DNA and yields mainly mono-nucleosomes. The resulting material can be processed directly or can be subjected to an optional chromatin immunoprecipitation step (MNase-ChIP-seq). De-crosslinked and purified DNA is then subjected to next-generation sequencing. The protocol presented here has been tailored for the analysis of nucleosome landscape in the malaria parasite, Plasmodium falciparum, but most steps are directly applicable to other cell types. We also discuss general considerations for experimental design and computational analysis, which are crucial for accurate investigation of the nucleosome landscape.
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36
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Chereji RV, Clark DJ. Major Determinants of Nucleosome Positioning. Biophys J 2018; 114:2279-2289. [PMID: 29628211 DOI: 10.1016/j.bpj.2018.03.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022] Open
Abstract
The compact structure of the nucleosome limits DNA accessibility and inhibits the binding of most sequence-specific proteins. Nucleosomes are not randomly located on the DNA but positioned with respect to the DNA sequence, suggesting models in which critical binding sites are either exposed in the linker, resulting in activation, or buried inside a nucleosome, resulting in repression. The mechanisms determining nucleosome positioning are therefore of paramount importance for understanding gene regulation and other events that occur in chromatin, such as transcription, replication, and repair. Here, we review our current understanding of the major determinants of nucleosome positioning: DNA sequence, nonhistone DNA-binding proteins, chromatin-remodeling enzymes, and transcription. We outline the major challenges for the future: elucidating the precise mechanisms of chromatin opening and promoter activation, identifying the complexes that occupy promoters, and understanding the multiscale problem of chromatin fiber organization.
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Affiliation(s)
- Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
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37
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胡 世. Prediction of Nucleosome Positioning Sequence for Yeast Genome. Biophysics (Nagoya-shi) 2018. [DOI: 10.12677/biphy.2018.61001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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38
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39
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Hu S, Chen X, Liao J, Chen Y, Zhao C, Zhang Y. CAM: A quality control pipeline for MNase-seq data. PLoS One 2017; 12:e0182771. [PMID: 28787030 PMCID: PMC5546596 DOI: 10.1371/journal.pone.0182771] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/24/2017] [Indexed: 11/19/2022] Open
Abstract
Nucleosome organization affects the accessibility of cis-elements to trans-acting factors. Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) is the most popular technology used to profile nucleosome organization on a genome-wide scale. Evaluating the data quality of MNase-seq data remains challenging, especially in mammalian. There is a strong need for a convenient and comprehensive approach to obtain dedicated quality control (QC) for MNase-seq data analysis. Here we developed CAM, which is a comprehensive QC pipeline for MNase-seq data. The CAM pipeline provides multiple informative QC measurements and nucleosome organization profiles on different potentially functional regions for given MNase-seq data. CAM also includes 268 historical MNase-seq datasets from human and mouse as a reference atlas for unbiased assessment. CAM is freely available at: http://www.tongji.edu.cn/~zhanglab/CAM.
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Affiliation(s)
- Sheng’en Hu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Xiaolan Chen
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Ji Liao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Yiqing Chen
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Chengchen Zhao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
| | - Yong Zhang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
- * E-mail:
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40
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Voong LN, Xi L, Wang JP, Wang X. Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping. Trends Genet 2017; 33:495-507. [PMID: 28693826 DOI: 10.1016/j.tig.2017.05.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/10/2017] [Accepted: 05/30/2017] [Indexed: 12/30/2022]
Abstract
Nucleosomes regulate the transcription output of the genome by occluding the underlying DNA sequences from DNA-binding proteins that must act on it. Knowledge of the precise locations of nucleosomes in the genome is thus essential towards understanding how transcription is regulated. Current nucleosome-mapping strategies involve digesting chromatin with nucleases or chemical cleavage followed by high-throughput sequencing. In this review, we compare the traditional micrococcal nuclease (MNase)-based approach with a chemical cleavage strategy, with discussion on the important insights each has uncovered about the role of nucleosomes in shaping transcriptional processes.
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Affiliation(s)
- Lilien N Voong
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Liqun Xi
- Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, IL 60208, USA.
| | - Xiaozhong Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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41
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Wedel C, Siegel TN. Genome-wide analysis of chromatin structures in Trypanosoma brucei using high-resolution MNase-ChIP-seq. Exp Parasitol 2017; 180:2-12. [PMID: 28286326 DOI: 10.1016/j.exppara.2017.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 02/24/2017] [Accepted: 03/07/2017] [Indexed: 11/16/2022]
Abstract
Specific DNA-protein interactions are the basis for many important cellular mechanisms like the regulation of gene expression or replication. Knowledge about the precise genomic locations of DNA-protein interactions is important because it provides insight into the regulation of these processes. Recently, we have adapted an approach that combines micrococcal nuclease (MNase) digestion of chromatin with chromatin immunoprecipitation in Trypanosoma brucei. Here, we describe in detail how this method can be used to map the genome-wide distribution of nucleosomes or other DNA-binding proteins at high resolution in T. brucei.
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Affiliation(s)
- Carolin Wedel
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Straße 2 / Bau D15, 97080 Würzburg, Germany
| | - T Nicolai Siegel
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Straße 2 / Bau D15, 97080 Würzburg, Germany.
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42
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Vainshtein Y, Rippe K, Teif VB. NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data. BMC Genomics 2017; 18:158. [PMID: 28196481 PMCID: PMC5309995 DOI: 10.1186/s12864-017-3580-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/10/2017] [Indexed: 12/21/2022] Open
Abstract
Background Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them. Results Here we introduce the NucTools suite of Perl scripts as well as MATLAB- and R-based visualization programs for a nucleosome-centred downstream analysis of deep sequencing data. NucTools accounts for the continuous distribution of nucleosome occupancy. It allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between different experimental conditions, and the estimation of the changes of integral chromatin properties such as the nucleosome repeat length. Furthermore, NucTools facilitates the annotation of nucleosome occupancy with other chromatin features like binding of transcription factors or architectural proteins, and epigenetic marks like histone modifications or DNA methylation. The applications of NucTools are demonstrated for the comparison of several datasets for nucleosome occupancy in mouse embryonic stem cells (ESCs) and mouse embryonic fibroblasts (MEFs). Conclusions The typical workflows of data processing and integrative analysis with NucTools reveal information on the interplay of nucleosome positioning with other features such as for example binding of a transcription factor CTCF, regions with stable and unstable nucleosomes, and domains of large organized chromatin K9me2 modifications (LOCKs). As potential limitations and problems we discuss how inter-replicate variability of MNase-seq experiments can be addressed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3580-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yevhen Vainshtein
- Functional Genomics Group, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Nobelstraße 12, 70569, Stuttgart, Germany.
| | - Karsten Rippe
- Research Group Genome Organization & Function, German Cancer Research Center (DKFZ) and Bioquant, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Vladimir B Teif
- School of Biological Sciences, University of Essex, Wivenhoe Park, CO4 3SQ, Colchester, UK.
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43
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Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions. Biophys J 2017; 112:505-511. [PMID: 28131316 DOI: 10.1016/j.bpj.2016.12.041] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 12/19/2016] [Accepted: 12/29/2016] [Indexed: 02/07/2023] Open
Abstract
Sequences that influence nucleosome positioning in promoter regions, and their relation to gene regulation, have been the topic of much research over the last decade. In yeast, significant nucleosome-depleted regions are found, which facilitate transcription. With the arrival of nucleosome positioning maps for the human genome, it was discovered that in our genome, unlike in that of yeast, promoters encode for high nucleosome occupancy. In this work, we look at the genomes of a range of different organisms, to provide a catalog of nucleosome positioning signals in promoters across the tree of life. We utilize a computational model of the nucleosome, based on crystallographic analyses of the structure and elasticity of the nucleosome, to predict the nucleosome positioning signals in promoter regions. To be able to apply our model to large genomic datasets, we introduce an approximative scheme that makes use of the limited range of correlations in nucleosomal sequence preferences to create a computationally efficient approximation of the full biophysical model. Our predictions show that a clear distinction between unicellular and multicellular life is visible in the intrinsically encoded nucleosome affinity. Furthermore, the strength of the nucleosome positioning signals correlates with the complexity of the organism. We conclude that encoding for high nucleosome occupancy, as in the human genome, is in fact a universal feature of multicellular life.
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González S, García A, Vázquez E, Serrano R, Sánchez M, Quintales L, Antequera F. Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome. Genome Res 2016; 26:1532-1543. [PMID: 27662899 PMCID: PMC5088595 DOI: 10.1101/gr.207241.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 09/19/2016] [Indexed: 12/18/2022]
Abstract
In the yeast genome, a large proportion of nucleosomes occupy well-defined and stable positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genome remains controversial. Through quantitative analysis of nucleosome positioning, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes in three species of Schizosaccharomyces and in Saccharomyces cerevisiae. This effect is equally detected in transcribed and nontranscribed regions, suggesting the existence of sequence elements that contribute to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is species-specific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open the possibility of designing coding and noncoding DNA molecules capable of directing their own nucleosomal organization.
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Affiliation(s)
- Sara González
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Alicia García
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Enrique Vázquez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Rebeca Serrano
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Luis Quintales
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain.,Departamento de Informática y Automática, Universidad de Salamanca/Facultad de Ciencias, 37007 Salamanca, Spain
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
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Awazu A. Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition. Bioinformatics 2016; 33:42-48. [PMID: 27563027 PMCID: PMC5860184 DOI: 10.1093/bioinformatics/btw562] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/02/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022] Open
Abstract
Motivation Nucleosome positioning plays important roles in many eukaryotic intranuclear processes, such as transcriptional regulation and chromatin structure formation. The investigations of nucleosome positioning rules provide a deeper understanding of these intracellular processes. Results Nucleosome positioning prediction was performed using a model consisting of three types of variables characterizing a DNA sequence—the number of five-nucleotide sequences, the number of three-nucleotide combinations in one period of a helix, and mono- and di-nucleotide distributions in DNA fragments. Using recently proposed stringent benchmark datasets with low biases for Saccharomyces cerevisiae, Homo sapiens, Caenorhabditis elegans and Drosophila melanogaster, the present model was shown to have a better prediction performance than the recently proposed predictors. This model was able to display the common and organism-dependent factors that affect nucleosome forming and inhibiting sequences as well. Therefore, the predictors developed here can accurately predict nucleosome positioning and help determine the key factors influencing this process. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Akinori Awazu
- Department of Mathematical and Life Sciences.,Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima, 739-8526, Japan
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Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach. PLoS One 2016; 11:e0156905. [PMID: 27272176 PMCID: PMC4896621 DOI: 10.1371/journal.pone.0156905] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/20/2016] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function.
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